[1] "ofn"        "-oTUCEC-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/UCEC-TP/22507145/UCEC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCEC-TP/22815333/transformed.cor.cli.txt"

nPatients in clinical file=548, in cluster file=248, common to both=248
[1] 197 248
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
           161             87 
  PTEN MUTATED PTEN WILD-TYPE 
           161             87 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              82              166 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              82              166 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            69            179 
  TP53 MUTATED TP53 WILD-TYPE 
            69            179 
[1] "CTCF MUTATION ANALYSIS"
[1] 3
  CTCF MUTATED CTCF WILD-TYPE 
            44            204 
  CTCF MUTATED CTCF WILD-TYPE 
            44            204 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             38             210 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             38             210 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             131              117 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             131              117 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              83              165 
  ARID1A MUTATED ARID1A WILD-TYPE 
              83              165 
[1] "ARHGAP35 MUTATION ANALYSIS"
[1] 3
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                36                212 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                36                212 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            52            196 
  KRAS MUTATED KRAS WILD-TYPE 
            52            196 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              74              174 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              74              174 
[1] "ZFHX3 MUTATION ANALYSIS"
[1] 3
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             44             204 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             44             204 
[1] "SPOP MUTATION ANALYSIS"
[1] 3
  SPOP MUTATED SPOP WILD-TYPE 
            21            227 
  SPOP MUTATED SPOP WILD-TYPE 
            21            227 
[1] "FGFR2 MUTATION ANALYSIS"
[1] 3
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             31             217 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             31             217 
[1] "TCP11L2 MUTATION ANALYSIS"
[1] 3
  TCP11L2 MUTATED TCP11L2 WILD-TYPE 
               14               234 
  TCP11L2 MUTATED TCP11L2 WILD-TYPE 
               14               234 
[1] "VPS11 MUTATION ANALYSIS"
[1] 3
  VPS11 MUTATED VPS11 WILD-TYPE 
             11             237 
  VPS11 MUTATED VPS11 WILD-TYPE 
             11             237 
[1] "PPP2R1A MUTATION ANALYSIS"
[1] 3
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               28               220 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               28               220 
[1] "MAX MUTATION ANALYSIS"
[1] 3
  MAX MUTATED MAX WILD-TYPE 
            9           239 
  MAX MUTATED MAX WILD-TYPE 
            9           239 
[1] "SOX17 MUTATION ANALYSIS"
[1] 3
  SOX17 MUTATED SOX17 WILD-TYPE 
              7             241 
  SOX17 MUTATED SOX17 WILD-TYPE 
              7             241 
[1] "CCND1 MUTATION ANALYSIS"
[1] 3
  CCND1 MUTATED CCND1 WILD-TYPE 
             14             234 
  CCND1 MUTATED CCND1 WILD-TYPE 
             14             234 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             9            239 
  NRAS MUTATED NRAS WILD-TYPE 
             9            239 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
             21             227 
  EP300 MUTATED EP300 WILD-TYPE 
             21             227 
[1] "KLHL8 MUTATION ANALYSIS"
[1] 3
  KLHL8 MUTATED KLHL8 WILD-TYPE 
             12             236 
  KLHL8 MUTATED KLHL8 WILD-TYPE 
             12             236 
[1] "ALG8 MUTATION ANALYSIS"
[1] 3
  ALG8 MUTATED ALG8 WILD-TYPE 
            11            237 
  ALG8 MUTATED ALG8 WILD-TYPE 
            11            237 
[1] "GNPTAB MUTATION ANALYSIS"
[1] 3
  GNPTAB MUTATED GNPTAB WILD-TYPE 
              20              228 
  GNPTAB MUTATED GNPTAB WILD-TYPE 
              20              228 
[1] "SIN3A MUTATION ANALYSIS"
[1] 3
  SIN3A MUTATED SIN3A WILD-TYPE 
             21             227 
  SIN3A MUTATED SIN3A WILD-TYPE 
             21             227 
[1] "ARID5B MUTATION ANALYSIS"
[1] 3
  ARID5B MUTATED ARID5B WILD-TYPE 
              29              219 
  ARID5B MUTATED ARID5B WILD-TYPE 
              29              219 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              14              234 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              14              234 
[1] "ZNF471 MUTATION ANALYSIS"
[1] 3
  ZNF471 MUTATED ZNF471 WILD-TYPE 
              15              233 
  ZNF471 MUTATED ZNF471 WILD-TYPE 
              15              233 
[1] "MORC4 MUTATION ANALYSIS"
[1] 3
  MORC4 MUTATED MORC4 WILD-TYPE 
             20             228 
  MORC4 MUTATED MORC4 WILD-TYPE 
             20             228 
[1] "SELP MUTATION ANALYSIS"
[1] 3
  SELP MUTATED SELP WILD-TYPE 
            10            238 
  SELP MUTATED SELP WILD-TYPE 
            10            238 
[1] "RBMX MUTATION ANALYSIS"
[1] 3
  RBMX MUTATED RBMX WILD-TYPE 
            12            236 
  RBMX MUTATED RBMX WILD-TYPE 
            12            236 
[1] "FAT1 MUTATION ANALYSIS"
[1] 3
  FAT1 MUTATED FAT1 WILD-TYPE 
            40            208 
  FAT1 MUTATED FAT1 WILD-TYPE 
            40            208 
[1] "MARK3 MUTATION ANALYSIS"
[1] 3
  MARK3 MUTATED MARK3 WILD-TYPE 
             11             237 
  MARK3 MUTATED MARK3 WILD-TYPE 
             11             237 
[1] "SOS1 MUTATION ANALYSIS"
[1] 3
  SOS1 MUTATED SOS1 WILD-TYPE 
            12            236 
  SOS1 MUTATED SOS1 WILD-TYPE 
            12            236 
[1] "RBBP6 MUTATION ANALYSIS"
[1] 3
  RBBP6 MUTATED RBBP6 WILD-TYPE 
             22             226 
  RBBP6 MUTATED RBBP6 WILD-TYPE 
             22             226 
[1] "ZNF263 MUTATION ANALYSIS"
[1] 3
  ZNF263 MUTATED ZNF263 WILD-TYPE 
               7              241 
  ZNF263 MUTATED ZNF263 WILD-TYPE 
               7              241 
[1] "INTS7 MUTATION ANALYSIS"
[1] 3
  INTS7 MUTATED INTS7 WILD-TYPE 
              8             240 
  INTS7 MUTATED INTS7 WILD-TYPE 
              8             240 
[1] "L1TD1 MUTATION ANALYSIS"
[1] 3
  L1TD1 MUTATED L1TD1 WILD-TYPE 
             16             232 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
             16             232 
[1] "NAT1 MUTATION ANALYSIS"
[1] 3
  NAT1 MUTATED NAT1 WILD-TYPE 
             7            241 
  NAT1 MUTATED NAT1 WILD-TYPE 
             7            241 
[1] "JAKMIP2 MUTATION ANALYSIS"
[1] 3
  JAKMIP2 MUTATED JAKMIP2 WILD-TYPE 
               12               236 
  JAKMIP2 MUTATED JAKMIP2 WILD-TYPE 
               12               236 
[1] "ING1 MUTATION ANALYSIS"
[1] 3
  ING1 MUTATED ING1 WILD-TYPE 
            12            236 
  ING1 MUTATED ING1 WILD-TYPE 
            12            236 
[1] "CCDC6 MUTATION ANALYSIS"
[1] 3
  CCDC6 MUTATED CCDC6 WILD-TYPE 
              6             242 
  CCDC6 MUTATED CCDC6 WILD-TYPE 
              6             242 
[1] "ZNF781 MUTATION ANALYSIS"
[1] 3
  ZNF781 MUTATED ZNF781 WILD-TYPE 
              10              238 
  ZNF781 MUTATED ZNF781 WILD-TYPE 
              10              238 
[1] "MKI67 MUTATION ANALYSIS"
[1] 3
  MKI67 MUTATED MKI67 WILD-TYPE 
             29             219 
  MKI67 MUTATED MKI67 WILD-TYPE 
             29             219 
[1] "EIF2S2 MUTATION ANALYSIS"
[1] 3
  EIF2S2 MUTATED EIF2S2 WILD-TYPE 
               9              239 
  EIF2S2 MUTATED EIF2S2 WILD-TYPE 
               9              239 
[1] "BCOR MUTATION ANALYSIS"
[1] 3
  BCOR MUTATED BCOR WILD-TYPE 
            30            218 
  BCOR MUTATED BCOR WILD-TYPE 
            30            218 
[1] "RASA1 MUTATION ANALYSIS"
[1] 3
  RASA1 MUTATED RASA1 WILD-TYPE 
             21             227 
  RASA1 MUTATED RASA1 WILD-TYPE 
             21             227 
[1] "DNER MUTATION ANALYSIS"
[1] 3
  DNER MUTATED DNER WILD-TYPE 
            18            230 
  DNER MUTATED DNER WILD-TYPE 
            18            230 
[1] "C9ORF23 MUTATION ANALYSIS"
[1] 3
  C9ORF23 MUTATED C9ORF23 WILD-TYPE 
                9               239 
  C9ORF23 MUTATED C9ORF23 WILD-TYPE 
                9               239 
[1] "CUX1 MUTATION ANALYSIS"
[1] 3
  CUX1 MUTATED CUX1 WILD-TYPE 
            21            227 
  CUX1 MUTATED CUX1 WILD-TYPE 
            21            227 
[1] "CDK17 MUTATION ANALYSIS"
[1] 3
  CDK17 MUTATED CDK17 WILD-TYPE 
             14             234 
  CDK17 MUTATED CDK17 WILD-TYPE 
             14             234 
[1] "USP28 MUTATION ANALYSIS"
[1] 3
  USP28 MUTATED USP28 WILD-TYPE 
             10             238 
  USP28 MUTATED USP28 WILD-TYPE 
             10             238 
[1] "MSH6 MUTATION ANALYSIS"
[1] 3
  MSH6 MUTATED MSH6 WILD-TYPE 
            17            231 
  MSH6 MUTATED MSH6 WILD-TYPE 
            17            231 
[1] "WDR45 MUTATION ANALYSIS"
[1] 3
  WDR45 MUTATED WDR45 WILD-TYPE 
             11             237 
  WDR45 MUTATED WDR45 WILD-TYPE 
             11             237 
[1] "C14ORF166B MUTATION ANALYSIS"
[1] 3
  C14ORF166B MUTATED C14ORF166B WILD-TYPE 
                   9                  239 
  C14ORF166B MUTATED C14ORF166B WILD-TYPE 
                   9                  239 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           29           219 
  ATM MUTATED ATM WILD-TYPE 
           29           219 
[1] "RAE1 MUTATION ANALYSIS"
[1] 3
  RAE1 MUTATED RAE1 WILD-TYPE 
            11            237 
  RAE1 MUTATED RAE1 WILD-TYPE 
            11            237 
[1] "ZNF485 MUTATION ANALYSIS"
[1] 3
  ZNF485 MUTATED ZNF485 WILD-TYPE 
               9              239 
  ZNF485 MUTATED ZNF485 WILD-TYPE 
               9              239 
[1] "POLE MUTATION ANALYSIS"
[1] 3
  POLE MUTATED POLE WILD-TYPE 
            27            221 
  POLE MUTATED POLE WILD-TYPE 
            27            221 
[1] "AHCYL1 MUTATION ANALYSIS"
[1] 3
  AHCYL1 MUTATED AHCYL1 WILD-TYPE 
               6              242 
  AHCYL1 MUTATED AHCYL1 WILD-TYPE 
               6              242 
[1] "ZNF334 MUTATION ANALYSIS"
[1] 3
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              17              231 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              17              231 
[1] "SACS MUTATION ANALYSIS"
[1] 3
  SACS MUTATED SACS WILD-TYPE 
            26            222 
  SACS MUTATED SACS WILD-TYPE 
            26            222 
[1] "MSH4 MUTATION ANALYSIS"
[1] 3
  MSH4 MUTATED MSH4 WILD-TYPE 
            15            233 
  MSH4 MUTATED MSH4 WILD-TYPE 
            15            233 
[1] "SLC26A8 MUTATION ANALYSIS"
[1] 3
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
               12               236 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
               12               236 
[1] "KIF20B MUTATION ANALYSIS"
[1] 3
  KIF20B MUTATED KIF20B WILD-TYPE 
              21              227 
  KIF20B MUTATED KIF20B WILD-TYPE 
              21              227 
[1] "RRAS2 MUTATION ANALYSIS"
[1] 3
  RRAS2 MUTATED RRAS2 WILD-TYPE 
              4             244 
  RRAS2 MUTATED RRAS2 WILD-TYPE 
              4             244 
[1] "CTNND1 MUTATION ANALYSIS"
[1] 3
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              19              229 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              19              229 
[1] "NFE2L3 MUTATION ANALYSIS"
[1] 3
  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
              12              236 
  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
              12              236 
[1] "FAM65B MUTATION ANALYSIS"
[1] 3
  FAM65B MUTATED FAM65B WILD-TYPE 
              16              232 
  FAM65B MUTATED FAM65B WILD-TYPE 
              16              232 
[1] "RNF43 MUTATION ANALYSIS"
[1] 3
  RNF43 MUTATED RNF43 WILD-TYPE 
             12             236 
  RNF43 MUTATED RNF43 WILD-TYPE 
             12             236 
[1] "MRPL47 MUTATION ANALYSIS"
[1] 3
  MRPL47 MUTATED MRPL47 WILD-TYPE 
               6              242 
  MRPL47 MUTATED MRPL47 WILD-TYPE 
               6              242 
[1] "TIGD4 MUTATION ANALYSIS"
[1] 3
  TIGD4 MUTATED TIGD4 WILD-TYPE 
             13             235 
  TIGD4 MUTATED TIGD4 WILD-TYPE 
             13             235 
[1] "FILIP1 MUTATION ANALYSIS"
[1] 3
  FILIP1 MUTATED FILIP1 WILD-TYPE 
              16              232 
  FILIP1 MUTATED FILIP1 WILD-TYPE 
              16              232 
[1] "SLC1A3 MUTATION ANALYSIS"
[1] 3
  SLC1A3 MUTATED SLC1A3 WILD-TYPE 
              12              236 
  SLC1A3 MUTATED SLC1A3 WILD-TYPE 
              12              236 
[1] "UFSP2 MUTATION ANALYSIS"
[1] 3
  UFSP2 MUTATED UFSP2 WILD-TYPE 
             11             237 
  UFSP2 MUTATED UFSP2 WILD-TYPE 
             11             237 
[1] "WBP4 MUTATION ANALYSIS"
[1] 3
  WBP4 MUTATED WBP4 WILD-TYPE 
             8            240 
  WBP4 MUTATED WBP4 WILD-TYPE 
             8            240 
[1] "TRIM59 MUTATION ANALYSIS"
[1] 3
  TRIM59 MUTATED TRIM59 WILD-TYPE 
               9              239 
  TRIM59 MUTATED TRIM59 WILD-TYPE 
               9              239 
[1] "RSBN1L MUTATION ANALYSIS"
[1] 3
  RSBN1L MUTATED RSBN1L WILD-TYPE 
              12              236 
  RSBN1L MUTATED RSBN1L WILD-TYPE 
              12              236 
[1] "SERHL2 MUTATION ANALYSIS"
[1] 3
  SERHL2 MUTATED SERHL2 WILD-TYPE 
               6              242 
  SERHL2 MUTATED SERHL2 WILD-TYPE 
               6              242 
[1] "OR52I2 MUTATION ANALYSIS"
[1] 3
  OR52I2 MUTATED OR52I2 WILD-TYPE 
               8              240 
  OR52I2 MUTATED OR52I2 WILD-TYPE 
               8              240 
[1] "SGK1 MUTATION ANALYSIS"
[1] 3
  SGK1 MUTATED SGK1 WILD-TYPE 
            13            235 
  SGK1 MUTATED SGK1 WILD-TYPE 
            13            235 
[1] "LNX2 MUTATION ANALYSIS"
[1] 3
  LNX2 MUTATED LNX2 WILD-TYPE 
            14            234 
  LNX2 MUTATED LNX2 WILD-TYPE 
            14            234 
[1] "ALPK2 MUTATION ANALYSIS"
[1] 3
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             19             229 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             19             229 
[1] "REV3L MUTATION ANALYSIS"
[1] 3
  REV3L MUTATED REV3L WILD-TYPE 
             20             228 
  REV3L MUTATED REV3L WILD-TYPE 
             20             228 
[1] "CAB39L MUTATION ANALYSIS"
[1] 3
  CAB39L MUTATED CAB39L WILD-TYPE 
               8              240 
  CAB39L MUTATED CAB39L WILD-TYPE 
               8              240 
[1] "ERBB3 MUTATION ANALYSIS"
[1] 3
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             17             231 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             17             231 
[1] "INPP4B MUTATION ANALYSIS"
[1] 3
  INPP4B MUTATED INPP4B WILD-TYPE 
              12              236 
  INPP4B MUTATED INPP4B WILD-TYPE 
              12              236 
[1] "C1ORF100 MUTATION ANALYSIS"
[1] 3
  C1ORF100 MUTATED C1ORF100 WILD-TYPE 
                 9                239 
  C1ORF100 MUTATED C1ORF100 WILD-TYPE 
                 9                239 
[1] "IL20 MUTATION ANALYSIS"
[1] 3
  IL20 MUTATED IL20 WILD-TYPE 
             7            241 
  IL20 MUTATED IL20 WILD-TYPE 
             7            241 
[1] "SLC44A3 MUTATION ANALYSIS"
[1] 3
  SLC44A3 MUTATED SLC44A3 WILD-TYPE 
                6               242 
  SLC44A3 MUTATED SLC44A3 WILD-TYPE 
                6               242 
[1] "TAP1 MUTATION ANALYSIS"
[1] 3
  TAP1 MUTATED TAP1 WILD-TYPE 
             8            240 
  TAP1 MUTATED TAP1 WILD-TYPE 
             8            240 
[1] "RHBDD3 MUTATION ANALYSIS"
[1] 3
  RHBDD3 MUTATED RHBDD3 WILD-TYPE 
               4              244 
  RHBDD3 MUTATED RHBDD3 WILD-TYPE 
               4              244 
[1] "BRDT MUTATION ANALYSIS"
[1] 3
  BRDT MUTATED BRDT WILD-TYPE 
            14            234 
  BRDT MUTATED BRDT WILD-TYPE 
            14            234 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           20           228 
  RB1 MUTATED RB1 WILD-TYPE 
           20           228 
[1] "MFAP5 MUTATION ANALYSIS"
[1] 3
  MFAP5 MUTATED MFAP5 WILD-TYPE 
              9             239 
  MFAP5 MUTATED MFAP5 WILD-TYPE 
              9             239 
[1] "NAA15 MUTATION ANALYSIS"
[1] 3
  NAA15 MUTATED NAA15 WILD-TYPE 
             14             234 
  NAA15 MUTATED NAA15 WILD-TYPE 
             14             234 
[1] "ZRANB3 MUTATION ANALYSIS"
[1] 3
  ZRANB3 MUTATED ZRANB3 WILD-TYPE 
               7              241 
  ZRANB3 MUTATED ZRANB3 WILD-TYPE 
               7              241 
[1] "SLC34A3 MUTATION ANALYSIS"
[1] 3
  SLC34A3 MUTATED SLC34A3 WILD-TYPE 
                6               242 
  SLC34A3 MUTATED SLC34A3 WILD-TYPE 
                6               242 
[1] "MLH3 MUTATION ANALYSIS"
[1] 3
  MLH3 MUTATED MLH3 WILD-TYPE 
            17            231 
  MLH3 MUTATED MLH3 WILD-TYPE 
            17            231 
[1] "CCDC147 MUTATION ANALYSIS"
[1] 3
  CCDC147 MUTATED CCDC147 WILD-TYPE 
               15               233 
  CCDC147 MUTATED CCDC147 WILD-TYPE 
               15               233 
[1] "ZNF662 MUTATION ANALYSIS"
[1] 3
  ZNF662 MUTATED ZNF662 WILD-TYPE 
              13              235 
  ZNF662 MUTATED ZNF662 WILD-TYPE 
              13              235 
[1] "PSMC4 MUTATION ANALYSIS"
[1] 3
  PSMC4 MUTATED PSMC4 WILD-TYPE 
             11             237 
  PSMC4 MUTATED PSMC4 WILD-TYPE 
             11             237 
[1] "CCDC160 MUTATION ANALYSIS"
[1] 3
  CCDC160 MUTATED CCDC160 WILD-TYPE 
               11               237 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
               11               237 
[1] "PPIL4 MUTATION ANALYSIS"
[1] 3
  PPIL4 MUTATED PPIL4 WILD-TYPE 
             11             237 
  PPIL4 MUTATED PPIL4 WILD-TYPE 
             11             237 
[1] "CCDC144A MUTATION ANALYSIS"
[1] 3
  CCDC144A MUTATED CCDC144A WILD-TYPE 
                18                230 
  CCDC144A MUTATED CCDC144A WILD-TYPE 
                18                230 
[1] "TUBGCP6 MUTATION ANALYSIS"
[1] 3
  TUBGCP6 MUTATED TUBGCP6 WILD-TYPE 
               20               228 
  TUBGCP6 MUTATED TUBGCP6 WILD-TYPE 
               20               228 
[1] "TTC39C MUTATION ANALYSIS"
[1] 3
  TTC39C MUTATED TTC39C WILD-TYPE 
               7              241 
  TTC39C MUTATED TTC39C WILD-TYPE 
               7              241 
[1] "COL8A1 MUTATION ANALYSIS"
[1] 3
  COL8A1 MUTATED COL8A1 WILD-TYPE 
              10              238 
  COL8A1 MUTATED COL8A1 WILD-TYPE 
              10              238 
[1] "PER3 MUTATION ANALYSIS"
[1] 3
  PER3 MUTATED PER3 WILD-TYPE 
            12            236 
  PER3 MUTATED PER3 WILD-TYPE 
            12            236 
[1] "MGA MUTATION ANALYSIS"
[1] 3
  MGA MUTATED MGA WILD-TYPE 
           26           222 
  MGA MUTATED MGA WILD-TYPE 
           26           222 
[1] "GPRASP1 MUTATION ANALYSIS"
[1] 3
  GPRASP1 MUTATED GPRASP1 WILD-TYPE 
               21               227 
  GPRASP1 MUTATED GPRASP1 WILD-TYPE 
               21               227 
[1] "PPM1D MUTATION ANALYSIS"
[1] 3
  PPM1D MUTATED PPM1D WILD-TYPE 
             11             237 
  PPM1D MUTATED PPM1D WILD-TYPE 
             11             237 
[1] "ZNF674 MUTATION ANALYSIS"
[1] 3
  ZNF674 MUTATED ZNF674 WILD-TYPE 
              14              234 
  ZNF674 MUTATED ZNF674 WILD-TYPE 
              14              234 
[1] "LIMK2 MUTATION ANALYSIS"
[1] 3
  LIMK2 MUTATED LIMK2 WILD-TYPE 
             12             236 
  LIMK2 MUTATED LIMK2 WILD-TYPE 
             12             236 
[1] "ZNF606 MUTATION ANALYSIS"
[1] 3
  ZNF606 MUTATED ZNF606 WILD-TYPE 
              16              232 
  ZNF606 MUTATED ZNF606 WILD-TYPE 
              16              232 
[1] "SFRP4 MUTATION ANALYSIS"
[1] 3
  SFRP4 MUTATED SFRP4 WILD-TYPE 
              8             240 
  SFRP4 MUTATED SFRP4 WILD-TYPE 
              8             240 
[1] "TXNRD1 MUTATION ANALYSIS"
[1] 3
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
               8              240 
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
               8              240 
[1] "LETMD1 MUTATION ANALYSIS"
[1] 3
  LETMD1 MUTATED LETMD1 WILD-TYPE 
               6              242 
  LETMD1 MUTATED LETMD1 WILD-TYPE 
               6              242 
[1] "ZNF721 MUTATION ANALYSIS"
[1] 3
  ZNF721 MUTATED ZNF721 WILD-TYPE 
              13              235 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
              13              235 
[1] "RASSF9 MUTATION ANALYSIS"
[1] 3
  RASSF9 MUTATED RASSF9 WILD-TYPE 
               9              239 
  RASSF9 MUTATED RASSF9 WILD-TYPE 
               9              239 
[1] "AGXT2 MUTATION ANALYSIS"
[1] 3
  AGXT2 MUTATED AGXT2 WILD-TYPE 
             11             237 
  AGXT2 MUTATED AGXT2 WILD-TYPE 
             11             237 
[1] "MECOM MUTATION ANALYSIS"
[1] 3
  MECOM MUTATED MECOM WILD-TYPE 
             12             236 
  MECOM MUTATED MECOM WILD-TYPE 
             12             236 
[1] "ATP6V1C2 MUTATION ANALYSIS"
[1] 3
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
                12                236 
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
                12                236 
[1] "DYM MUTATION ANALYSIS"
[1] 3
  DYM MUTATED DYM WILD-TYPE 
           10           238 
  DYM MUTATED DYM WILD-TYPE 
           10           238 
[1] "TAB3 MUTATION ANALYSIS"
[1] 3
  TAB3 MUTATED TAB3 WILD-TYPE 
            18            230 
  TAB3 MUTATED TAB3 WILD-TYPE 
            18            230 
[1] "ZNF649 MUTATION ANALYSIS"
[1] 3
  ZNF649 MUTATED ZNF649 WILD-TYPE 
              14              234 
  ZNF649 MUTATED ZNF649 WILD-TYPE 
              14              234 
[1] "FN1 MUTATION ANALYSIS"
[1] 3
  FN1 MUTATED FN1 WILD-TYPE 
           24           224 
  FN1 MUTATED FN1 WILD-TYPE 
           24           224 
[1] "CCDC150 MUTATION ANALYSIS"
[1] 3
  CCDC150 MUTATED CCDC150 WILD-TYPE 
               11               237 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
               11               237 
[1] "KIF21A MUTATION ANALYSIS"
[1] 3
  KIF21A MUTATED KIF21A WILD-TYPE 
              15              233 
  KIF21A MUTATED KIF21A WILD-TYPE 
              15              233 
[1] "BHLHB9 MUTATION ANALYSIS"
[1] 3
  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
               8              240 
  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
               8              240 
[1] "EXOSC9 MUTATION ANALYSIS"
[1] 3
  EXOSC9 MUTATED EXOSC9 WILD-TYPE 
              10              238 
  EXOSC9 MUTATED EXOSC9 WILD-TYPE 
              10              238 
[1] "ZKSCAN1 MUTATION ANALYSIS"
[1] 3
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                7               241 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                7               241 
[1] "OR8B8 MUTATION ANALYSIS"
[1] 3
  OR8B8 MUTATED OR8B8 WILD-TYPE 
              7             241 
  OR8B8 MUTATED OR8B8 WILD-TYPE 
              7             241 
[1] "SENP7 MUTATION ANALYSIS"
[1] 3
  SENP7 MUTATED SENP7 WILD-TYPE 
             12             236 
  SENP7 MUTATED SENP7 WILD-TYPE 
             12             236 
[1] "WDR65 MUTATION ANALYSIS"
[1] 3
  WDR65 MUTATED WDR65 WILD-TYPE 
              6             242 
  WDR65 MUTATED WDR65 WILD-TYPE 
              6             242 
[1] "NRIP1 MUTATION ANALYSIS"
[1] 3
  NRIP1 MUTATED NRIP1 WILD-TYPE 
             13             235 
  NRIP1 MUTATED NRIP1 WILD-TYPE 
             13             235 
[1] "MCTP1 MUTATION ANALYSIS"
[1] 3
  MCTP1 MUTATED MCTP1 WILD-TYPE 
             13             235 
  MCTP1 MUTATED MCTP1 WILD-TYPE 
             13             235 
[1] "CCDC146 MUTATION ANALYSIS"
[1] 3
  CCDC146 MUTATED CCDC146 WILD-TYPE 
               14               234 
  CCDC146 MUTATED CCDC146 WILD-TYPE 
               14               234 
[1] "ZNF620 MUTATION ANALYSIS"
[1] 3
  ZNF620 MUTATED ZNF620 WILD-TYPE 
               9              239 
  ZNF620 MUTATED ZNF620 WILD-TYPE 
               9              239 
[1] "PTPN12 MUTATION ANALYSIS"
[1] 3
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              10              238 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              10              238 
[1] "RIOK3 MUTATION ANALYSIS"
[1] 3
  RIOK3 MUTATED RIOK3 WILD-TYPE 
              9             239 
  RIOK3 MUTATED RIOK3 WILD-TYPE 
              9             239 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
             17             231 
  CASP8 MUTATED CASP8 WILD-TYPE 
             17             231 
[1] "GFAP MUTATION ANALYSIS"
[1] 3
  GFAP MUTATED GFAP WILD-TYPE 
             6            242 
  GFAP MUTATED GFAP WILD-TYPE 
             6            242 
[1] "OMA1 MUTATION ANALYSIS"
[1] 3
  OMA1 MUTATED OMA1 WILD-TYPE 
            10            238 
  OMA1 MUTATED OMA1 WILD-TYPE 
            10            238 
[1] "DENND3 MUTATION ANALYSIS"
[1] 3
  DENND3 MUTATED DENND3 WILD-TYPE 
              15              233 
  DENND3 MUTATED DENND3 WILD-TYPE 
              15              233 
[1] "CHEK2 MUTATION ANALYSIS"
[1] 3
  CHEK2 MUTATED CHEK2 WILD-TYPE 
             12             236 
  CHEK2 MUTATED CHEK2 WILD-TYPE 
             12             236 
[1] "ZMYM2 MUTATION ANALYSIS"
[1] 3
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
             17             231 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
             17             231 
[1] "EPC2 MUTATION ANALYSIS"
[1] 3
  EPC2 MUTATED EPC2 WILD-TYPE 
             5            243 
  EPC2 MUTATED EPC2 WILD-TYPE 
             5            243 
[1] "DEPDC1B MUTATION ANALYSIS"
[1] 3
  DEPDC1B MUTATED DEPDC1B WILD-TYPE 
               11               237 
  DEPDC1B MUTATED DEPDC1B WILD-TYPE 
               11               237 
[1] "C3AR1 MUTATION ANALYSIS"
[1] 3
  C3AR1 MUTATED C3AR1 WILD-TYPE 
              7             241 
  C3AR1 MUTATED C3AR1 WILD-TYPE 
              7             241 
[1] "STK3 MUTATION ANALYSIS"
[1] 3
  STK3 MUTATED STK3 WILD-TYPE 
            10            238 
  STK3 MUTATED STK3 WILD-TYPE 
            10            238 
[1] "FOXJ3 MUTATION ANALYSIS"
[1] 3
  FOXJ3 MUTATED FOXJ3 WILD-TYPE 
             10             238 
  FOXJ3 MUTATED FOXJ3 WILD-TYPE 
             10             238 
[1] "EPS8 MUTATION ANALYSIS"
[1] 3
  EPS8 MUTATED EPS8 WILD-TYPE 
            12            236 
  EPS8 MUTATED EPS8 WILD-TYPE 
            12            236 
[1] "ZNF385B MUTATION ANALYSIS"
[1] 3
  ZNF385B MUTATED ZNF385B WILD-TYPE 
                7               241 
  ZNF385B MUTATED ZNF385B WILD-TYPE 
                7               241 
[1] "EFCAB4B MUTATION ANALYSIS"
[1] 3
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
               11               237 
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
               11               237 
[1] "NPRL2 MUTATION ANALYSIS"
[1] 3
  NPRL2 MUTATED NPRL2 WILD-TYPE 
              5             243 
  NPRL2 MUTATED NPRL2 WILD-TYPE 
              5             243 
[1] "ATF6 MUTATION ANALYSIS"
[1] 3
  ATF6 MUTATED ATF6 WILD-TYPE 
            14            234 
  ATF6 MUTATED ATF6 WILD-TYPE 
            14            234 
[1] "LIMA1 MUTATION ANALYSIS"
[1] 3
  LIMA1 MUTATED LIMA1 WILD-TYPE 
              8             240 
  LIMA1 MUTATED LIMA1 WILD-TYPE 
              8             240 
[1] "PPIG MUTATION ANALYSIS"
[1] 3
  PPIG MUTATED PPIG WILD-TYPE 
            16            232 
  PPIG MUTATED PPIG WILD-TYPE 
            16            232 
[1] "ZNF774 MUTATION ANALYSIS"
[1] 3
  ZNF774 MUTATED ZNF774 WILD-TYPE 
              10              238 
  ZNF774 MUTATED ZNF774 WILD-TYPE 
              10              238 
[1] "MUTED MUTATION ANALYSIS"
[1] 3
  MUTED MUTATED MUTED WILD-TYPE 
              7             241 
  MUTED MUTATED MUTED WILD-TYPE 
              7             241 
[1] "TPX2 MUTATION ANALYSIS"
[1] 3
  TPX2 MUTATED TPX2 WILD-TYPE 
             6            242 
  TPX2 MUTATED TPX2 WILD-TYPE 
             6            242 
[1] "PARG MUTATION ANALYSIS"
[1] 3
  PARG MUTATED PARG WILD-TYPE 
             9            239 
  PARG MUTATED PARG WILD-TYPE 
             9            239 
[1] "PSMD3 MUTATION ANALYSIS"
[1] 3
  PSMD3 MUTATED PSMD3 WILD-TYPE 
             11             237 
  PSMD3 MUTATED PSMD3 WILD-TYPE 
             11             237 
[1] "STRN3 MUTATION ANALYSIS"
[1] 3
  STRN3 MUTATED STRN3 WILD-TYPE 
             12             236 
  STRN3 MUTATED STRN3 WILD-TYPE 
             12             236 
[1] "MLL4 MUTATION ANALYSIS"
[1] 3
  MLL4 MUTATED MLL4 WILD-TYPE 
            30            218 
  MLL4 MUTATED MLL4 WILD-TYPE 
            30            218 
[1] "MSN MUTATION ANALYSIS"
[1] 3
  MSN MUTATED MSN WILD-TYPE 
           15           233 
  MSN MUTATED MSN WILD-TYPE 
           15           233 
[1] "MAPK8 MUTATION ANALYSIS"
[1] 3
  MAPK8 MUTATED MAPK8 WILD-TYPE 
             11             237 
  MAPK8 MUTATED MAPK8 WILD-TYPE 
             11             237 
[1] "RBL2 MUTATION ANALYSIS"
[1] 3
  RBL2 MUTATED RBL2 WILD-TYPE 
            12            236 
  RBL2 MUTATED RBL2 WILD-TYPE 
            12            236 
[1] "PDGFRA MUTATION ANALYSIS"
[1] 3
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              12              236 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              12              236 
[1] "TMEM62 MUTATION ANALYSIS"
[1] 3
  TMEM62 MUTATED TMEM62 WILD-TYPE 
               9              239 
  TMEM62 MUTATED TMEM62 WILD-TYPE 
               9              239 
[1] "RG9MTD3 MUTATION ANALYSIS"
[1] 3
  RG9MTD3 MUTATED RG9MTD3 WILD-TYPE 
                8               240 
  RG9MTD3 MUTATED RG9MTD3 WILD-TYPE 
                8               240 
[1] "KANK4 MUTATION ANALYSIS"
[1] 3
  KANK4 MUTATED KANK4 WILD-TYPE 
             11             237 
  KANK4 MUTATED KANK4 WILD-TYPE 
             11             237 
[1] "MYOM1 MUTATION ANALYSIS"
[1] 3
  MYOM1 MUTATED MYOM1 WILD-TYPE 
             23             225 
  MYOM1 MUTATED MYOM1 WILD-TYPE 
             23             225 
[1] "MORC3 MUTATION ANALYSIS"
[1] 3
  MORC3 MUTATED MORC3 WILD-TYPE 
             10             238 
  MORC3 MUTATED MORC3 WILD-TYPE 
             10             238 
[1] "CCDC82 MUTATION ANALYSIS"
[1] 3
  CCDC82 MUTATED CCDC82 WILD-TYPE 
              12              236 
  CCDC82 MUTATED CCDC82 WILD-TYPE 
              12              236 
[1] "B3GALT5 MUTATION ANALYSIS"
[1] 3
  B3GALT5 MUTATED B3GALT5 WILD-TYPE 
                4               244 
  B3GALT5 MUTATED B3GALT5 WILD-TYPE 
                4               244 
[1] "NOC3L MUTATION ANALYSIS"
[1] 3
  NOC3L MUTATED NOC3L WILD-TYPE 
             11             237 
  NOC3L MUTATED NOC3L WILD-TYPE 
             11             237 
[1] "NSUN4 MUTATION ANALYSIS"
[1] 3
  NSUN4 MUTATED NSUN4 WILD-TYPE 
              6             242 
  NSUN4 MUTATED NSUN4 WILD-TYPE 
              6             242 
[1] "ASXL2 MUTATION ANALYSIS"
[1] 3
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             14             234 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             14             234 
[1] "CHD4 MUTATION ANALYSIS"
[1] 3
  CHD4 MUTATED CHD4 WILD-TYPE 
            35            213 
  CHD4 MUTATED CHD4 WILD-TYPE 
            35            213 
[1] "FCN1 MUTATION ANALYSIS"
[1] 3
  FCN1 MUTATED FCN1 WILD-TYPE 
             7            241 
  FCN1 MUTATED FCN1 WILD-TYPE 
             7            241 
[1] "NIPA2 MUTATION ANALYSIS"
[1] 3
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              8             240 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              8             240 
[1] "C14ORF118 MUTATION ANALYSIS"
[1] 3
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                 13                 235 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                 13                 235 
[1] "THAP5 MUTATION ANALYSIS"
[1] 3
  THAP5 MUTATED THAP5 WILD-TYPE 
              6             242 
  THAP5 MUTATED THAP5 WILD-TYPE 
              6             242 
[1] "ZNF611 MUTATION ANALYSIS"
[1] 3
  ZNF611 MUTATED ZNF611 WILD-TYPE 
              12              236 
  ZNF611 MUTATED ZNF611 WILD-TYPE 
              12              236 
[1] "ZCCHC18 MUTATION ANALYSIS"
[1] 3
  ZCCHC18 MUTATED ZCCHC18 WILD-TYPE 
                6               242 
  ZCCHC18 MUTATED ZCCHC18 WILD-TYPE 
                6               242 
[1] "PRKCE MUTATION ANALYSIS"
[1] 3
  PRKCE MUTATED PRKCE WILD-TYPE 
              9             239 
  PRKCE MUTATED PRKCE WILD-TYPE 
              9             239 
[1] "BMP2K MUTATION ANALYSIS"
[1] 3
  BMP2K MUTATED BMP2K WILD-TYPE 
             13             235 
  BMP2K MUTATED BMP2K WILD-TYPE 
             13             235 
[1] "PRPF38B MUTATION ANALYSIS"
[1] 3
  PRPF38B MUTATED PRPF38B WILD-TYPE 
               11               237 
  PRPF38B MUTATED PRPF38B WILD-TYPE 
               11               237 
[1] "LGMN MUTATION ANALYSIS"
[1] 3
  LGMN MUTATED LGMN WILD-TYPE 
             7            241 
  LGMN MUTATED LGMN WILD-TYPE 
             7            241 
[1] "SSH2 MUTATION ANALYSIS"
[1] 3
  SSH2 MUTATED SSH2 WILD-TYPE 
            12            236 
  SSH2 MUTATED SSH2 WILD-TYPE 
            12            236 
[1] "EMR1 MUTATION ANALYSIS"
[1] 3
  EMR1 MUTATED EMR1 WILD-TYPE 
            11            237 
  EMR1 MUTATED EMR1 WILD-TYPE 
            11            237 
[1] "OR5AK2 MUTATION ANALYSIS"
[1] 3
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
               5              243 
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
               5              243 
[1] "C1ORF101 MUTATION ANALYSIS"
[1] 3
  C1ORF101 MUTATED C1ORF101 WILD-TYPE 
                12                236 
  C1ORF101 MUTATED C1ORF101 WILD-TYPE 
                12                236 
[1] "ZNF534 MUTATION ANALYSIS"
[1] 3
  ZNF534 MUTATED ZNF534 WILD-TYPE 
               9              239 
  ZNF534 MUTATED ZNF534 WILD-TYPE 
               9              239 
[1] "FAM122A MUTATION ANALYSIS"
[1] 3
  FAM122A MUTATED FAM122A WILD-TYPE 
                6               242 
  FAM122A MUTATED FAM122A WILD-TYPE 
                6               242 
[1] "data2feature, selection=ALL"
 [1] "VITAL_STATUS"                        
 [2] "DAYS_TO_DEATH"                       
 [3] "DAYS_TO_LAST_FOLLOWUP"               
 [4] "TUMOR_TISSUE_SITE"                   
 [5] "PATHOLOGIC_STAGE"                    
 [6] "PATHOLOGY_T_STAGE"                   
 [7] "PATHOLOGY_N_STAGE"                   
 [8] "PATHOLOGY_M_STAGE"                   
 [9] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[10] "DAYS_TO_LAST_KNOWN_ALIVE"            
[11] "RADIATION_THERAPY"                   
[12] "HISTOLOGICAL_TYPE"                   
[13] "RESIDUAL_TUMOR"                      

Input Data has 13 rows and 248 columns.

[1] "Last Follow UP"
Variable 1:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 2:'DAYS_TO_DEATH':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 3:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=209,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 4:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 5:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 10:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 11:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[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] "****** SUMMARY ***** "
Output Data has 248 columns, 1 survival variables, and 3 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "RADIATION_THERAPY" "HISTOLOGICAL_TYPE" "RESIDUAL_TUMOR"   
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = PTEN MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  PTEN MUTATED   147  14
  PTEN WILD-TYPE  68  19
  PTEN MUTATED PTEN WILD-TYPE 
           161             87 
  PTEN MUTATED PTEN WILD-TYPE 
            14             19 
$`PTEN MUTATED`
TCGA-A5-A0GM TCGA-BG-A0MS TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-A5-A0G9 
       60.53        61.87        12.56        19.79         4.44        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ 
       17.85        32.78       105.37        74.10        46.55        73.87 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 
       28.27        54.02        23.21        68.65        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AP-A051 
       24.62        29.06        28.77        42.35        15.95       129.80 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A0LD TCGA-AP-A0LE 
       23.31        86.07        48.03        23.87       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       66.25        46.72        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       49.22        25.08        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       88.24        71.51        35.34        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JR TCGA-B5-A0JS 
       60.66        61.08        40.11        77.39        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 
       55.30        86.01        69.27        71.44        36.49        72.62 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11H 
       57.76        64.21        63.55        13.45        59.84        88.34 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        19.56        19.50        19.59        18.41        17.36 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MQ TCGA-BG-A0MT 
       74.63        41.52        48.56        23.47        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VW TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       20.28        15.42        52.01        52.64        52.83        56.58 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BK-A0C9 TCGA-BK-A0CA 
       13.78        14.73        14.01        15.45        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       35.90        31.00        24.99        24.33        85.55        78.21 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       61.87        67.99        30.74        97.41       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UM TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       82.39        86.93        73.25        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       66.48        16.83         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
        1.74        21.99        30.08         1.91         3.68        29.33 
TCGA-D1-A165 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
        0.66        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y 
       31.07        33.63        10.65         0.69         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
       30.44         1.28        28.01        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.78        11.15        24.30         2.33        22.92 

$`PTEN WILD-TYPE`
TCGA-A5-A0GI TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP 
       88.18       110.63        57.80        93.99        67.66        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-EY-A212 
       27.88        80.38        22.06        66.41        51.55        10.19 
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0GD TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 
       46.95        37.02       112.54        65.75        60.53        37.91 
TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05P 
       20.25        21.99        63.91        45.53        36.89        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LL TCGA-AP-A0LM 
       48.79       125.42        36.36        97.71        83.97        27.12 
TCGA-AP-A1DQ TCGA-AX-A062 TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 
       46.78        45.99        35.74        37.78        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0K0 TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11F TCGA-B5-A11G 
       71.24        48.59        27.29        27.85       185.79       113.36 
TCGA-B5-A11I TCGA-B5-A11U TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       75.72        16.73        16.57        50.89        11.87        18.61 
TCGA-BG-A0MO TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0YU TCGA-BG-A18C TCGA-BG-A2AE 
       43.04        51.06        34.29        14.83        15.45        23.70 
TCGA-BK-A0CC TCGA-BS-A0T9 TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0U5 TCGA-BS-A0U9 
       35.08        46.95         4.80        77.95        96.49        92.88 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A15V 
       81.57        72.72        29.95         8.55        22.55        39.48 
TCGA-D1-A15X TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16G TCGA-D1-A16I 
       29.88        32.58        15.72        36.10        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16S TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       29.92        18.67        28.08        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  PTEN MUTATED PTEN WILD-TYPE 
          0.56           4.80 
  PTEN MUTATED PTEN WILD-TYPE 
        129.80         185.79 
  PTEN MUTATED PTEN WILD-TYPE 
         35.21          36.39 
[1] "0.6 - 129.8 (35.2)" "4.8 - 185.8 (36.4)"
[1] "hr=" "2.3"
D1V2, binary
                cls
clus               0   1
  PTEN MUTATED   108  53
  PTEN WILD-TYPE  49  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED    108   53
  PTEN WILD-TYPE   49   38
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO           108             49
  YES           53             38
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PTEN MUTATED                                       159
  PTEN WILD-TYPE                                      41
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  PTEN MUTATED                               1
  PTEN WILD-TYPE                             3
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  PTEN MUTATED                                   1
  PTEN WILD-TYPE                                43
D1V3, multiclass
                                         clus
vv                                        PTEN MUTATED PTEN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA          159             41
  MIXED SEROUS AND ENDOMETRIOID                      1              3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  1             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED   114   7   1  11
  PTEN WILD-TYPE  58   3   6   7
D1V4, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0          114             58
  R1            7              3
  R2            1              6
  RX           11              7
[1] 4 2
[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 = PIK3R1 MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2                0   1
  PIK3R1 MUTATED    68  14
  PIK3R1 WILD-TYPE 147  19
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              82              166 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              14               19 
$`PIK3R1 MUTATED`
TCGA-B5-A0JN TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-A5-A0G9 TCGA-A5-A0GE TCGA-A5-A0GU 
       80.38        66.41        61.87        83.51       105.37        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0R7 TCGA-A5-A0R9 TCGA-A5-A0VO TCGA-A5-A0VQ 
       54.02        23.21        17.59        24.62        28.77        15.95 
TCGA-AJ-A23M TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A0LH TCGA-AP-A0LO 
       20.25        86.07        48.03        23.87        36.36        33.40 
TCGA-AX-A05S TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A063 
       13.58        29.69        80.55        88.24        71.51        79.46 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JR 
       27.39        60.66        61.08        40.11        77.39        56.91 
TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K3 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       71.44        36.49        27.29        13.45        59.84       185.79 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11N TCGA-B5-A11R TCGA-B5-A11V TCGA-B5-A11W 
       88.34        54.44        61.68        77.23        19.56        19.50 
TCGA-B5-A11Z TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M9 TCGA-BG-A0MG TCGA-BG-A0MI 
       17.36        20.19        35.21        74.63        48.56        23.47 
TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0W1 TCGA-BG-A18B TCGA-BK-A139 TCGA-BS-A0T9 
       20.28        51.06        52.83        15.45        31.00        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0U5 TCGA-BS-A0U9 TCGA-BS-A0UA 
       24.33        85.55        78.21        96.49        92.88       114.90 
TCGA-BS-A0UV TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZS TCGA-D1-A101 TCGA-D1-A103 
       73.25        16.83         8.55         4.87         1.74        21.99 
TCGA-D1-A15W TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A169 
       30.08         3.68        29.33        32.58         0.66        37.32 
TCGA-D1-A16Q TCGA-D1-A16X TCGA-D1-A176 TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       10.65         3.65        30.15         7.00         0.99        30.44 
TCGA-D1-A17M TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17U 
       10.22         1.78        11.15        22.92 

$`PIK3R1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-BG-A0M6 TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO 
       36.39        27.88        22.06        51.55        12.56        19.79 
TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0GA TCGA-A5-A0GB 
        4.44        10.19        46.95        37.02        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      112.54        74.10        65.75        60.53        46.55        73.87 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-AP-A051 
       68.65        37.91        19.59        29.06        42.35       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05P 
       21.99        23.31        63.91        45.53        36.89        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LI 
       48.79       125.42       117.99       110.37        66.25        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05T TCGA-AX-A060 TCGA-AX-A062 
       49.22        25.08        46.78        33.21        35.34        45.99 
TCGA-AX-A064 TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       49.87        35.74        37.78        34.65        25.51        71.24 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0K0 TCGA-B5-A0K2 
       86.37        55.30        86.01        69.27        48.59        72.62 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A11G TCGA-B5-A11I 
       57.76        64.21        63.55        27.85       113.36        75.72 
TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11X 
       44.78        85.78        32.09        73.28        16.73        19.59 
TCGA-B5-A11Y TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0M0 
       18.41        16.57        50.89        11.87        18.61        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0MC TCGA-BG-A0MO TCGA-BG-A0MQ 
       20.94        71.24        63.68        41.52        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 
       21.17        15.42        52.01        34.29        52.64        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18C TCGA-BG-A2AE 
       14.83        13.78        14.73        14.01        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13C TCGA-BS-A0TE 
       35.90        34.98        35.90        35.08        24.99         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UF 
       77.95        61.87        67.99        30.74        97.41        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 
       82.39        81.57        86.93        72.72        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZU TCGA-D1-A0ZV 
       83.64        66.48        29.95         0.56        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A167 TCGA-D1-A168 
       22.55        39.48        29.88         1.91        15.72        36.10 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y 
       29.92        31.07        33.63         0.69        18.67        17.49 
TCGA-D1-A174 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
       19.53        18.02         1.58         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17N TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A1NU TCGA-D1-A1NX 
       26.37         1.51        24.30         2.33        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
            0.66             0.56 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
          185.79           129.80 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
          31.790           36.375 
[1] "0.7 - 185.8 (31.8)" "0.6 - 129.8 (36.4)"
[1] "hr=" "1.6"
D2V2, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED    55  27
  PIK3R1 WILD-TYPE 102  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED     55   27
  PIK3R1 WILD-TYPE  102   64
     clus
vv    PIK3R1 MUTATED PIK3R1 WILD-TYPE
  NO              55              102
  YES             27               64
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PIK3R1 MUTATED                                        79
  PIK3R1 WILD-TYPE                                     121
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  PIK3R1 MUTATED                               1
  PIK3R1 WILD-TYPE                             3
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  PIK3R1 MUTATED                                   2
  PIK3R1 WILD-TYPE                                42
D2V3, multiclass
                                         clus
vv                                        PIK3R1 MUTATED PIK3R1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             79              121
  MIXED SEROUS AND ENDOMETRIOID                        1                3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    2               42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PIK3R1 MUTATED    55   4   2   5
  PIK3R1 WILD-TYPE 117   6   5  13
D2V4, multiclass
    clus
vv   PIK3R1 MUTATED PIK3R1 WILD-TYPE
  R0             55              117
  R1              4                6
  R2              2                5
  RX              5               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"

Clustering(3) Variable = TP53 MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  TP53 MUTATED    52  17
  TP53 WILD-TYPE 163  16
  TP53 MUTATED TP53 WILD-TYPE 
            69            179 
  TP53 MUTATED TP53 WILD-TYPE 
            17             16 
$`TP53 MUTATED`
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A2HF 
      110.63        57.80        93.99        67.66        36.39        27.88 
TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-EY-A212 TCGA-A5-A0G3 
       80.38        22.06        66.41        12.56        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0GW TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-AJ-A23M 
       37.02        65.75        23.21        37.91        17.59        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        48.03        63.91        45.53        36.89 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AX-A060 
       48.79       125.42        36.36        97.71        46.78        35.34 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0K3 TCGA-B5-A11E 
       35.74        37.78        25.51        71.24        27.29        59.84 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11N TCGA-B5-A1MU TCGA-BG-A0M7 TCGA-BG-A18C 
       75.72        54.44        61.68        50.89        63.68        15.45 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0UF TCGA-BS-A0UV 
       35.08        31.00        61.87        92.88        85.84        73.25 
TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16G TCGA-D1-A16I 
       83.64        22.55        39.48        37.32        27.42        11.51 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NX 
       31.07        18.67        17.49        28.08        13.22        18.25 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

$`TP53 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-BG-A0MS TCGA-BG-A0VT TCGA-D1-A0ZO TCGA-D1-A102 
       88.18        60.53        61.87        51.55        19.79         4.44 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX 
       60.53        46.55        73.87        28.27        54.02        68.65 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.59        24.62        29.06        28.77        42.35        15.95 
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
      129.80        86.07        23.87        20.91       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       66.25        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AX-A05S TCGA-AX-A05T 
       61.64        80.78        49.22        25.08        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A063 
       29.69        80.55        88.24        71.51        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0J0 TCGA-AX-A0J1 
       49.87        27.39        60.66        61.08        40.11        77.39 
TCGA-AX-A1C7 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       34.65        56.91        86.37        55.30        86.01        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 
       71.44        48.59        36.49        72.62        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        13.45       185.79       113.36        88.34 
TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       44.78        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       71.24        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.73        14.01        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       35.90        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
        4.80        77.95        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
      114.90        82.39        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       63.58        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W 
        4.87        28.67        23.93         1.74        21.99        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       15.72        36.10        36.36        37.51        36.79         2.63 
TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A174 
       29.92        33.63        10.65         0.69         3.65        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-DI-A0WH 
       11.15        24.30         2.33        22.92        16.31 

  TP53 MUTATED TP53 WILD-TYPE 
          9.34           0.56 
  TP53 MUTATED TP53 WILD-TYPE 
        125.42         185.79 
  TP53 MUTATED TP53 WILD-TYPE 
         37.32          34.29 
[1] "9.3 - 125.4 (37.3)" "0.6 - 185.8 (34.3)"
[1] "hr=" "2.6"
D3V2, binary
                cls
clus               0   1
  TP53 MUTATED    42  27
  TP53 WILD-TYPE 115  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     42   27
  TP53 WILD-TYPE  115   64
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            42            115
  YES           27             64
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  TP53 MUTATED                                        27
  TP53 WILD-TYPE                                     173
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  TP53 MUTATED                               3
  TP53 WILD-TYPE                             1
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  TP53 MUTATED                                  39
  TP53 WILD-TYPE                                 5
D3V3, multiclass
                                         clus
vv                                        TP53 MUTATED TP53 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           27            173
  MIXED SEROUS AND ENDOMETRIOID                      3              1
  SEROUS ENDOMETRIAL ADENOCARCINOMA                 39              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TP53 MUTATED    46   6   4   5
  TP53 WILD-TYPE 126   4   3  13
D3V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           46            126
  R1            6              4
  R2            4              3
  RX            5             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"

Clustering(4) Variable = CTCF MUTATION ANALYSIS
D4V1, survival
                sevent
clus2              0   1
  CTCF MUTATED    41   3
  CTCF WILD-TYPE 174  30
  CTCF MUTATED CTCF WILD-TYPE 
            44            204 
  CTCF MUTATED CTCF WILD-TYPE 
             3             30 
$`CTCF MUTATED`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GA TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0R9 
       88.18        60.53        17.85        74.10        46.55        24.62 
TCGA-A5-A0VO TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LP 
       28.77       129.80        48.03        83.97        27.12        61.64 
TCGA-AX-A05T TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A06H TCGA-AX-A0J0 TCGA-B5-A0JV 
       33.21        88.24        71.51        27.39        40.11        86.01 
TCGA-B5-A0K7 TCGA-B5-A11R TCGA-B5-A11X TCGA-B5-A11Y TCGA-BG-A0LX TCGA-BG-A0M4 
       63.55        77.23        19.59        18.41        20.19        71.24 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A186 TCGA-BK-A0C9 
       74.63        41.52        43.04        59.74        13.78        35.90 
TCGA-BS-A0T9 TCGA-BS-A0U5 TCGA-BS-A0UJ TCGA-BS-A0UM TCGA-BS-A0V6 TCGA-D1-A0ZR 
       46.95        96.49        82.39        86.93        89.59         0.56 
TCGA-D1-A0ZV TCGA-D1-A161 TCGA-D1-A16D TCGA-D1-A16Q TCGA-D1-A16X TCGA-D1-A17D 
       23.93        29.33        37.51        10.65         3.65        30.44 
TCGA-D1-A17S TCGA-D1-A17U 
       24.30        22.92 

$`CTCF WILD-TYPE`
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A2HF 
      110.63        57.80        93.99        67.66        36.39        27.88 
TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV 
       80.38        22.06        66.41        61.87        51.55        12.56 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 
       19.79         4.44        10.19        46.95        37.02        83.51 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ 
       32.78       112.54       105.37        65.75        60.53        73.87 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        54.02        23.21        68.65        37.91        17.59 
TCGA-A5-A0R8 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       19.59        29.06        42.35        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LQ 
       36.36        97.71        46.72        82.52        33.40        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05U TCGA-AX-A05W 
       49.22        25.08        46.78        13.58        29.69        80.55 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06L TCGA-AX-A0IS 
       35.34        45.99        79.46        49.87        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        55.30        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K8 
       36.49        72.62        27.29        57.76        64.21        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11S 
       54.44        44.78        61.68        85.78        32.09        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       16.73        19.56        19.50        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M7 
       11.87        18.61        19.33        20.94        35.21        63.68 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       48.56        23.47        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0CA 
       14.73        14.01        15.45        15.45        23.70        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0TA TCGA-BS-A0TC 
       35.90        35.08        31.00        24.99        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U7 
       78.21         4.80        77.95        61.87        67.99        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        92.88       114.90        85.84        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       73.25        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        8.55         4.87        28.67        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A163 
       39.48        30.08        29.88         1.91         3.68        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16E 
        0.66        15.72        36.10        37.32        36.36        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
        0.69        18.67        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        1.58         7.00         0.99         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17T 
       26.37        10.22         1.51         1.78        11.15         2.33 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  CTCF MUTATED CTCF WILD-TYPE 
          0.56           0.66 
  CTCF MUTATED CTCF WILD-TYPE 
        129.80         185.79 
  CTCF MUTATED CTCF WILD-TYPE 
        42.280         35.275 
[1] "0.6 - 129.8 (42.3)" "0.7 - 185.8 (35.3)"
[1] "hr=" "2.4"
D4V2, binary
                cls
clus               0   1
  CTCF MUTATED    27  17
  CTCF WILD-TYPE 130  74
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     27   17
  CTCF WILD-TYPE  130   74
     clus
vv    CTCF MUTATED CTCF WILD-TYPE
  NO            27            130
  YES           17             74
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CTCF MUTATED                                        44
  CTCF WILD-TYPE                                     156
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  CTCF MUTATED                               0
  CTCF WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  CTCF MUTATED                                   0
  CTCF WILD-TYPE                                44
D4V3, multiclass
                                         clus
vv                                        CTCF MUTATED CTCF WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           44            156
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CTCF MUTATED    34   2   1   2
  CTCF WILD-TYPE 138   8   6  16
D4V4, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  R0           34            138
  R1            2              8
  R2            1              6
  RX            2             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"

Clustering(5) Variable = FBXW7 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED    34   4
  FBXW7 WILD-TYPE 181  29
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             38             210 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              4              29 
$`FBXW7 MUTATED`
TCGA-A5-A0GP TCGA-A5-A0R8 TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A05A 
       46.55        19.59        42.35       129.80        86.07        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05P TCGA-AP-A0LM TCGA-AX-A05S TCGA-AX-A05Z 
       45.53        36.89        20.91        27.12        13.58        71.51 
TCGA-AX-A0IU TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-B5-A0JY TCGA-B5-A11E 
       35.74        40.11        34.65        25.51        69.27        59.84 
TCGA-B5-A11N TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A13C TCGA-BS-A0TC TCGA-BS-A0U8 
       61.68        35.90        34.98        24.99        85.55        97.41 
TCGA-D1-A0ZP TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15X TCGA-D1-A160 TCGA-D1-A16G 
       29.95         1.74        21.99        29.88         3.68        27.42 
TCGA-D1-A16I TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A17Q TCGA-DI-A1NN TCGA-E6-A1LZ 
       11.51         3.65        17.49         1.78        35.38        79.10 
TCGA-EO-A1Y5 TCGA-FI-A2EX 
       10.92         9.34 

$`FBXW7 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        37.91        17.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 
       28.77        15.95        20.25        21.99        23.31        48.03 
TCGA-AP-A05N TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       23.87        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05T 
       61.64        80.78        49.22        25.08        46.78        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        80.55        88.24        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0J1 
       49.87        27.39        60.66        61.08        37.78        77.39 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       71.24        56.91        86.37        55.30        86.01        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        13.45       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       75.72        54.44        44.78        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       15.45        15.45        23.70        35.90        35.08        31.00 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        24.33        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        92.88       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 
       82.39        81.57        86.93        72.72        73.25        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       63.58        83.64        66.48        16.83         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A15W 
        4.87        28.67        23.93        22.55        39.48        30.08 
TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        1.91        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16J 
       37.32        36.36        37.51        36.79         2.63        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A174 
       31.07        33.63        10.65         0.69        18.67        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2F8 
       16.31        37.71        22.03        77.33        59.01        30.67 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           1.74            0.56 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         129.80          185.79 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         34.815          36.375 
[1] "1.7 - 129.8 (34.8)" "0.6 - 185.8 (36.4)"
[1] "hr=" "1.2"
D5V2, binary
                 cls
clus                0   1
  FBXW7 MUTATED    26  12
  FBXW7 WILD-TYPE 131  79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     26   12
  FBXW7 WILD-TYPE  131   79
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO             26             131
  YES            12              79
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  FBXW7 MUTATED                                        23
  FBXW7 WILD-TYPE                                     177
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  FBXW7 MUTATED                               1
  FBXW7 WILD-TYPE                             3
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  FBXW7 MUTATED                                  14
  FBXW7 WILD-TYPE                                30
D5V3, multiclass
                                         clus
vv                                        FBXW7 MUTATED FBXW7 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            23             177
  MIXED SEROUS AND ENDOMETRIOID                       1               3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  14              30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FBXW7 MUTATED    26   2   1   5
  FBXW7 WILD-TYPE 146   8   6  13
D5V4, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  R0            26             146
  R1             2               8
  R2             1               6
  RX             5              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"

Clustering(6) Variable = PIK3CA MUTATION ANALYSIS
D6V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED   119  12
  PIK3CA WILD-TYPE  96  21
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             131              117 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              12               21 
$`PIK3CA MUTATED`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A1CP 
       88.18        60.53       110.63        57.80        67.66        36.39 
TCGA-AX-A2HF TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-A5-A0GA 
       27.88        22.06        66.41        19.79         4.44        17.85 
TCGA-A5-A0GB TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0RA 
       32.78        60.53        46.55        68.65        37.91        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
       42.35        15.95        20.25        21.99        23.31        86.07 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      125.42       117.99       110.37        66.25        36.36        46.72 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       27.12        82.52        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05T TCGA-AX-A05W TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       46.78        33.21        80.55        71.51        35.34        45.99 
TCGA-AX-A064 TCGA-AX-A0J0 TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       49.87        40.11        86.37        55.30        86.01        69.27 
TCGA-B5-A0K0 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A11F 
       48.59        72.62        27.29        64.21        63.55       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11R 
      113.36        88.34        75.72        44.78        85.78        77.23 
TCGA-B5-A11S TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A1MU TCGA-BG-A0M0 TCGA-BG-A0M4 
       73.28        19.59        18.41        50.89        19.33        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0RY 
       63.68        74.63        41.52        59.74        21.17        15.42 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A186 TCGA-BG-A187 
       34.29        52.64        52.83        56.58        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BS-A0TC TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0UF TCGA-BS-A0UJ 
       35.90        85.55        77.95        67.99        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        86.93        72.72        73.25        89.59        63.58 
TCGA-BS-A0WQ TCGA-D1-A0ZP TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A103 TCGA-D1-A15V 
       66.48        29.95        28.67        23.93        21.99        39.48 
TCGA-D1-A15X TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D 
       29.88        29.33        32.58        36.10        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79         2.63        27.42        29.92        31.07        33.63 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A174 TCGA-D1-A17A TCGA-D1-A17F TCGA-D1-A17H 
        0.69        18.67        19.53         1.58         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T 
       28.08        26.37        10.22         1.78        24.30         2.33 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-E6-A1LZ TCGA-EO-A1Y8 TCGA-FI-A2D2 
       13.22        18.25        79.10        37.71        77.33 

$`PIK3CA WILD-TYPE`
TCGA-AP-A0LF TCGA-B5-A0JN TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-EY-A212 
       93.99        80.38        61.87        51.55        12.56        10.19 
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       46.95        37.02        83.51       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0R7 
       65.75        73.87        28.27        54.02        23.21        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0VO TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A05A 
       19.59        24.62        28.77       129.80        48.03        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LI 
       45.53        36.89        23.87        20.91        48.79        97.71 
TCGA-AP-A0LL TCGA-AP-A0LO TCGA-AX-A05S TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A063 
       83.97        33.40        13.58        29.69        88.24        79.46 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        61.08        35.74        37.78        77.39 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JZ TCGA-B5-A0K1 
       34.65        25.51        71.24        56.91        71.44        36.49 
TCGA-B5-A0K4 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11J TCGA-B5-A11N 
       57.76        27.85        13.45        59.84        54.44        61.68 
TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Z TCGA-B5-A121 
       32.09        16.73        19.56        19.50        17.36        16.57 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0MG 
       11.87        18.61        20.19        20.94        35.21        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0YU 
       23.47        43.04        20.28        51.06        52.01        14.83 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD 
       35.08        31.00        24.99        46.95        24.33        78.21 
TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
        4.80        61.87        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0V8 TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
      114.90        83.64        16.83         8.55         0.56         4.87 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A165 
       22.55         1.74        30.08         1.91         3.68         0.66 
TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16Q TCGA-D1-A16X TCGA-D1-A16Y 
       15.72        37.32        11.51        10.65         3.65        17.49 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17N 
       30.15        18.02         7.00         0.99        30.44         1.51 
TCGA-D1-A17R TCGA-D1-A17U TCGA-DI-A0WH TCGA-DI-A1NN TCGA-EO-A1Y5 TCGA-EY-A1GS 
       11.15        22.92        16.31        35.38        10.92        22.03 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.69             0.56 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          185.79           129.80 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           39.48            30.67 
[1] "0.7 - 185.8 (39.5)" "0.6 - 129.8 (30.7)"
[1] "hr=" "2.4"
D6V2, binary
                  cls
clus                0  1
  PIK3CA MUTATED   83 48
  PIK3CA WILD-TYPE 74 43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     83   48
  PIK3CA WILD-TYPE   74   43
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              83               74
  YES             48               43
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PIK3CA MUTATED                                       109
  PIK3CA WILD-TYPE                                      91
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  PIK3CA MUTATED                               3
  PIK3CA WILD-TYPE                             1
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  PIK3CA MUTATED                                  19
  PIK3CA WILD-TYPE                                25
D6V3, multiclass
                                         clus
vv                                        PIK3CA MUTATED PIK3CA WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            109               91
  MIXED SEROUS AND ENDOMETRIOID                        3                1
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   19               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  PIK3CA MUTATED   92  4  1 11
  PIK3CA WILD-TYPE 80  6  6  7
D6V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0             92               80
  R1              4                6
  R2              1                6
  RX             11                7
[1] 4 2
[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 = ARID1A MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    80   3
  ARID1A WILD-TYPE 135  30
  ARID1A MUTATED ARID1A WILD-TYPE 
              83              165 
  ARID1A MUTATED ARID1A WILD-TYPE 
               3               30 
$`ARID1A MUTATED`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AX-A2HF TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-A5-A0GB 
       88.18        60.53        27.88        12.56        19.79        32.78 
TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-AP-A051 
       74.10        46.55        73.87        37.91        19.59       129.80 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LL 
       86.07        48.03        23.87       110.37        66.25        83.97 
TCGA-AP-A0LM TCGA-AX-A05T TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       27.12        33.21        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A0IS TCGA-AX-A0J0 TCGA-B5-A0JS TCGA-B5-A0JV 
       45.99        79.46        61.08        40.11        86.37        86.01 
TCGA-B5-A0JY TCGA-B5-A0K0 TCGA-B5-A0K4 TCGA-B5-A11E TCGA-B5-A11M TCGA-B5-A11O 
       69.27        48.59        57.76        59.84        44.78        85.78 
TCGA-B5-A11R TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A121 TCGA-BG-A0LX TCGA-BG-A0M3 
       77.23        19.50        19.59        16.57        20.19        35.21 
TCGA-BG-A0M9 TCGA-BG-A0MG TCGA-BG-A0MT TCGA-BG-A0VV TCGA-BG-A18A TCGA-BG-A18B 
       74.63        48.56        21.17        51.06        14.01        15.45 
TCGA-BG-A2AE TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BS-A0TC TCGA-BS-A0TG TCGA-BS-A0TJ 
       23.70        34.98        35.90        85.55        77.95        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UM TCGA-BS-A0UV 
       96.49        97.41       114.90        82.39        86.93        73.25 
TCGA-BS-A0V6 TCGA-D1-A0ZN TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A15W TCGA-D1-A15X 
       89.59        16.83         4.87        28.67        30.08        29.88 
TCGA-D1-A160 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        3.68        15.72        36.10        36.36        37.51        36.79 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16X TCGA-D1-A176 TCGA-D1-A17A TCGA-D1-A17C 
       33.63        10.65         3.65        30.15         1.58         0.99 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17T 
       28.01        26.37         1.78        11.15         2.33 

$`ARID1A WILD-TYPE`
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP TCGA-B5-A0JN 
      110.63        57.80        93.99        67.66        36.39        80.38 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-D1-A102 TCGA-EY-A212 
       22.06        66.41        61.87        51.55         4.44        10.19 
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GE 
       46.95        37.02        83.51        17.85       112.54       105.37 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       65.75        60.53        28.27        54.02        23.21        68.65 
TCGA-A5-A0R7 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        24.62        29.06        28.77        42.35        15.95 
TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       20.25        21.99        23.31        63.91        45.53        36.89 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LH TCGA-AP-A0LI 
       20.91        48.79       125.42       117.99        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       46.72        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05U TCGA-AX-A064 TCGA-AX-A06H 
       25.08        46.78        13.58        29.69        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       60.66        35.74        37.78        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 
       71.24        56.91        55.30        71.44        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       27.29        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11N TCGA-B5-A11Q 
      113.36        88.34        75.72        54.44        61.68        32.09 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A1MU 
       73.28        16.73        19.56        18.41        17.36        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M7 
       11.87        18.61        19.33        20.94        71.24        63.68 
TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MU TCGA-BG-A0RY 
       41.52        23.47        43.04        59.74        20.28        15.42 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A139 
       13.78        14.73        15.45        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TI 
       24.99        46.95        24.33        78.21         4.80        61.87 
TCGA-BS-A0U7 TCGA-BS-A0U9 TCGA-BS-A0UF TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V7 
       30.74        92.88        85.84        81.57        72.72        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZV 
       83.64        66.48        29.95         8.55         0.56        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15Z TCGA-D1-A161 
       22.55         1.74        21.99        39.48         1.91        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A169 TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       32.58         0.66        37.32         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 
       29.92        31.07         0.69        18.67        17.49        19.53 
TCGA-D1-A177 TCGA-D1-A17B TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17K TCGA-D1-A17M 
       18.02         7.00        30.44         1.28        28.08        10.22 
TCGA-D1-A17N TCGA-D1-A17S TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
        1.51        24.30        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.99             0.56 
  ARID1A MUTATED ARID1A WILD-TYPE 
          129.80           185.79 
  ARID1A MUTATED ARID1A WILD-TYPE 
           37.51            34.65 
[1] "1.0 - 129.8 (37.5)" "0.6 - 185.8 (34.6)"
[1] "hr=" "5.5"
D7V2, binary
                  cls
clus                 0   1
  ARID1A MUTATED    49  34
  ARID1A WILD-TYPE 108  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     49   34
  ARID1A WILD-TYPE  108   57
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO              49              108
  YES             34               57
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ARID1A MUTATED                                        78
  ARID1A WILD-TYPE                                     122
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ARID1A MUTATED                               1
  ARID1A WILD-TYPE                             3
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ARID1A MUTATED                                   4
  ARID1A WILD-TYPE                                40
D7V3, multiclass
                                         clus
vv                                        ARID1A MUTATED ARID1A WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             78              122
  MIXED SEROUS AND ENDOMETRIOID                        1                3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    4               40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ARID1A MUTATED    61   3   0   5
  ARID1A WILD-TYPE 111   7   7  13
D7V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             61              111
  R1              3                7
  R2              0                7
  RX              5               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"

Clustering(8) Variable = ARHGAP35 MUTATION ANALYSIS
D8V1, survival
                    sevent
clus2                  0   1
  ARHGAP35 MUTATED    31   5
  ARHGAP35 WILD-TYPE 184  28
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                36                212 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 5                 28 
$`ARHGAP35 MUTATED`
TCGA-B5-A0JN TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0VP TCGA-AJ-A23M TCGA-AP-A051 
       80.38        37.02       105.37        42.35        20.25       129.80 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A0LM 
       23.31        86.07        48.03        63.91        36.89        27.12 
TCGA-AX-A05U TCGA-AX-A05Z TCGA-AX-A064 TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A11E 
       29.69        71.51        49.87        40.11        77.39        59.84 
TCGA-B5-A11H TCGA-B5-A11Y TCGA-BG-A0MQ TCGA-BK-A0C9 TCGA-BS-A0UF TCGA-BS-A0UL 
       88.34        18.41        59.74        35.90        85.84        81.57 
TCGA-BS-A0UV TCGA-BS-A0WQ TCGA-D1-A103 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A16G 
       73.25        66.48        21.99        32.58         0.66        27.42 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A17F TCGA-D1-A17Q TCGA-E6-A1LZ TCGA-EY-A1GS 
        3.65        17.49         1.28         1.78        79.10        22.03 

$`ARHGAP35 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       36.39        27.88        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G9 
       12.56        19.79         4.44        10.19        46.95        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
       17.85        32.78       112.54        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        73.87        28.27        54.02        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       37.91        17.59        19.59        24.62        29.06        28.77 
TCGA-A5-A0VQ TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       15.95        21.99        45.53        23.87        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05W 
       49.22        25.08        46.78        13.58        33.21        80.55 
TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A06H TCGA-AX-A06L 
       88.24        35.34        45.99        79.46        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       61.08        35.74        37.78        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        86.37        55.30        86.01        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I 
       63.55        27.85        13.45       185.79       113.36        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        19.59        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       48.56        23.47        43.04        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       23.70        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 
      114.90        82.39        86.93        72.72        89.59        63.58 
TCGA-BS-A0V8 TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       83.64        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W 
       28.67        23.93        22.55         1.74        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A167 TCGA-D1-A168 
       29.88         1.91         3.68        29.33        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16I 
       37.32        36.36        37.51        36.79         2.63        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
       30.44        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-FI-A2D2 TCGA-FI-A2EW 
       16.31        35.38        10.92        37.71        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
              0.66               0.56 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
            129.80             185.79 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
            41.230             35.275 
[1] "0.7 - 129.8 (41.2)" "0.6 - 185.8 (35.3)"
[1] "hr=" "1"  
D8V2, binary
                    cls
clus                   0   1
  ARHGAP35 MUTATED    25  11
  ARHGAP35 WILD-TYPE 132  80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP35 MUTATED     25   11
  ARHGAP35 WILD-TYPE  132   80
     clus
vv    ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  NO                25                132
  YES               11                 80
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ARHGAP35 MUTATED                                        28
  ARHGAP35 WILD-TYPE                                     172
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  ARHGAP35 MUTATED                               0
  ARHGAP35 WILD-TYPE                             4
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  ARHGAP35 MUTATED                                   8
  ARHGAP35 WILD-TYPE                                36
D8V3, multiclass
                                         clus
vv                                        ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               28                172
  MIXED SEROUS AND ENDOMETRIOID                          0                  4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      8                 36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ARHGAP35 MUTATED    25   2   1   2
  ARHGAP35 WILD-TYPE 147   8   6  16
D8V4, multiclass
    clus
vv   ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  R0               25                147
  R1                2                  8
  R2                1                  6
  RX                2                 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"

Clustering(9) Variable = KRAS MUTATION ANALYSIS
D9V1, survival
                sevent
clus2              0   1
  KRAS MUTATED    49   3
  KRAS WILD-TYPE 166  30
  KRAS MUTATED KRAS WILD-TYPE 
            52            196 
  KRAS MUTATED KRAS WILD-TYPE 
             3             30 
$`KRAS MUTATED`
TCGA-BG-A0M8 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GP TCGA-A5-A0VO TCGA-AP-A056 
       66.41        17.85        32.78        46.55        28.77        86.07 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LM TCGA-AP-A0LT 
       20.91       117.99       110.37        66.25        27.12        49.22 
TCGA-AX-A05W TCGA-AX-A060 TCGA-AX-A0J0 TCGA-B5-A0JS TCGA-B5-A0JV TCGA-B5-A0K3 
       80.55        35.34        40.11        86.37        86.01        27.29 
TCGA-B5-A0K6 TCGA-B5-A11E TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       64.21        59.84        54.44        44.78        61.68        85.78 
TCGA-B5-A11W TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0VW TCGA-BG-A0VZ TCGA-BG-A187 
       19.50        74.63        41.52        52.01        52.64        14.73 
TCGA-BG-A18B TCGA-BG-A2AE TCGA-BS-A0TC TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U8 
       15.45        23.70        85.55        77.95        67.99        97.41 
TCGA-BS-A0UL TCGA-BS-A0V7 TCGA-D1-A0ZS TCGA-D1-A101 TCGA-D1-A15W TCGA-D1-A15X 
       81.57        63.58         4.87         1.74        30.08        29.88 
TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A168 TCGA-D1-A16D TCGA-D1-A16F TCGA-D1-A16O 
        3.68        32.58        36.10        37.51         2.63        33.63 
TCGA-D1-A16Y TCGA-D1-A17A TCGA-D1-A17H TCGA-D1-A17U 
       17.49         1.58        28.01        22.92 

$`KRAS WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT 
       36.39        27.88        80.38        22.06        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
       83.51       112.54       105.37        74.10        65.75        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       73.87        28.27        54.02        23.21        68.65        37.91 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A 
       20.25       129.80        21.99        23.31        48.03        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LH 
       45.53        36.89        23.87        48.79       125.42        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        46.72        83.97        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       80.78        25.08        46.78        13.58        33.21        29.69 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       88.24        71.51        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        61.08        35.74        37.78        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0JY TCGA-B5-A0JZ 
       25.51        71.24        56.91        55.30        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K7 TCGA-B5-A0K8 
       48.59        36.49        72.62        57.76        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11Q 
       13.45       185.79       113.36        88.34        75.72        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11X TCGA-B5-A11Y 
       77.23        73.28        16.73        19.56        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0MG 
       19.33        20.94        35.21        71.24        63.68        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       51.06        34.29        52.83        56.58        14.83        13.78 
TCGA-BG-A18A TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       14.01        15.45        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE 
       31.00        24.99        46.95        24.33        78.21         4.80 
TCGA-BS-A0TI TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       61.87        96.49        30.74        92.88       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V8 
       82.39        86.93        72.72        73.25        89.59        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZU 
       66.48        16.83        29.95         8.55         0.56        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15Z TCGA-D1-A161 
       23.93        22.55        21.99        39.48         1.91        29.33 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16E TCGA-D1-A16G 
        0.66        15.72        37.32        36.36        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       11.51        29.92        31.07        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17B TCGA-D1-A17C 
        3.65        19.53        30.15        18.02         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
       30.44         1.28        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A1NU TCGA-D1-A1NX 
        1.78        11.15        24.30         2.33        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  KRAS MUTATED KRAS WILD-TYPE 
          1.58           0.56 
  KRAS MUTATED KRAS WILD-TYPE 
        117.99         185.79 
  KRAS MUTATED KRAS WILD-TYPE 
        40.815         35.295 
[1] "1.6 - 118.0 (40.8)" "0.6 - 185.8 (35.3)"
[1] "hr=" "2.9"
D9V2, binary
                cls
clus               0   1
  KRAS MUTATED    32  20
  KRAS WILD-TYPE 125  71
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     32   20
  KRAS WILD-TYPE  125   71
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO            32            125
  YES           20             71
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  KRAS MUTATED                                        51
  KRAS WILD-TYPE                                     149
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  KRAS MUTATED                               0
  KRAS WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  KRAS MUTATED                                   1
  KRAS WILD-TYPE                                43
D9V3, multiclass
                                         clus
vv                                        KRAS MUTATED KRAS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           51            149
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  1             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KRAS MUTATED    34   1   0   5
  KRAS WILD-TYPE 138   9   7  13
D9V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           34            138
  R1            1              9
  R2            0              7
  RX            5             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"

Clustering(10) Variable = CTNNB1 MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2                0   1
  CTNNB1 MUTATED    66   8
  CTNNB1 WILD-TYPE 149  25
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              74              174 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               8               25 
$`CTNNB1 MUTATED`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-BG-A0VT TCGA-D1-A102 TCGA-A5-A0GN TCGA-A5-A0GU 
       88.18        60.53        51.55         4.44        60.53        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R9 TCGA-A5-A0VO TCGA-A5-A0VQ 
       54.02        23.21        68.65        24.62        28.77        15.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A0LE TCGA-AP-A0LG 
       23.31        86.07        48.03        23.87       110.37        66.25 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LV TCGA-AX-A05T 
       46.72        83.97        27.12        82.52        25.08        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A062 TCGA-AX-A0IS TCGA-AX-A0J0 TCGA-AX-A0J1 
       29.69        80.55        45.99        61.08        40.11        77.39 
TCGA-B5-A0JT TCGA-B5-A0JY TCGA-B5-A0K0 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A11E 
       55.30        69.27        48.59        64.21        63.55        59.84 
TCGA-B5-A11F TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A121 
      185.79        16.73        19.56        19.59        17.36        16.57 
TCGA-BG-A0LW TCGA-BG-A0M3 TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MU 
       18.61        35.21        48.56        23.47        43.04        20.28 
TCGA-BG-A0VX TCGA-BG-A0W2 TCGA-BG-A187 TCGA-BK-A0CB TCGA-BS-A0T9 TCGA-BS-A0TG 
       34.29        56.58        14.73        35.90        46.95        77.95 
TCGA-BS-A0UJ TCGA-BS-A0UT TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       82.39        72.72        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZQ TCGA-D1-A0ZU TCGA-D1-A103 TCGA-D1-A15Z TCGA-D1-A165 TCGA-D1-A16B 
        8.55        28.67        21.99         1.91         0.66        36.36 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A17C TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       10.65         0.69         0.99        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T 
       24.30         2.33 

$`CTNNB1 WILD-TYPE`
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A2HF 
      110.63        57.80        93.99        67.66        36.39        27.88 
TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0YV TCGA-D1-A0ZO 
       80.38        22.06        66.41        61.87        12.56        19.79 
TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       10.19        46.95        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ 
      112.54       105.37        74.10        65.75        46.55        73.87 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-AJ-A23M 
       37.91        17.59        19.59        29.06        42.35        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05P 
      129.80        21.99        63.91        45.53        36.89        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LO 
       48.79       125.42       117.99        36.36        97.71        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05Y 
       61.64        80.78        49.22        46.78        13.58        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       71.51        35.34        79.46        49.87        27.39        60.66 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       35.74        37.78        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       86.37        86.01        71.44        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       57.76        27.85        13.45       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LX 
       73.28        19.50        18.41        50.89        11.87        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       19.33        20.94        71.24        63.68        74.63        41.52 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VZ 
       59.74        21.17        15.42        51.06        52.01        52.64 
TCGA-BG-A0W1 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       52.83        14.83        13.78        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       23.70        35.90        34.98        35.08        31.00        24.99 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0TJ 
       24.33        85.55        78.21         4.80        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        92.88       114.90        85.84 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-D1-A0ZP TCGA-D1-A0ZR 
       81.57        86.93        73.25        89.59        29.95         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W 
        4.87        23.93        22.55         1.74        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 
       29.88         3.68        29.33        32.58        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       37.32        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       29.92        31.07        33.63        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17D 
       19.53        30.15        18.02         1.58         7.00        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17Q TCGA-D1-A17U 
        1.28        28.01        28.08        26.37         1.78        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            0.66             0.56 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          185.79           129.80 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          35.555           36.000 
[1] "0.7 - 185.8 (35.6)" "0.6 - 129.8 (36.0)"
[1] "hr=" "1.2"
D10V2, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    50  24
  CTNNB1 WILD-TYPE 107  67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     50   24
  CTNNB1 WILD-TYPE  107   67
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO              50              107
  YES             24               67
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CTNNB1 MUTATED                                        74
  CTNNB1 WILD-TYPE                                     126
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  CTNNB1 MUTATED                               0
  CTNNB1 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  CTNNB1 MUTATED                                   0
  CTNNB1 WILD-TYPE                                44
D10V3, multiclass
                                         clus
vv                                        CTNNB1 MUTATED CTNNB1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             74              126
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CTNNB1 MUTATED    55   3   1   3
  CTNNB1 WILD-TYPE 117   7   6  15
D10V4, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0             55              117
  R1              3                7
  R2              1                6
  RX              3               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"

Clustering(11) Variable = ZFHX3 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2               0   1
  ZFHX3 MUTATED    38   6
  ZFHX3 WILD-TYPE 177  27
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             44             204 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
              6              27 
$`ZFHX3 MUTATED`
TCGA-A5-A0G9 TCGA-A5-A0GB TCGA-A5-A0GP TCGA-A5-A0GV TCGA-AP-A051 TCGA-AP-A054 
       83.51        32.78        46.55        54.02       129.80        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A0L9 TCGA-AP-A0LD 
       86.07        48.03        63.91        23.87       125.42       117.99 
TCGA-AP-A0LG TCGA-AP-A0LM TCGA-AP-A0LT TCGA-AX-A05Z TCGA-AX-A063 TCGA-AX-A06H 
       66.25        27.12        49.22        71.51        79.46        27.39 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JR TCGA-B5-A0JY TCGA-B5-A0K9 TCGA-B5-A11E 
       40.11        77.39        56.91        69.27        13.45        59.84 
TCGA-B5-A11Y TCGA-BG-A0VZ TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BS-A0TA TCGA-BS-A0TC 
       18.41        52.64        15.45        35.90        24.33        85.55 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UM TCGA-BS-A0UV TCGA-D1-A0ZS 
      114.90        85.84        82.39        86.93        73.25         4.87 
TCGA-D1-A103 TCGA-D1-A163 TCGA-D1-A16F TCGA-D1-A16I TCGA-D1-A176 TCGA-D1-A17D 
       21.99        32.58         2.63        11.51        30.15        30.44 
TCGA-D1-A17F TCGA-D1-A17Q 
        1.28         1.78 

$`ZFHX3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ 
       37.02        17.85       112.54       105.37        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       60.53        73.87        28.27        23.21        68.65        37.91 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP 
       17.59        19.59        24.62        29.06        28.77        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05P 
       15.95        20.25        21.99        45.53        36.89        20.91 
TCGA-AP-A0L8 TCGA-AP-A0LE TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
       48.79       110.37        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LV TCGA-AP-A1DQ 
       82.52        33.40        61.64        80.78        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       45.99        49.87        60.66        61.08        35.74        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       34.65        25.51        71.24        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       64.21        63.55        27.85       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0W1 
       20.28        15.42        51.06        52.01        34.29        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A2AE TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       23.70        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       46.95        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UL TCGA-BS-A0UT 
       96.49        30.74        97.41        92.88        81.57        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        8.55         0.56        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A177 
        0.69        18.67         3.65        17.49        19.53        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        1.58         7.00         0.99        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       10.22         1.51        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
           1.28            0.56 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
         129.80          185.79 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
         48.625          35.275 
[1] "1.3 - 129.8 (48.6)" "0.6 - 185.8 (35.3)"
[1] "hr=" "1.3"
D11V2, binary
                 cls
clus                0   1
  ZFHX3 MUTATED    33  11
  ZFHX3 WILD-TYPE 124  80
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED     33   11
  ZFHX3 WILD-TYPE  124   80
     clus
vv    ZFHX3 MUTATED ZFHX3 WILD-TYPE
  NO             33             124
  YES            11              80
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZFHX3 MUTATED                                        41
  ZFHX3 WILD-TYPE                                     159
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  ZFHX3 MUTATED                               0
  ZFHX3 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZFHX3 MUTATED                                   3
  ZFHX3 WILD-TYPE                                41
D11V3, multiclass
                                         clus
vv                                        ZFHX3 MUTATED ZFHX3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            41             159
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   3              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZFHX3 MUTATED    34   3   0   2
  ZFHX3 WILD-TYPE 138   7   7  16
D11V4, multiclass
    clus
vv   ZFHX3 MUTATED ZFHX3 WILD-TYPE
  R0            34             138
  R1             3               7
  R2             0               7
  RX             2              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"

Clustering(12) Variable = SPOP MUTATION ANALYSIS
D12V1, survival
                sevent
clus2              0   1
  SPOP MUTATED    20   1
  SPOP WILD-TYPE 195  32
  SPOP MUTATED SPOP WILD-TYPE 
            21            227 
  SPOP MUTATED SPOP WILD-TYPE 
             1             32 
$`SPOP MUTATED`
TCGA-D1-A0ZO TCGA-A5-A0RA TCGA-AP-A059 TCGA-AP-A0L8 TCGA-AX-A05Z TCGA-AX-A062 
       19.79        29.06        48.03        48.79        71.51        45.99 
TCGA-AX-A063 TCGA-B5-A0JY TCGA-B5-A0K0 TCGA-B5-A11Y TCGA-BG-A0M3 TCGA-BG-A0M7 
       79.46        69.27        48.59        18.41        35.21        63.68 
TCGA-BS-A0UF TCGA-BS-A0UT TCGA-D1-A0ZQ TCGA-D1-A103 TCGA-D1-A167 TCGA-D1-A168 
       85.84        72.72         8.55        21.99        15.72        36.10 
TCGA-D1-A17D TCGA-DI-A1NN TCGA-FI-A2EW 
       30.44        35.38        59.01 

$`SPOP WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       51.55        12.56         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 
       28.77        42.35        15.95        20.25       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A064 
       33.21        29.69        80.55        88.24        35.34        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        61.08        35.74        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       77.39        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       55.30        86.01        71.44        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.56        19.50        19.59        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 
       11.87        18.61        20.19        19.33        20.94        71.24 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ 
       96.49        30.74        97.41        92.88       114.90        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        86.93        73.25        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       66.48        16.83        29.95         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93        22.55         1.74        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A169 
        1.91         3.68        29.33        32.58         0.66        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        7.00         0.99         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-E6-A1LZ TCGA-EO-A1Y5 
       22.92        13.22        18.25        16.31        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33         9.34        30.67 

  SPOP MUTATED SPOP WILD-TYPE 
          8.55           0.56 
  SPOP MUTATED SPOP WILD-TYPE 
         85.84         185.79 
  SPOP MUTATED SPOP WILD-TYPE 
         45.99          35.74 
[1] "8.6 - 85.8 (46.0)"  "0.6 - 185.8 (35.7)"
[1] "hr=" "3"  
D12V2, binary
                cls
clus               0   1
  SPOP MUTATED    13   8
  SPOP WILD-TYPE 144  83
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPOP MUTATED     13    8
  SPOP WILD-TYPE  144   83
     clus
vv    SPOP MUTATED SPOP WILD-TYPE
  NO            13            144
  YES            8             83
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SPOP MUTATED                                        18
  SPOP WILD-TYPE                                     182
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  SPOP MUTATED                               0
  SPOP WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  SPOP MUTATED                                   3
  SPOP WILD-TYPE                                41
D12V3, multiclass
                                         clus
vv                                        SPOP MUTATED SPOP WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           18            182
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  3             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SPOP MUTATED    17   1   0   0
  SPOP WILD-TYPE 155   9   7  18
D12V4, multiclass
    clus
vv   SPOP MUTATED SPOP WILD-TYPE
  R0           17            155
  R1            1              9
  R2            0              7
  RX            0             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"

Clustering(13) Variable = FGFR2 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  FGFR2 MUTATED    29   2
  FGFR2 WILD-TYPE 186  31
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             31             217 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
              2              31 
$`FGFR2 MUTATED`
TCGA-BG-A0MS TCGA-A5-A0GQ TCGA-A5-A0GW TCGA-AP-A056 TCGA-AP-A0LM TCGA-AP-A0LP 
       61.87        73.87        23.21        86.07        27.12        61.64 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JR 
       79.46        49.87        27.39        40.11        77.39        56.91 
TCGA-B5-A0JT TCGA-B5-A0K1 TCGA-B5-A11E TCGA-B5-A11Y TCGA-B5-A121 TCGA-BG-A0LX 
       55.30        36.49        59.84        18.41        16.57        20.19 
TCGA-BG-A0M7 TCGA-BG-A0MQ TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BS-A0UV TCGA-D1-A15X 
       63.68        59.74        15.42        51.06        73.25        29.88 
TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A16F TCGA-D1-A16I TCGA-DI-A0WH TCGA-EO-A1Y8 
        1.91        29.33         2.63        11.51        16.31        37.71 
TCGA-FI-A2EW 
       59.01 

$`FGFR2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0VT 
       36.39        27.88        80.38        22.06        66.41        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX 
       65.75        60.53        46.55        28.27        54.02        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       37.91        17.59        19.59        24.62        29.06        28.77 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
       42.35        15.95        20.25       129.80        21.99        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       48.03        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LQ 
       97.71        46.72        83.97        82.52        33.40        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       49.22        25.08        46.78        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A06L 
       80.55        88.24        71.51        35.34        45.99        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       61.08        35.74        37.78        34.65        25.51        71.24 
TCGA-B5-A0JS TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K2 
       86.37        86.01        69.27        71.44        48.59        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A1MU TCGA-B5-A1MY 
       19.56        19.50        19.59        17.36        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M9 
       18.61        19.33        20.94        35.21        71.24        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MT TCGA-BG-A0MU 
       41.52        48.56        23.47        43.04        21.17        20.28 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
      114.90        85.84        82.39        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A160 TCGA-D1-A163 
        1.74        21.99        39.48        30.08         3.68        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EX 
       35.38        79.10        10.92        22.03        77.33         9.34 
TCGA-FI-A2F8 
       30.67 

  FGFR2 MUTATED FGFR2 WILD-TYPE 
           1.91            0.56 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
          86.07          185.79 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
          40.11           35.38 
[1] "1.9 - 86.1 (40.1)"  "0.6 - 185.8 (35.4)"
[1] "hr=" "2.1"
D13V2, binary
                 cls
clus                0   1
  FGFR2 MUTATED    19  12
  FGFR2 WILD-TYPE 138  79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR2 MUTATED     19   12
  FGFR2 WILD-TYPE  138   79
     clus
vv    FGFR2 MUTATED FGFR2 WILD-TYPE
  NO             19             138
  YES            12              79
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  FGFR2 MUTATED                                        27
  FGFR2 WILD-TYPE                                     173
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  FGFR2 MUTATED                               0
  FGFR2 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  FGFR2 MUTATED                                   4
  FGFR2 WILD-TYPE                                40
D13V3, multiclass
                                         clus
vv                                        FGFR2 MUTATED FGFR2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            27             173
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   4              40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FGFR2 MUTATED    23   1   0   0
  FGFR2 WILD-TYPE 149   9   7  18
D13V4, multiclass
    clus
vv   FGFR2 MUTATED FGFR2 WILD-TYPE
  R0            23             149
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(14) Variable = TCP11L2 MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  TCP11L2 MUTATED    14   0
  TCP11L2 WILD-TYPE 201  33
  TCP11L2 MUTATED TCP11L2 WILD-TYPE 
               14               234 
  TCP11L2 MUTATED TCP11L2 WILD-TYPE 
                0                33 
$`TCP11L2 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 
      129.80        86.07        48.03        71.51        35.34        79.46 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A11E TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UV 
       40.11        77.39        59.84       114.90        85.84        73.25 
TCGA-D1-A167 TCGA-D1-A17Q 
       15.72         1.78 

$`TCP11L2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A062 
       13.58        33.21        29.69        80.55        88.24        45.99 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       86.01        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       92.88        82.39        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       29.33        32.58         0.66        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       10.22         1.51        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  TCP11L2 MUTATED TCP11L2 WILD-TYPE 
             1.78              0.56 
  TCP11L2 MUTATED TCP11L2 WILD-TYPE 
           129.80            185.79 
  TCP11L2 MUTATED TCP11L2 WILD-TYPE 
           72.380            35.145 
[1] "1.8 - 129.8 (72.4)" "0.6 - 185.8 (35.1)"
[1] "hr="     "8.1e+07"
D14V2, binary
                   cls
clus                  0   1
  TCP11L2 MUTATED    10   4
  TCP11L2 WILD-TYPE 147  87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TCP11L2 MUTATED     10    4
  TCP11L2 WILD-TYPE  147   87
     clus
vv    TCP11L2 MUTATED TCP11L2 WILD-TYPE
  NO               10               147
  YES               4                87
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  TCP11L2 MUTATED                                        14
  TCP11L2 WILD-TYPE                                     186
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  TCP11L2 MUTATED                               0
  TCP11L2 WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  TCP11L2 MUTATED                                   0
  TCP11L2 WILD-TYPE                                44
D14V3, multiclass
                                         clus
vv                                        TCP11L2 MUTATED TCP11L2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              14               186
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     0                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TCP11L2 MUTATED    11   2   0   0
  TCP11L2 WILD-TYPE 161   8   7  18
D14V4, multiclass
    clus
vv   TCP11L2 MUTATED TCP11L2 WILD-TYPE
  R0              11               161
  R1               2                 8
  R2               0                 7
  RX               0                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"

Clustering(15) Variable = VPS11 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  VPS11 MUTATED    10   1
  VPS11 WILD-TYPE 205  32
  VPS11 MUTATED VPS11 WILD-TYPE 
             11             237 
  VPS11 MUTATED VPS11 WILD-TYPE 
              1              32 
$`VPS11 MUTATED`
TCGA-BG-A0YV TCGA-A5-A0GA TCGA-A5-A0VP TCGA-AP-A051 TCGA-AX-A0J1 TCGA-B5-A11E 
       12.56        17.85        42.35       129.80        77.39        59.84 
TCGA-B5-A11Y TCGA-BG-A0MQ TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A15X 
       18.41        59.74        85.84        73.25        29.88 

$`VPS11 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       51.55        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ 
       83.51        32.78       112.54       105.37        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
       28.77        15.95        20.25        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       48.03        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        40.11        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        86.37        55.30        86.01        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        13.45       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MT TCGA-BG-A0MU 
       41.52        48.56        23.47        43.04        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       31.00        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       97.41        92.88       114.90        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z 
       22.55         1.74        21.99        39.48        30.08         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       18.67         3.65        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  VPS11 MUTATED VPS11 WILD-TYPE 
          12.56            0.56 
  VPS11 MUTATED VPS11 WILD-TYPE 
         129.80          185.79 
  VPS11 MUTATED VPS11 WILD-TYPE 
          59.74           35.74 
[1] "12.6 - 129.8 (59.7)" "0.6 - 185.8 (35.7)" 
[1] "hr=" "1.9"
D15V2, binary
                 cls
clus                0   1
  VPS11 MUTATED     6   5
  VPS11 WILD-TYPE 151  86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS11 MUTATED      6    5
  VPS11 WILD-TYPE  151   86
     clus
vv    VPS11 MUTATED VPS11 WILD-TYPE
  NO              6             151
  YES             5              86
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  VPS11 MUTATED                                         9
  VPS11 WILD-TYPE                                     191
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  VPS11 MUTATED                               0
  VPS11 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  VPS11 MUTATED                                   2
  VPS11 WILD-TYPE                                42
D15V3, multiclass
                                         clus
vv                                        VPS11 MUTATED VPS11 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             9             191
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   2              42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  VPS11 MUTATED     9   0   0   0
  VPS11 WILD-TYPE 163  10   7  18
D15V4, multiclass
    clus
vv   VPS11 MUTATED VPS11 WILD-TYPE
  R0             9             163
  R1             0              10
  R2             0               7
  RX             0              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"

Clustering(16) Variable = PPP2R1A MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  PPP2R1A MUTATED    24   4
  PPP2R1A WILD-TYPE 191  29
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               28               220 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
                4                29 
$`PPP2R1A MUTATED`
TCGA-AP-A05D TCGA-BG-A0M6 TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       57.80        22.06         4.44        10.19        46.95        37.02 
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AP-A1DQ TCGA-AX-A063 
      129.80        86.07        48.03        27.12        46.78        79.46 
TCGA-AX-A0J1 TCGA-AX-A1C8 TCGA-B5-A0JY TCGA-B5-A0K6 TCGA-B5-A0K8 TCGA-B5-A11G 
       77.39        25.51        69.27        64.21        27.85       113.36 
TCGA-BG-A0VW TCGA-BK-A0CC TCGA-BS-A0UJ TCGA-BS-A0UM TCGA-D1-A15V TCGA-D1-A167 
       52.01        35.08        82.39        86.93        39.48        15.72 
TCGA-D1-A169 TCGA-D1-A16S TCGA-EO-A1Y8 TCGA-FI-A2D2 
       37.32        18.67        37.71        77.33 

$`PPP2R1A WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP 
       88.18        60.53       110.63        93.99        67.66        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV 
       27.88        80.38        66.41        61.87        51.55        12.56 
TCGA-D1-A0ZO TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       19.79        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AX-A05S TCGA-AX-A05T 
       61.64        80.78        49.22        25.08        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       40.11        34.65        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       86.01        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H 
       57.76        63.55        13.45        59.84       185.79        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ 
       21.17        20.28        15.42        51.06        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       31.00        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        92.88       114.90        85.84        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       73.25        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       22.55         1.74        21.99        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A16B 
        3.68        29.33        32.58         0.66        36.10        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y 
       31.07        33.63        10.65         0.69         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EY-A1GS TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        59.01         9.34        30.67 

  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
             4.44              0.56 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
           129.80            185.79 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
           46.865            35.095 
[1] "4.4 - 129.8 (46.9)" "0.6 - 185.8 (35.1)"
[1] "hr=" "1.2"
D16V2, binary
                   cls
clus                  0   1
  PPP2R1A MUTATED    19   9
  PPP2R1A WILD-TYPE 138  82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R1A MUTATED     19    9
  PPP2R1A WILD-TYPE  138   82
     clus
vv    PPP2R1A MUTATED PPP2R1A WILD-TYPE
  NO               19               138
  YES               9                82
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PPP2R1A MUTATED                                        15
  PPP2R1A WILD-TYPE                                     185
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  PPP2R1A MUTATED                               1
  PPP2R1A WILD-TYPE                             3
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  PPP2R1A MUTATED                                  12
  PPP2R1A WILD-TYPE                                32
D16V3, multiclass
                                         clus
vv                                        PPP2R1A MUTATED PPP2R1A WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              15               185
  MIXED SEROUS AND ENDOMETRIOID                         1                 3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    12                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PPP2R1A MUTATED    21   1   0   2
  PPP2R1A WILD-TYPE 151   9   7  16
D16V4, multiclass
    clus
vv   PPP2R1A MUTATED PPP2R1A WILD-TYPE
  R0              21               151
  R1               1                 9
  R2               0                 7
  RX               2                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"

Clustering(17) Variable = MAX MUTATION ANALYSIS
D17V1, survival
               sevent
clus2             0   1
  MAX MUTATED     8   1
  MAX WILD-TYPE 207  32
  MAX MUTATED MAX WILD-TYPE 
            9           239 
  MAX MUTATED MAX WILD-TYPE 
            1            32 
$`MAX MUTATED`
TCGA-A5-A0GI TCGA-AP-A059 TCGA-AX-A063 TCGA-AX-A0J0 TCGA-B5-A0K2 TCGA-B5-A11E 
       88.18        48.03        79.46        40.11        72.62        59.84 
TCGA-B5-A11O TCGA-BS-A0T9 TCGA-D1-A17L 
       85.78        46.95        26.37 

$`MAX WILD-TYPE`
TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP 
       60.53       110.63        57.80        93.99        67.66        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        86.07        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       71.51        35.34        45.99        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       61.08        35.74        37.78        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       71.24        56.91        86.37        55.30        86.01        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       71.44        48.59        36.49        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        13.45       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11Q TCGA-B5-A11R 
       75.72        54.44        44.78        61.68        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       35.08        31.00        24.99        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        92.88       114.90        85.84        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       86.93        72.72        73.25        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17M TCGA-D1-A17N 
       30.44         1.28        28.01        28.08        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.78        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  MAX MUTATED MAX WILD-TYPE 
        26.37          0.56 
  MAX MUTATED MAX WILD-TYPE 
        88.18        185.79 
  MAX MUTATED MAX WILD-TYPE 
        59.84         35.34 
[1] "26.4 - 88.2 (59.8)" "0.6 - 185.8 (35.3)"
[1] "hr=" "1.6"
D17V2, binary
               cls
clus              0   1
  MAX MUTATED     6   3
  MAX WILD-TYPE 151  88
[1] "tbl2"
               cls
clus            [,1] [,2]
  MAX MUTATED      6    3
  MAX WILD-TYPE  151   88
     clus
vv    MAX MUTATED MAX WILD-TYPE
  NO            6           151
  YES           3            88
[1] 2 2
[1] FALSE
               vv
clus            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MAX MUTATED                                         9
  MAX WILD-TYPE                                     191
               vv
clus            MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  MAX MUTATED                               0                                 0
  MAX WILD-TYPE                             4                                44
D17V3, multiclass
                                         clus
vv                                        MAX MUTATED MAX WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           9           191
  MIXED SEROUS AND ENDOMETRIOID                     0             4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                 0            44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  MAX MUTATED     5   0   1   0
  MAX WILD-TYPE 167  10   6  18
D17V4, multiclass
    clus
vv   MAX MUTATED MAX WILD-TYPE
  R0           5           167
  R1           0            10
  R2           1             6
  RX           0            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"

Clustering(18) Variable = SOX17 MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2               0   1
  SOX17 MUTATED     7   0
  SOX17 WILD-TYPE 208  33
  SOX17 MUTATED SOX17 WILD-TYPE 
              7             241 
  SOX17 MUTATED SOX17 WILD-TYPE 
              0              33 
$`SOX17 MUTATED`
TCGA-AP-A05P TCGA-B5-A0K4 TCGA-BG-A0W1 TCGA-BG-A18A TCGA-BK-A13C TCGA-BS-A0UT 
       20.91        57.76        52.83        14.01        24.99        72.72 
TCGA-D1-A0ZR 
        0.56 

$`SOX17 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
      129.80        21.99        23.31        86.07        48.03        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       45.53        36.89        23.87        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        61.08        35.74        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       77.39        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       55.30        86.01        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       72.62        27.29        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       44.78        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 
       15.42        51.06        52.01        34.29        52.64        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       14.83        13.78        14.73        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BS-A0T9 
       35.90        34.98        35.90        35.08        31.00        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UV TCGA-BS-A0V6 
       85.84        82.39        81.57        86.93        73.25        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  SOX17 MUTATED SOX17 WILD-TYPE 
           0.56            0.66 
  SOX17 MUTATED SOX17 WILD-TYPE 
          72.72          185.79 
  SOX17 MUTATED SOX17 WILD-TYPE 
          24.99           35.90 
[1] "0.6 - 72.7 (25.0)"  "0.7 - 185.8 (35.9)"
[1] "hr="     "9200000"
D18V2, binary
                 cls
clus                0   1
  SOX17 MUTATED     5   2
  SOX17 WILD-TYPE 152  89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SOX17 MUTATED      5    2
  SOX17 WILD-TYPE  152   89
     clus
vv    SOX17 MUTATED SOX17 WILD-TYPE
  NO              5             152
  YES             2              89
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SOX17 MUTATED                                         7
  SOX17 WILD-TYPE                                     193
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  SOX17 MUTATED                               0
  SOX17 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  SOX17 MUTATED                                   0
  SOX17 WILD-TYPE                                44
D18V3, multiclass
                                         clus
vv                                        SOX17 MUTATED SOX17 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             7             193
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SOX17 MUTATED     5   0   0   1
  SOX17 WILD-TYPE 167  10   7  17
D18V4, multiclass
    clus
vv   SOX17 MUTATED SOX17 WILD-TYPE
  R0             5             167
  R1             0              10
  R2             0               7
  RX             1              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"

Clustering(19) Variable = CCND1 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  CCND1 MUTATED    13   1
  CCND1 WILD-TYPE 202  32
  CCND1 MUTATED CCND1 WILD-TYPE 
             14             234 
  CCND1 MUTATED CCND1 WILD-TYPE 
              1              32 
$`CCND1 MUTATED`
TCGA-D1-A0ZO TCGA-AP-A054 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A063 
       19.79        23.31        27.12        71.51        45.99        79.46 
TCGA-AX-A0J0 TCGA-B5-A0JV TCGA-BG-A0MQ TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-D1-A0ZU 
       40.11        86.01        59.74        67.99        96.49        28.67 
TCGA-D1-A16D TCGA-D1-A17D 
       37.51        30.44 

$`CCND1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       51.55        12.56         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        86.07        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       77.39        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       55.30        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       44.78        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       48.56        23.47        43.04        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       77.95        61.87        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       85.84        82.39        81.57        86.93        72.72        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        8.55         0.56         4.87        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
        0.99         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  CCND1 MUTATED CCND1 WILD-TYPE 
          19.79            0.56 
  CCND1 MUTATED CCND1 WILD-TYPE 
          96.49          185.79 
  CCND1 MUTATED CCND1 WILD-TYPE 
          43.05           35.56 
[1] "19.8 - 96.5 (43.0)" "0.6 - 185.8 (35.6)"
[1] "hr=" "2.2"
D19V2, binary
                 cls
clus                0   1
  CCND1 MUTATED     7   7
  CCND1 WILD-TYPE 150  84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCND1 MUTATED      7    7
  CCND1 WILD-TYPE  150   84
     clus
vv    CCND1 MUTATED CCND1 WILD-TYPE
  NO              7             150
  YES             7              84
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CCND1 MUTATED                                        14
  CCND1 WILD-TYPE                                     186
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  CCND1 MUTATED                               0
  CCND1 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  CCND1 MUTATED                                   0
  CCND1 WILD-TYPE                                44
D19V3, multiclass
                                         clus
vv                                        CCND1 MUTATED CCND1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            14             186
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CCND1 MUTATED    10   2   0   1
  CCND1 WILD-TYPE 162   8   7  17
D19V4, multiclass
    clus
vv   CCND1 MUTATED CCND1 WILD-TYPE
  R0            10             162
  R1             2               8
  R2             0               7
  RX             1              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"

Clustering(20) Variable = NRAS MUTATION ANALYSIS
D20V1, survival
                sevent
clus2              0   1
  NRAS MUTATED     9   0
  NRAS WILD-TYPE 206  33
  NRAS MUTATED NRAS WILD-TYPE 
             9            239 
  NRAS MUTATED NRAS WILD-TYPE 
             0             33 
$`NRAS MUTATED`
TCGA-A5-A0GH TCGA-A5-A0VQ TCGA-AP-A0L9 TCGA-AX-A0J0 TCGA-B5-A0JV TCGA-BS-A0TD 
       74.10        15.95       125.42        40.11        86.01        78.21 
TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A17F 
       82.39        73.25         1.28 

$`NRAS WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 
       29.06        28.77        42.35        20.25       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       23.87        20.91        48.79       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       61.08        35.74        37.78        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JY TCGA-B5-A0JZ 
       71.24        56.91        86.37        55.30        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       24.33        85.55         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        92.88       114.90        85.84 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        86.93        72.72        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
       30.44        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.78        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  NRAS MUTATED NRAS WILD-TYPE 
          1.28           0.56 
  NRAS MUTATED NRAS WILD-TYPE 
        125.42         185.79 
  NRAS MUTATED NRAS WILD-TYPE 
         74.10          35.38 
[1] "1.3 - 125.4 (74.1)" "0.6 - 185.8 (35.4)"
[1] "hr="     "2.7e+07"
D20V2, binary
                cls
clus               0   1
  NRAS MUTATED     7   2
  NRAS WILD-TYPE 150  89
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      7    2
  NRAS WILD-TYPE  150   89
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             7            150
  YES            2             89
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  NRAS MUTATED                                         8
  NRAS WILD-TYPE                                     192
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  NRAS MUTATED                               0
  NRAS WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  NRAS MUTATED                                   1
  NRAS WILD-TYPE                                43
D20V3, multiclass
                                         clus
vv                                        NRAS MUTATED NRAS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            8            192
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  1             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NRAS MUTATED     8   0   0   0
  NRAS WILD-TYPE 164  10   7  18
D20V4, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  R0            8            164
  R1            0             10
  R2            0              7
  RX            0             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"

Clustering(21) Variable = EP300 MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2               0   1
  EP300 MUTATED    20   1
  EP300 WILD-TYPE 195  32
  EP300 MUTATED EP300 WILD-TYPE 
             21             227 
  EP300 MUTATED EP300 WILD-TYPE 
              1              32 
$`EP300 MUTATED`
TCGA-A5-A0GH TCGA-AP-A0LM TCGA-AP-A0LQ TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY 
       74.10        27.12        80.78        71.51        40.11        69.27 
TCGA-B5-A11E TCGA-B5-A11G TCGA-BG-A0LX TCGA-BG-A0MG TCGA-BG-A0MU TCGA-BG-A0RY 
       59.84       113.36        20.19        48.56        20.28        15.42 
TCGA-BK-A0C9 TCGA-BS-A0TA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-D1-A0ZR TCGA-D1-A160 
       35.90        24.33        85.84        82.39         0.56         3.68 
TCGA-D1-A16X TCGA-D1-A177 TCGA-D1-A17Q 
        3.65        18.02         1.78 

$`EP300 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       82.52        33.40        61.64        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        55.30        86.01        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       27.85        13.45       185.79        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       44.78        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0M0 TCGA-BG-A0M2 
       16.57        50.89        11.87        18.61        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MI 
       35.21        71.24        63.68        74.63        41.52        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       43.04        59.74        21.17        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0CA TCGA-BK-A0CB 
       14.01        15.45        15.45        23.70        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TC TCGA-BS-A0TD 
       35.08        31.00        24.99        46.95        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       97.41        92.88       114.90        81.57        86.93        72.72 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       73.25        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
       29.95         8.55         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       17.49        19.53        30.15         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.51        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  EP300 MUTATED EP300 WILD-TYPE 
           0.56            0.66 
  EP300 MUTATED EP300 WILD-TYPE 
         113.36          185.79 
  EP300 MUTATED EP300 WILD-TYPE 
           35.9            35.9 
[1] "0.6 - 113.4 (35.9)" "0.7 - 185.8 (35.9)"
[1] "hr=" "2.9"
D21V2, binary
                 cls
clus                0   1
  EP300 MUTATED    15   6
  EP300 WILD-TYPE 142  85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     15    6
  EP300 WILD-TYPE  142   85
     clus
vv    EP300 MUTATED EP300 WILD-TYPE
  NO             15             142
  YES             6              85
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  EP300 MUTATED                                        21
  EP300 WILD-TYPE                                     179
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  EP300 MUTATED                               0
  EP300 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  EP300 MUTATED                                   0
  EP300 WILD-TYPE                                44
D21V3, multiclass
                                         clus
vv                                        EP300 MUTATED EP300 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            21             179
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EP300 MUTATED    16   1   0   1
  EP300 WILD-TYPE 156   9   7  17
D21V4, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  R0            16             156
  R1             1               9
  R2             0               7
  RX             1              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"

Clustering(22) Variable = KLHL8 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2               0   1
  KLHL8 MUTATED    11   1
  KLHL8 WILD-TYPE 204  32
  KLHL8 MUTATED KLHL8 WILD-TYPE 
             12             236 
  KLHL8 MUTATED KLHL8 WILD-TYPE 
              1              32 
$`KLHL8 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY 
      129.80        48.03        71.51        40.11        77.39        69.27 
TCGA-B5-A0K9 TCGA-B5-A11Q TCGA-BG-A0VX TCGA-BG-A18B TCGA-BS-A0UV TCGA-D1-A17Q 
       13.45        32.09        34.29        15.45        73.25         1.78 

$`KLHL8 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        86.07        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       61.08        35.74        37.78        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        55.30        86.01        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       27.85        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11R TCGA-B5-A11S 
       54.44        44.78        61.68        85.78        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       15.42        51.06        52.01        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18C TCGA-BG-A2AE 
       14.83        13.78        14.73        14.01        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
      114.90        85.84        82.39        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       18.67         3.65        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  KLHL8 MUTATED KLHL8 WILD-TYPE 
           1.78            0.56 
  KLHL8 MUTATED KLHL8 WILD-TYPE 
         129.80          185.79 
  KLHL8 MUTATED KLHL8 WILD-TYPE 
          44.07           35.82 
[1] "1.8 - 129.8 (44.1)" "0.6 - 185.8 (35.8)"
[1] "hr=" "2"  
D22V2, binary
                 cls
clus                0   1
  KLHL8 MUTATED     7   5
  KLHL8 WILD-TYPE 150  86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL8 MUTATED      7    5
  KLHL8 WILD-TYPE  150   86
     clus
vv    KLHL8 MUTATED KLHL8 WILD-TYPE
  NO              7             150
  YES             5              86
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  KLHL8 MUTATED                                        12
  KLHL8 WILD-TYPE                                     188
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  KLHL8 MUTATED                               0
  KLHL8 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  KLHL8 MUTATED                                   0
  KLHL8 WILD-TYPE                                44
D22V3, multiclass
                                         clus
vv                                        KLHL8 MUTATED KLHL8 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            12             188
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KLHL8 MUTATED     6   1   0   2
  KLHL8 WILD-TYPE 166   9   7  16
D22V4, multiclass
    clus
vv   KLHL8 MUTATED KLHL8 WILD-TYPE
  R0             6             166
  R1             1               9
  R2             0               7
  RX             2              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"

Clustering(23) Variable = ALG8 MUTATION ANALYSIS
D23V1, survival
                sevent
clus2              0   1
  ALG8 MUTATED    10   1
  ALG8 WILD-TYPE 205  32
  ALG8 MUTATED ALG8 WILD-TYPE 
            11            237 
  ALG8 MUTATED ALG8 WILD-TYPE 
             1             32 
$`ALG8 MUTATED`
TCGA-A5-A0GJ TCGA-AP-A0LM TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A0J1 TCGA-B5-A11E 
       65.75        27.12        88.24        71.51        77.39        59.84 
TCGA-BS-A0TA TCGA-BS-A0UJ TCGA-D1-A103 TCGA-D1-A167 TCGA-D1-A17F 
       24.33        82.39        21.99        15.72         1.28 

$`ALG8 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A060 
       46.78        13.58        33.21        29.69        80.55        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        40.11        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        86.37        55.30        86.01        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        13.45       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TC 
       35.90        35.08        31.00        24.99        46.95        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UL 
       30.74        97.41        92.88       114.90        85.84        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       86.93        72.72        73.25        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W 
       28.67        23.93        22.55         1.74        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17H 
       18.02         1.58         7.00         0.99        30.44        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  ALG8 MUTATED ALG8 WILD-TYPE 
          1.28           0.56 
  ALG8 MUTATED ALG8 WILD-TYPE 
         88.24         185.79 
  ALG8 MUTATED ALG8 WILD-TYPE 
         59.84          35.90 
[1] "1.3 - 88.2 (59.8)"  "0.6 - 185.8 (35.9)"
[1] "hr=" "1.6"
D23V2, binary
                cls
clus               0   1
  ALG8 MUTATED     8   3
  ALG8 WILD-TYPE 149  88
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG8 MUTATED      8    3
  ALG8 WILD-TYPE  149   88
     clus
vv    ALG8 MUTATED ALG8 WILD-TYPE
  NO             8            149
  YES            3             88
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ALG8 MUTATED                                        11
  ALG8 WILD-TYPE                                     189
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  ALG8 MUTATED                               0
  ALG8 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  ALG8 MUTATED                                   0
  ALG8 WILD-TYPE                                44
D23V3, multiclass
                                         clus
vv                                        ALG8 MUTATED ALG8 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           11            189
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ALG8 MUTATED     8   1   0   1
  ALG8 WILD-TYPE 164   9   7  17
D23V4, multiclass
    clus
vv   ALG8 MUTATED ALG8 WILD-TYPE
  R0            8            164
  R1            1              9
  R2            0              7
  RX            1             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"

Clustering(24) Variable = GNPTAB MUTATION ANALYSIS
D24V1, survival
                  sevent
clus2                0   1
  GNPTAB MUTATED    20   0
  GNPTAB WILD-TYPE 195  33
  GNPTAB MUTATED GNPTAB WILD-TYPE 
              20              228 
  GNPTAB MUTATED GNPTAB WILD-TYPE 
               0               33 
$`GNPTAB MUTATED`
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 
       86.07        48.03        27.12        71.51        40.11        77.39 
TCGA-B5-A0JY TCGA-B5-A0K4 TCGA-B5-A11E TCGA-B5-A11J TCGA-B5-A11N TCGA-BS-A0UF 
       69.27        57.76        59.84        54.44        61.68        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A160 TCGA-D1-A167 TCGA-D1-A16X 
       82.39        73.25        21.99         3.68        15.72         3.65 
TCGA-D1-A17Q TCGA-DI-A1NN 
        1.78        35.38 

$`GNPTAB WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
      129.80        21.99        23.31        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       35.74        37.78        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       72.62        27.29        64.21        63.55        27.85        13.45 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11M TCGA-B5-A11O 
      185.79       113.36        88.34        75.72        44.78        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        86.93        72.72        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W 
       28.67        23.93        22.55         1.74        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A168 
       29.88         1.91        29.33        32.58         0.66        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       18.67        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       26.37        10.22         1.51        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-E6-A1LZ TCGA-EO-A1Y5 
       22.92        13.22        18.25        16.31        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  GNPTAB MUTATED GNPTAB WILD-TYPE 
            1.78             0.56 
  GNPTAB MUTATED GNPTAB WILD-TYPE 
           86.07           185.79 
  GNPTAB MUTATED GNPTAB WILD-TYPE 
          56.100           35.275 
[1] "1.8 - 86.1 (56.1)"  "0.6 - 185.8 (35.3)"
[1] "hr="     "7.7e+07"
D24V2, binary
                  cls
clus                 0   1
  GNPTAB MUTATED    16   4
  GNPTAB WILD-TYPE 141  87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GNPTAB MUTATED     16    4
  GNPTAB WILD-TYPE  141   87
     clus
vv    GNPTAB MUTATED GNPTAB WILD-TYPE
  NO              16              141
  YES              4               87
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  GNPTAB MUTATED                                        19
  GNPTAB WILD-TYPE                                     181
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  GNPTAB MUTATED                               0
  GNPTAB WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  GNPTAB MUTATED                                   1
  GNPTAB WILD-TYPE                                43
D24V3, multiclass
                                         clus
vv                                        GNPTAB MUTATED GNPTAB WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             19              181
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    1               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GNPTAB MUTATED    14   1   0   0
  GNPTAB WILD-TYPE 158   9   7  18
D24V4, multiclass
    clus
vv   GNPTAB MUTATED GNPTAB WILD-TYPE
  R0             14              158
  R1              1                9
  R2              0                7
  RX              0               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"

Clustering(25) Variable = SIN3A MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2               0   1
  SIN3A MUTATED    20   1
  SIN3A WILD-TYPE 195  32
  SIN3A MUTATED SIN3A WILD-TYPE 
             21             227 
  SIN3A MUTATED SIN3A WILD-TYPE 
              1              32 
$`SIN3A MUTATED`
TCGA-A5-A0GW TCGA-A5-A0VP TCGA-AP-A0LM TCGA-AX-A060 TCGA-AX-A0J0 TCGA-AX-A0J1 
       23.21        42.35        27.12        35.34        40.11        77.39 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11R TCGA-B5-A11X 
       69.27        59.84       185.79        88.34        77.23        19.59 
TCGA-BG-A0VX TCGA-BG-A2AE TCGA-BS-A0TJ TCGA-BS-A0UF TCGA-D1-A103 TCGA-D1-A15X 
       34.29        23.70        67.99        85.84        21.99        29.88 
TCGA-D1-A167 TCGA-D1-A17H TCGA-D1-A17R 
       15.72        28.01        11.15 

$`SIN3A WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       54.02        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 
       29.06        28.77        15.95        20.25       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       35.74        37.78        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N 
       13.45       113.36        75.72        54.44        44.78        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       85.78        32.09        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VZ 
       21.17        20.28        15.42        51.06        52.01        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        15.45        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       31.00        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
        4.80        77.95        61.87        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       92.88       114.90        82.39        81.57        86.93        72.72 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       73.25        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 
       22.55         1.74        39.48        30.08         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       29.33        32.58         0.66        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
        0.99        30.44         1.28        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.51         1.78        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  SIN3A MUTATED SIN3A WILD-TYPE 
          11.15            0.56 
  SIN3A MUTATED SIN3A WILD-TYPE 
         185.79          129.80 
  SIN3A MUTATED SIN3A WILD-TYPE 
          35.34           35.90 
[1] "11.2 - 185.8 (35.3)" "0.6 - 129.8 (35.9)" 
[1] "hr=" "3.3"
D25V2, binary
                 cls
clus                0   1
  SIN3A MUTATED    10  11
  SIN3A WILD-TYPE 147  80
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIN3A MUTATED     10   11
  SIN3A WILD-TYPE  147   80
     clus
vv    SIN3A MUTATED SIN3A WILD-TYPE
  NO             10             147
  YES            11              80
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SIN3A MUTATED                                        20
  SIN3A WILD-TYPE                                     180
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  SIN3A MUTATED                               0
  SIN3A WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  SIN3A MUTATED                                   1
  SIN3A WILD-TYPE                                43
D25V3, multiclass
                                         clus
vv                                        SIN3A MUTATED SIN3A WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            20             180
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SIN3A MUTATED    12   1   0   1
  SIN3A WILD-TYPE 160   9   7  17
D25V4, multiclass
    clus
vv   SIN3A MUTATED SIN3A WILD-TYPE
  R0            12             160
  R1             1               9
  R2             0               7
  RX             1              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"

Clustering(26) Variable = ARID5B MUTATION ANALYSIS
D26V1, survival
                  sevent
clus2                0   1
  ARID5B MUTATED    24   5
  ARID5B WILD-TYPE 191  28
  ARID5B MUTATED ARID5B WILD-TYPE 
              29              219 
  ARID5B MUTATED ARID5B WILD-TYPE 
               5               28 
$`ARID5B MUTATED`
TCGA-D1-A0ZO TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GP TCGA-A5-A0GU TCGA-A5-A0GW 
       19.79        83.51        17.85        46.55        28.27        23.21 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N 
       29.06        28.77        23.31        86.07        48.03        23.87 
TCGA-AP-A0LD TCGA-AP-A0LT TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A06H TCGA-B5-A0JT 
      117.99        49.22        88.24        71.51        27.39        55.30 
TCGA-B5-A11N TCGA-BG-A0M2 TCGA-BG-A0MC TCGA-BS-A0TC TCGA-BS-A0U7 TCGA-BS-A0U8 
       61.68        20.94        41.52        85.55        30.74        97.41 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-D1-A17F 
       85.84        82.39        81.57        73.25         1.28 

$`ARID5B WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       51.55        12.56         4.44        10.19        46.95        37.02 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
       32.78       112.54       105.37        74.10        65.75        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       73.87        54.02        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 
       24.62        42.35        15.95        20.25       129.80        21.99 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       63.91        45.53        36.89        20.91        48.79       125.42 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LV 
       27.12        82.52        33.40        61.64        80.78        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A060 
       46.78        13.58        33.21        29.69        80.55        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       45.99        79.46        49.87        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       37.78        40.11        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        86.01        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       75.72        54.44        44.78        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MG 
       19.33        35.21        71.24        63.68        74.63        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       24.99        46.95        24.33        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UM 
       61.87        67.99        96.49        92.88       114.90        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17H 
       18.02         1.58         7.00         0.99        30.44        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  ARID5B MUTATED ARID5B WILD-TYPE 
            1.28             0.56 
  ARID5B MUTATED ARID5B WILD-TYPE 
          117.99           185.79 
  ARID5B MUTATED ARID5B WILD-TYPE 
           48.03            35.38 
[1] "1.3 - 118.0 (48.0)" "0.6 - 185.8 (35.4)"
[1] "hr=" "1.1"
D26V2, binary
                  cls
clus                 0   1
  ARID5B MUTATED    23   6
  ARID5B WILD-TYPE 134  85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5B MUTATED     23    6
  ARID5B WILD-TYPE  134   85
     clus
vv    ARID5B MUTATED ARID5B WILD-TYPE
  NO              23              134
  YES              6               85
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ARID5B MUTATED                                        29
  ARID5B WILD-TYPE                                     171
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ARID5B MUTATED                               0
  ARID5B WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ARID5B MUTATED                                   0
  ARID5B WILD-TYPE                                44
D26V3, multiclass
                                         clus
vv                                        ARID5B MUTATED ARID5B WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             29              171
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ARID5B MUTATED    23   3   0   0
  ARID5B WILD-TYPE 149   7   7  18
D26V4, multiclass
    clus
vv   ARID5B MUTATED ARID5B WILD-TYPE
  R0             23              149
  R1              3                7
  R2              0                7
  RX              0               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"

Clustering(27) Variable = NFE2L2 MUTATION ANALYSIS
D27V1, survival
                  sevent
clus2                0   1
  NFE2L2 MUTATED    13   1
  NFE2L2 WILD-TYPE 202  32
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              14              234 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               1               32 
$`NFE2L2 MUTATED`
TCGA-A5-A0G9 TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GW TCGA-AX-A05W TCGA-B5-A0JT 
       83.51        74.10        46.55        23.21        80.55        55.30 
TCGA-B5-A11R TCGA-B5-A11Y TCGA-BG-A0M4 TCGA-BK-A0C9 TCGA-BS-A0U7 TCGA-D1-A16E 
       77.23        18.41        71.24        35.90        30.74        36.79 
TCGA-D1-A17Q TCGA-D1-A17U 
        1.78        22.92 

$`NFE2L2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GJ 
       37.02        17.85        32.78       112.54       105.37        65.75 
TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 
       60.53        73.87        28.27        54.02        68.65        37.91 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP 
       17.59        19.59        24.62        29.06        28.77        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
       15.95        20.25       129.80        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       48.03        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       37.78        40.11        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        86.01        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        19.59        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       20.94        35.21        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       23.70        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       61.87        67.99        96.49        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       85.84        82.39        81.57        86.93        72.72        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       37.32        36.36        37.51         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       26.37        10.22         1.51        11.15        24.30         2.33 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            1.78             0.56 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           83.51           185.79 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           41.67            35.56 
[1] "1.8 - 83.5 (41.7)"  "0.6 - 185.8 (35.6)"
[1] "hr=" "2"  
D27V2, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED    11   3
  NFE2L2 WILD-TYPE 146  88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     11    3
  NFE2L2 WILD-TYPE  146   88
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  NO              11              146
  YES              3               88
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  NFE2L2 MUTATED                                        14
  NFE2L2 WILD-TYPE                                     186
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  NFE2L2 MUTATED                               0
  NFE2L2 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  NFE2L2 MUTATED                                   0
  NFE2L2 WILD-TYPE                                44
D27V3, multiclass
                                         clus
vv                                        NFE2L2 MUTATED NFE2L2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             14              186
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NFE2L2 MUTATED    11   0   0   0
  NFE2L2 WILD-TYPE 161  10   7  18
D27V4, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  R0             11              161
  R1              0               10
  R2              0                7
  RX              0               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"

Clustering(28) Variable = ZNF471 MUTATION ANALYSIS
D28V1, survival
                  sevent
clus2                0   1
  ZNF471 MUTATED    13   2
  ZNF471 WILD-TYPE 202  31
  ZNF471 MUTATED ZNF471 WILD-TYPE 
              15              233 
  ZNF471 MUTATED ZNF471 WILD-TYPE 
               2               31 
$`ZNF471 MUTATED`
TCGA-A5-A0GP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       46.55       129.80        86.07        27.12        71.51        40.11 
TCGA-B5-A0JY TCGA-BS-A0T9 TCGA-BS-A0U7 TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 
       69.27        46.95        30.74        85.84        73.25        21.99 
TCGA-D1-A167 TCGA-D1-A16X TCGA-D1-A17Q 
       15.72         3.65         1.78 

$`ZNF471 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       29.06        28.77        42.35        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        48.03        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        80.55        88.24        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       37.78        77.39        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       35.08        31.00        24.99        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U8 
        4.80        77.95        61.87        67.99        96.49        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       92.88       114.90        82.39        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       29.33        32.58         0.66        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y 
       31.07        33.63        10.65         0.69        18.67        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.51        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  ZNF471 MUTATED ZNF471 WILD-TYPE 
            1.78             0.56 
  ZNF471 MUTATED ZNF471 WILD-TYPE 
          129.80           185.79 
  ZNF471 MUTATED ZNF471 WILD-TYPE 
           46.55            35.74 
[1] "1.8 - 129.8 (46.5)" "0.6 - 185.8 (35.7)"
[1] "hr=" "1.2"
D28V2, binary
                  cls
clus                 0   1
  ZNF471 MUTATED    12   3
  ZNF471 WILD-TYPE 145  88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF471 MUTATED     12    3
  ZNF471 WILD-TYPE  145   88
     clus
vv    ZNF471 MUTATED ZNF471 WILD-TYPE
  NO              12              145
  YES              3               88
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZNF471 MUTATED                                        15
  ZNF471 WILD-TYPE                                     185
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ZNF471 MUTATED                               0
  ZNF471 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZNF471 MUTATED                                   0
  ZNF471 WILD-TYPE                                44
D28V3, multiclass
                                         clus
vv                                        ZNF471 MUTATED ZNF471 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             15              185
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF471 MUTATED    12   1   1   0
  ZNF471 WILD-TYPE 160   9   6  18
D28V4, multiclass
    clus
vv   ZNF471 MUTATED ZNF471 WILD-TYPE
  R0             12              160
  R1              1                9
  R2              1                6
  RX              0               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"

Clustering(29) Variable = MORC4 MUTATION ANALYSIS
D29V1, survival
                 sevent
clus2               0   1
  MORC4 MUTATED    20   0
  MORC4 WILD-TYPE 195  33
  MORC4 MUTATED MORC4 WILD-TYPE 
             20             228 
  MORC4 MUTATED MORC4 WILD-TYPE 
              0              33 
$`MORC4 MUTATED`
TCGA-A5-A0GN TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0L9 TCGA-AP-A0LG TCGA-AP-A0LM 
       60.53        86.07        48.03       125.42        66.25        27.12 
TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11Y 
       71.51        40.11        77.39        69.27        59.84        18.41 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BS-A0UF TCGA-BS-A0V7 TCGA-D1-A163 TCGA-D1-A16Q 
       34.29        52.64        85.84        63.58        32.58        10.65 
TCGA-D1-A16X TCGA-D1-A177 
        3.65        18.02 

$`MORC4 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LH TCGA-AP-A0LI 
       20.91        48.79       117.99       110.37        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       49.22        25.08        46.78        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       80.55        88.24        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       27.39        60.66        61.08        35.74        37.78        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       19.59        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0W1 
       21.17        20.28        15.42        51.06        52.01        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       31.00        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       97.41        92.88       114.90        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        73.25        89.59        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        1.91         3.68        29.33         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16R TCGA-D1-A16S 
       11.51        29.92        31.07        33.63         0.69        18.67 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       17.49        19.53        30.15         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  MORC4 MUTATED MORC4 WILD-TYPE 
           3.65            0.56 
  MORC4 MUTATED MORC4 WILD-TYPE 
         125.42          185.79 
  MORC4 MUTATED MORC4 WILD-TYPE 
          56.24           35.36 
[1] "3.6 - 125.4 (56.2)" "0.6 - 185.8 (35.4)"
[1] "hr="     "7.8e+07"
D29V2, binary
                 cls
clus                0   1
  MORC4 MUTATED    12   8
  MORC4 WILD-TYPE 145  83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC4 MUTATED     12    8
  MORC4 WILD-TYPE  145   83
     clus
vv    MORC4 MUTATED MORC4 WILD-TYPE
  NO             12             145
  YES             8              83
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MORC4 MUTATED                                        19
  MORC4 WILD-TYPE                                     181
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  MORC4 MUTATED                               0
  MORC4 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  MORC4 MUTATED                                   1
  MORC4 WILD-TYPE                                43
D29V3, multiclass
                                         clus
vv                                        MORC4 MUTATED MORC4 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            19             181
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MORC4 MUTATED    15   1   0   1
  MORC4 WILD-TYPE 157   9   7  17
D29V4, multiclass
    clus
vv   MORC4 MUTATED MORC4 WILD-TYPE
  R0            15             157
  R1             1               9
  R2             0               7
  RX             1              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"

Clustering(30) Variable = SELP MUTATION ANALYSIS
D30V1, survival
                sevent
clus2              0   1
  SELP MUTATED     9   1
  SELP WILD-TYPE 206  32
  SELP MUTATED SELP WILD-TYPE 
            10            238 
  SELP MUTATED SELP WILD-TYPE 
             1             32 
$`SELP MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A05Z TCGA-B5-A0JY TCGA-BS-A0TE 
      129.80        86.07        48.03        71.51        69.27         4.80 
TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A16X 
       85.84        73.25        21.99         3.65 

$`SELP WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.74        37.78        40.11        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       71.24        56.91        86.37        55.30        86.01        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       24.33        85.55        78.21        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ 
       96.49        30.74        97.41        92.88       114.90        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        86.93        72.72        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W 
       28.67        23.93        22.55         1.74        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
       10.65         0.69        18.67        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  SELP MUTATED SELP WILD-TYPE 
          3.65           0.56 
  SELP MUTATED SELP WILD-TYPE 
        129.80         185.79 
  SELP MUTATED SELP WILD-TYPE 
         70.39          35.56 
[1] "3.6 - 129.8 (70.4)" "0.6 - 185.8 (35.6)"
[1] "hr=" "1.8"
D30V2, binary
                cls
clus               0   1
  SELP MUTATED     8   2
  SELP WILD-TYPE 149  89
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELP MUTATED      8    2
  SELP WILD-TYPE  149   89
     clus
vv    SELP MUTATED SELP WILD-TYPE
  NO             8            149
  YES            2             89
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SELP MUTATED                                        10
  SELP WILD-TYPE                                     190
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  SELP MUTATED                               0
  SELP WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  SELP MUTATED                                   0
  SELP WILD-TYPE                                44
D30V3, multiclass
                                         clus
vv                                        SELP MUTATED SELP WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           10            190
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SELP MUTATED     7   1   1   0
  SELP WILD-TYPE 165   9   6  18
D30V4, multiclass
    clus
vv   SELP MUTATED SELP WILD-TYPE
  R0            7            165
  R1            1              9
  R2            1              6
  RX            0             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"

Clustering(31) Variable = RBMX MUTATION ANALYSIS
D31V1, survival
                sevent
clus2              0   1
  RBMX MUTATED    10   2
  RBMX WILD-TYPE 205  31
  RBMX MUTATED RBMX WILD-TYPE 
            12            236 
  RBMX MUTATED RBMX WILD-TYPE 
             2             31 
$`RBMX MUTATED`
TCGA-D1-A0ZO TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AX-A05S 
       19.79        23.31        48.03       117.99       110.37        13.58 
TCGA-AX-A060 TCGA-B5-A0JZ TCGA-BG-A0LX TCGA-BS-A0UF TCGA-BS-A0UM TCGA-D1-A17Q 
       35.34        71.44        20.19        85.84        86.93         1.78 

$`RBMX WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       51.55        12.56         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        86.07        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
       20.91        48.79       125.42        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05T TCGA-AX-A05U 
       80.78        49.22        25.08        46.78        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       80.55        88.24        71.51        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        61.08        35.74        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       77.39        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       55.30        86.01        69.27        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       44.78        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0M0 TCGA-BG-A0M2 
       16.57        50.89        11.87        18.61        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       92.88       114.90        82.39        81.57        72.72        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       18.67         3.65        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  RBMX MUTATED RBMX WILD-TYPE 
          1.78           0.56 
  RBMX MUTATED RBMX WILD-TYPE 
        117.99         185.79 
  RBMX MUTATED RBMX WILD-TYPE 
        41.685         35.900 
[1] "1.8 - 118.0 (41.7)" "0.6 - 185.8 (35.9)"
[1] "hr=" "1.1"
D31V2, binary
                cls
clus               0   1
  RBMX MUTATED     7   5
  RBMX WILD-TYPE 150  86
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      7    5
  RBMX WILD-TYPE  150   86
     clus
vv    RBMX MUTATED RBMX WILD-TYPE
  NO             7            150
  YES            5             86
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  RBMX MUTATED                                        12
  RBMX WILD-TYPE                                     188
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  RBMX MUTATED                               0
  RBMX WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  RBMX MUTATED                                   0
  RBMX WILD-TYPE                                44
D31V3, multiclass
                                         clus
vv                                        RBMX MUTATED RBMX WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           12            188
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RBMX MUTATED     8   2   1   0
  RBMX WILD-TYPE 164   8   6  18
D31V4, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  R0            8            164
  R1            2              8
  R2            1              6
  RX            0             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"

Clustering(32) Variable = FAT1 MUTATION ANALYSIS
D32V1, survival
                sevent
clus2              0   1
  FAT1 MUTATED    39   1
  FAT1 WILD-TYPE 176  32
  FAT1 MUTATED FAT1 WILD-TYPE 
            40            208 
  FAT1 MUTATED FAT1 WILD-TYPE 
             1             32 
$`FAT1 MUTATED`
TCGA-D1-A0ZO TCGA-A5-A0GB TCGA-A5-A0GH TCGA-A5-A0GW TCGA-A5-A0VP TCGA-AP-A051 
       19.79        32.78        74.10        23.21        42.35       129.80 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H TCGA-AP-A0LM TCGA-AP-A0LT TCGA-AX-A05Z 
       86.07        48.03        45.53        27.12        49.22        71.51 
TCGA-AX-A060 TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JT TCGA-B5-A0JY TCGA-B5-A0JZ 
       35.34        40.11        77.39        55.30        69.27        71.44 
TCGA-B5-A11E TCGA-B5-A11H TCGA-B5-A11R TCGA-B5-A11Y TCGA-BG-A0MG TCGA-BK-A0CC 
       59.84        88.34        77.23        18.41        48.56        35.08 
TCGA-BK-A139 TCGA-BS-A0TC TCGA-BS-A0U8 TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UV 
       31.00        85.55        97.41        85.84        82.39        73.25 
TCGA-D1-A0ZQ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A160 TCGA-D1-A167 TCGA-D1-A169 
        8.55         1.74        21.99         3.68        15.72        37.32 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A17M TCGA-D1-A17Q 
       19.53        30.15        10.22         1.78 

$`FAT1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       51.55        12.56         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GJ TCGA-A5-A0GN 
       83.51        17.85       112.54       105.37        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 
       46.55        73.87        28.27        54.02        68.65        37.91 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        28.77        15.95 
TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N 
       20.25        21.99        23.31        63.91        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       61.64        80.78        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       29.69        80.55        88.24        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       27.39        60.66        61.08        35.74        37.78        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JV TCGA-B5-A0K0 
       25.51        71.24        56.91        86.37        86.01        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J 
       27.85        13.45       185.79       113.36        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U 
       44.78        61.68        85.78        32.09        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.56        19.50        19.59        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MO 
       71.24        63.68        74.63        41.52        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD 
       34.98        35.90        24.99        46.95        24.33        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       92.88       114.90        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZR 
       63.58        83.64        66.48        16.83        29.95         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A15W 
        4.87        28.67        23.93        22.55        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A168 
       29.88         1.91        29.33        32.58         0.66        36.10 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        3.65        17.49        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17N 
       30.44         1.28        28.01        28.08        26.37         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  FAT1 MUTATED FAT1 WILD-TYPE 
          1.74           0.56 
  FAT1 MUTATED FAT1 WILD-TYPE 
        129.80         185.79 
  FAT1 MUTATED FAT1 WILD-TYPE 
        43.940         35.295 
[1] "1.7 - 129.8 (43.9)" "0.6 - 185.8 (35.3)"
[1] "hr=" "6.7"
D32V2, binary
                cls
clus               0   1
  FAT1 MUTATED    26  14
  FAT1 WILD-TYPE 131  77
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED     26   14
  FAT1 WILD-TYPE  131   77
     clus
vv    FAT1 MUTATED FAT1 WILD-TYPE
  NO            26            131
  YES           14             77
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  FAT1 MUTATED                                        38
  FAT1 WILD-TYPE                                     162
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  FAT1 MUTATED                               0
  FAT1 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  FAT1 MUTATED                                   2
  FAT1 WILD-TYPE                                42
D32V3, multiclass
                                         clus
vv                                        FAT1 MUTATED FAT1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           38            162
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  2             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FAT1 MUTATED    28   2   0   2
  FAT1 WILD-TYPE 144   8   7  16
D32V4, multiclass
    clus
vv   FAT1 MUTATED FAT1 WILD-TYPE
  R0           28            144
  R1            2              8
  R2            0              7
  RX            2             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"

Clustering(33) Variable = MARK3 MUTATION ANALYSIS
D33V1, survival
                 sevent
clus2               0   1
  MARK3 MUTATED    10   1
  MARK3 WILD-TYPE 205  32
  MARK3 MUTATED MARK3 WILD-TYPE 
             11             237 
  MARK3 MUTATED MARK3 WILD-TYPE 
              1              32 
$`MARK3 MUTATED`
TCGA-A5-A0GW TCGA-AP-A051 TCGA-AP-A056 TCGA-AX-A05S TCGA-AX-A05Z TCGA-AX-A0J0 
       23.21       129.80        86.07        13.58        71.51        40.11 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11H TCGA-BS-A0UV TCGA-D1-A17Q 
       69.27        59.84        88.34        73.25         1.78 

$`MARK3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       54.02        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       29.06        28.77        42.35        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        48.03        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        80.55        88.24        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       37.78        77.39        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
       13.45       185.79       113.36        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       92.88       114.90        85.84        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  MARK3 MUTATED MARK3 WILD-TYPE 
           1.78            0.56 
  MARK3 MUTATED MARK3 WILD-TYPE 
         129.80          185.79 
  MARK3 MUTATED MARK3 WILD-TYPE 
          69.27           35.38 
[1] "1.8 - 129.8 (69.3)" "0.6 - 185.8 (35.4)"
[1] "hr=" "2.1"
D33V2, binary
                 cls
clus                0   1
  MARK3 MUTATED     8   3
  MARK3 WILD-TYPE 149  88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MARK3 MUTATED      8    3
  MARK3 WILD-TYPE  149   88
     clus
vv    MARK3 MUTATED MARK3 WILD-TYPE
  NO              8             149
  YES             3              88
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MARK3 MUTATED                                        11
  MARK3 WILD-TYPE                                     189
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  MARK3 MUTATED                               0
  MARK3 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  MARK3 MUTATED                                   0
  MARK3 WILD-TYPE                                44
D33V3, multiclass
                                         clus
vv                                        MARK3 MUTATED MARK3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            11             189
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MARK3 MUTATED     6   1   1   0
  MARK3 WILD-TYPE 166   9   6  18
D33V4, multiclass
    clus
vv   MARK3 MUTATED MARK3 WILD-TYPE
  R0             6             166
  R1             1               9
  R2             1               6
  RX             0              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"

Clustering(34) Variable = SOS1 MUTATION ANALYSIS
D34V1, survival
                sevent
clus2              0   1
  SOS1 MUTATED    12   0
  SOS1 WILD-TYPE 203  33
  SOS1 MUTATED SOS1 WILD-TYPE 
            12            236 
  SOS1 MUTATED SOS1 WILD-TYPE 
             0             33 
$`SOS1 MUTATED`
TCGA-A5-A0GP TCGA-A5-A0R9 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LJ TCGA-AP-A0LM 
       46.55        24.62        86.07        48.03        46.72        27.12 
TCGA-AP-A0LQ TCGA-AX-A0J0 TCGA-B5-A0JR TCGA-B5-A0JY TCGA-BG-A0RY TCGA-D1-A176 
       80.78        40.11        56.91        69.27        15.42        30.15 

$`SOS1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0RA 
       23.21        68.65        37.91        17.59        19.59        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 
       28.77        42.35        15.95        20.25       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       23.31        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LT 
       97.71        83.97        82.52        33.40        61.64        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        61.08        35.74        37.78        77.39 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       34.65        25.51        71.24        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        44.78        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW 
       43.04        59.74        21.17        20.28        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       85.84        82.39        81.57        86.93        72.72        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A177 TCGA-D1-A17A 
       18.67         3.65        17.49        19.53        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  SOS1 MUTATED SOS1 WILD-TYPE 
         15.42           0.56 
  SOS1 MUTATED SOS1 WILD-TYPE 
         86.07         185.79 
  SOS1 MUTATED SOS1 WILD-TYPE 
        46.635         35.560 
[1] "15.4 - 86.1 (46.6)" "0.6 - 185.8 (35.6)"
[1] "hr="     "2.6e+07"
D34V2, binary
                cls
clus               0   1
  SOS1 MUTATED     8   4
  SOS1 WILD-TYPE 149  87
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS1 MUTATED      8    4
  SOS1 WILD-TYPE  149   87
     clus
vv    SOS1 MUTATED SOS1 WILD-TYPE
  NO             8            149
  YES            4             87
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SOS1 MUTATED                                        12
  SOS1 WILD-TYPE                                     188
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  SOS1 MUTATED                               0
  SOS1 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  SOS1 MUTATED                                   0
  SOS1 WILD-TYPE                                44
D34V3, multiclass
                                         clus
vv                                        SOS1 MUTATED SOS1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           12            188
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SOS1 MUTATED    10   0   0   0
  SOS1 WILD-TYPE 162  10   7  18
D34V4, multiclass
    clus
vv   SOS1 MUTATED SOS1 WILD-TYPE
  R0           10            162
  R1            0             10
  R2            0              7
  RX            0             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"

Clustering(35) Variable = RBBP6 MUTATION ANALYSIS
D35V1, survival
                 sevent
clus2               0   1
  RBBP6 MUTATED    21   1
  RBBP6 WILD-TYPE 194  32
  RBBP6 MUTATED RBBP6 WILD-TYPE 
             22             226 
  RBBP6 MUTATED RBBP6 WILD-TYPE 
              1              32 
$`RBBP6 MUTATED`
TCGA-A5-A0GM TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       60.53        42.35       129.80        23.31        86.07        48.03 
TCGA-AP-A0LM TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-BS-A0TJ 
       27.12        77.39        69.27        59.84        61.68        67.99 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A0ZS TCGA-D1-A103 TCGA-D1-A165 
       85.84        82.39        73.25         4.87        21.99         0.66 
TCGA-D1-A16X TCGA-D1-A177 TCGA-D1-A17C TCGA-D1-A17Q 
        3.65        18.02         0.99         1.78 

$`RBBP6 WILD-TYPE`
TCGA-A5-A0GI TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP 
       88.18       110.63        57.80        93.99        67.66        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A05A 
       29.06        28.77        15.95        20.25        21.99        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89        23.87        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37        66.25        36.36        97.71        46.72 
TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       83.97        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        61.08        35.74        37.78        40.11 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       86.01        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       57.76        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O 
      113.36        88.34        75.72        54.44        44.78        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UL 
       96.49        30.74        97.41        92.88       114.90        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZU TCGA-D1-A0ZV 
       16.83        29.95         8.55         0.56        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       22.55         1.74        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
        3.68        29.33        32.58        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17D 
       17.49        19.53        30.15         1.58         7.00        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  RBBP6 MUTATED RBBP6 WILD-TYPE 
           0.66            0.56 
  RBBP6 MUTATED RBBP6 WILD-TYPE 
         129.80          185.79 
  RBBP6 MUTATED RBBP6 WILD-TYPE 
         53.935          35.560 
[1] "0.7 - 129.8 (53.9)" "0.6 - 185.8 (35.6)"
[1] "hr=" "3.4"
D35V2, binary
                 cls
clus                0   1
  RBBP6 MUTATED    15   7
  RBBP6 WILD-TYPE 142  84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP6 MUTATED     15    7
  RBBP6 WILD-TYPE  142   84
     clus
vv    RBBP6 MUTATED RBBP6 WILD-TYPE
  NO             15             142
  YES             7              84
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  RBBP6 MUTATED                                        22
  RBBP6 WILD-TYPE                                     178
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  RBBP6 MUTATED                               0
  RBBP6 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  RBBP6 MUTATED                                   0
  RBBP6 WILD-TYPE                                44
D35V3, multiclass
                                         clus
vv                                        RBBP6 MUTATED RBBP6 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            22             178
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RBBP6 MUTATED    18   1   0   0
  RBBP6 WILD-TYPE 154   9   7  18
D35V4, multiclass
    clus
vv   RBBP6 MUTATED RBBP6 WILD-TYPE
  R0            18             154
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(36) Variable = ZNF263 MUTATION ANALYSIS
D36V1, survival
                  sevent
clus2                0   1
  ZNF263 MUTATED     7   0
  ZNF263 WILD-TYPE 208  33
  ZNF263 MUTATED ZNF263 WILD-TYPE 
               7              241 
  ZNF263 MUTATED ZNF263 WILD-TYPE 
               0               33 
$`ZNF263 MUTATED`
TCGA-A5-A0GB TCGA-AP-A0LM TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A11G TCGA-D1-A101 
       32.78        27.12        71.51        69.27       113.36         1.74 
TCGA-D1-A17Q 
        1.78 

$`ZNF263 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       37.02        83.51        17.85       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       85.84        82.39        81.57        86.93        72.72        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       26.37        10.22         1.51        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  ZNF263 MUTATED ZNF263 WILD-TYPE 
            1.74             0.56 
  ZNF263 MUTATED ZNF263 WILD-TYPE 
          113.36           185.79 
  ZNF263 MUTATED ZNF263 WILD-TYPE 
           32.78            35.90 
[1] "1.7 - 113.4 (32.8)" "0.6 - 185.8 (35.9)"
[1] "hr="     "2.6e+07"
D36V2, binary
                  cls
clus                 0   1
  ZNF263 MUTATED     5   2
  ZNF263 WILD-TYPE 152  89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF263 MUTATED      5    2
  ZNF263 WILD-TYPE  152   89
     clus
vv    ZNF263 MUTATED ZNF263 WILD-TYPE
  NO               5              152
  YES              2               89
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZNF263 MUTATED                                         7
  ZNF263 WILD-TYPE                                     193
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ZNF263 MUTATED                               0
  ZNF263 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZNF263 MUTATED                                   0
  ZNF263 WILD-TYPE                                44
D36V3, multiclass
                                         clus
vv                                        ZNF263 MUTATED ZNF263 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              7              193
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF263 MUTATED     3   1   0   1
  ZNF263 WILD-TYPE 169   9   7  17
D36V4, multiclass
    clus
vv   ZNF263 MUTATED ZNF263 WILD-TYPE
  R0              3              169
  R1              1                9
  R2              0                7
  RX              1               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"

Clustering(37) Variable = INTS7 MUTATION ANALYSIS
D37V1, survival
                 sevent
clus2               0   1
  INTS7 MUTATED     8   0
  INTS7 WILD-TYPE 207  33
  INTS7 MUTATED INTS7 WILD-TYPE 
              8             240 
  INTS7 MUTATED INTS7 WILD-TYPE 
              0              33 
$`INTS7 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-BS-A0UF 
      129.80        86.07        71.51        40.11        69.27        85.84 
TCGA-BS-A0UJ TCGA-D1-A167 
       82.39        15.72 

$`INTS7 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       61.08        35.74        37.78        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       71.24        56.91        86.37        55.30        86.01        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        86.93        72.72        73.25        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  INTS7 MUTATED INTS7 WILD-TYPE 
          15.72            0.56 
  INTS7 MUTATED INTS7 WILD-TYPE 
         129.80          185.79 
  INTS7 MUTATED INTS7 WILD-TYPE 
          76.95           35.36 
[1] "15.7 - 129.8 (77.0)" "0.6 - 185.8 (35.4)" 
[1] "hr="     "2.7e+07"
D37V2, binary
                 cls
clus                0   1
  INTS7 MUTATED     6   2
  INTS7 WILD-TYPE 151  89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS7 MUTATED      6    2
  INTS7 WILD-TYPE  151   89
     clus
vv    INTS7 MUTATED INTS7 WILD-TYPE
  NO              6             151
  YES             2              89
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  INTS7 MUTATED                                         8
  INTS7 WILD-TYPE                                     192
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  INTS7 MUTATED                               0
  INTS7 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  INTS7 MUTATED                                   0
  INTS7 WILD-TYPE                                44
D37V3, multiclass
                                         clus
vv                                        INTS7 MUTATED INTS7 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             8             192
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  INTS7 MUTATED     6   1   0   0
  INTS7 WILD-TYPE 166   9   7  18
D37V4, multiclass
    clus
vv   INTS7 MUTATED INTS7 WILD-TYPE
  R0             6             166
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(38) Variable = L1TD1 MUTATION ANALYSIS
D38V1, survival
                 sevent
clus2               0   1
  L1TD1 MUTATED    16   0
  L1TD1 WILD-TYPE 199  33
  L1TD1 MUTATED L1TD1 WILD-TYPE 
             16             232 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
              0              33 
$`L1TD1 MUTATED`
TCGA-D1-A0ZO TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       19.79        86.07        48.03        27.12        71.51        40.11 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-BG-A0VX TCGA-BS-A0TC TCGA-BS-A0UF 
       69.27        59.84        61.68        34.29        85.55        85.84 
TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A167 TCGA-D1-A17Q 
       73.25        21.99        15.72         1.78 

$`L1TD1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       51.55        12.56         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        80.55        88.24        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       37.78        77.39        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       13.45       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       44.78        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       51.06        52.01        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        24.33        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 
       82.39        81.57        86.93        72.72        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V 
        4.87        28.67        23.93        22.55         1.74        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69        18.67         3.65        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  L1TD1 MUTATED L1TD1 WILD-TYPE 
           1.78            0.56 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
          86.07          185.79 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
         53.935          35.560 
[1] "1.8 - 86.1 (53.9)"  "0.6 - 185.8 (35.6)"
[1] "hr="     "2.7e+07"
D38V2, binary
                 cls
clus                0   1
  L1TD1 MUTATED    12   4
  L1TD1 WILD-TYPE 145  87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1TD1 MUTATED     12    4
  L1TD1 WILD-TYPE  145   87
     clus
vv    L1TD1 MUTATED L1TD1 WILD-TYPE
  NO             12             145
  YES             4              87
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  L1TD1 MUTATED                                        16
  L1TD1 WILD-TYPE                                     184
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  L1TD1 MUTATED                               0
  L1TD1 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  L1TD1 MUTATED                                   0
  L1TD1 WILD-TYPE                                44
D38V3, multiclass
                                         clus
vv                                        L1TD1 MUTATED L1TD1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            16             184
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  L1TD1 MUTATED    11   1   0   1
  L1TD1 WILD-TYPE 161   9   7  17
D38V4, multiclass
    clus
vv   L1TD1 MUTATED L1TD1 WILD-TYPE
  R0            11             161
  R1             1               9
  R2             0               7
  RX             1              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"

Clustering(39) Variable = NAT1 MUTATION ANALYSIS
D39V1, survival
                sevent
clus2              0   1
  NAT1 MUTATED     6   1
  NAT1 WILD-TYPE 209  32
  NAT1 MUTATED NAT1 WILD-TYPE 
             7            241 
  NAT1 MUTATED NAT1 WILD-TYPE 
             1             32 
$`NAT1 MUTATED`
TCGA-A5-A0GB TCGA-AP-A054 TCGA-B5-A0JZ TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 
       32.78        23.31        71.44        85.84        73.25        21.99 
TCGA-D1-A17Q 
        1.78 

$`NAT1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       37.02        83.51        17.85       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        86.07        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       71.51        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        61.08        35.74        37.78        40.11        77.39 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       86.01        69.27        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       92.88       114.90        82.39        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       26.37        10.22         1.51        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  NAT1 MUTATED NAT1 WILD-TYPE 
          1.78           0.56 
  NAT1 MUTATED NAT1 WILD-TYPE 
         85.84         185.79 
  NAT1 MUTATED NAT1 WILD-TYPE 
         32.78          35.90 
[1] "1.8 - 85.8 (32.8)"  "0.6 - 185.8 (35.9)"
[1] "hr=" "1.1"
D39V2, binary
                cls
clus               0   1
  NAT1 MUTATED     5   2
  NAT1 WILD-TYPE 152  89
[1] "tbl2"
                cls
clus             [,1] [,2]
  NAT1 MUTATED      5    2
  NAT1 WILD-TYPE  152   89
     clus
vv    NAT1 MUTATED NAT1 WILD-TYPE
  NO             5            152
  YES            2             89
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  NAT1 MUTATED                                         7
  NAT1 WILD-TYPE                                     193
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  NAT1 MUTATED                               0
  NAT1 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  NAT1 MUTATED                                   0
  NAT1 WILD-TYPE                                44
D39V3, multiclass
                                         clus
vv                                        NAT1 MUTATED NAT1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            7            193
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NAT1 MUTATED     5   1   0   0
  NAT1 WILD-TYPE 167   9   7  18
D39V4, multiclass
    clus
vv   NAT1 MUTATED NAT1 WILD-TYPE
  R0            5            167
  R1            1              9
  R2            0              7
  RX            0             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"

Clustering(40) Variable = JAKMIP2 MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  JAKMIP2 MUTATED    11   1
  JAKMIP2 WILD-TYPE 204  32
  JAKMIP2 MUTATED JAKMIP2 WILD-TYPE 
               12               236 
  JAKMIP2 MUTATED JAKMIP2 WILD-TYPE 
                1                32 
$`JAKMIP2 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
      129.80        86.07        48.03        27.12        71.51        40.11 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0TC TCGA-BS-A0TE TCGA-BS-A0UF TCGA-BS-A0UV 
       69.27        59.84        85.55         4.80        85.84        73.25 

$`JAKMIP2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        80.55        88.24        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       37.78        77.39        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       13.45       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       44.78        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TG 
       31.00        24.99        46.95        24.33        78.21        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
      114.90        82.39        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  JAKMIP2 MUTATED JAKMIP2 WILD-TYPE 
             4.80              0.56 
  JAKMIP2 MUTATED JAKMIP2 WILD-TYPE 
           129.80            185.79 
  JAKMIP2 MUTATED JAKMIP2 WILD-TYPE 
           70.390            35.275 
[1] "4.8 - 129.8 (70.4)" "0.6 - 185.8 (35.3)"
[1] "hr=" "2.5"
D40V2, binary
                   cls
clus                  0   1
  JAKMIP2 MUTATED     9   3
  JAKMIP2 WILD-TYPE 148  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  JAKMIP2 MUTATED      9    3
  JAKMIP2 WILD-TYPE  148   88
     clus
vv    JAKMIP2 MUTATED JAKMIP2 WILD-TYPE
  NO                9               148
  YES               3                88
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  JAKMIP2 MUTATED                                        12
  JAKMIP2 WILD-TYPE                                     188
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  JAKMIP2 MUTATED                               0
  JAKMIP2 WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  JAKMIP2 MUTATED                                   0
  JAKMIP2 WILD-TYPE                                44
D40V3, multiclass
                                         clus
vv                                        JAKMIP2 MUTATED JAKMIP2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              12               188
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     0                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  JAKMIP2 MUTATED     8   1   1   0
  JAKMIP2 WILD-TYPE 164   9   6  18
D40V4, multiclass
    clus
vv   JAKMIP2 MUTATED JAKMIP2 WILD-TYPE
  R0               8               164
  R1               1                 9
  R2               1                 6
  RX               0                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"

Clustering(41) Variable = ING1 MUTATION ANALYSIS
D41V1, survival
                sevent
clus2              0   1
  ING1 MUTATED    12   0
  ING1 WILD-TYPE 203  33
  ING1 MUTATED ING1 WILD-TYPE 
            12            236 
  ING1 MUTATED ING1 WILD-TYPE 
             0             33 
$`ING1 MUTATED`
TCGA-A5-A0VP TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-B5-A0JY TCGA-B5-A11E 
       42.35        86.07        48.03        27.12        69.27        59.84 
TCGA-B5-A11W TCGA-BG-A0M9 TCGA-BS-A0TC TCGA-D1-A168 TCGA-D1-A17C TCGA-D1-A17Q 
       19.50        74.63        85.55        36.10         0.99         1.78 

$`ING1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       24.62        29.06        28.77        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.74        37.78        40.11        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       71.24        56.91        86.37        55.30        86.01        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        13.45       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11X TCGA-B5-A11Y 
       77.23        73.28        16.73        19.56        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0MC 
       19.33        20.94        35.21        71.24        63.68        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE 
       31.00        24.99        46.95        24.33        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       92.88       114.90        85.84        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       72.72        73.25        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       15.72        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
       18.02         1.58         7.00        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  ING1 MUTATED ING1 WILD-TYPE 
          0.99           0.56 
  ING1 MUTATED ING1 WILD-TYPE 
         86.07         185.79 
  ING1 MUTATED ING1 WILD-TYPE 
         45.19          35.56 
[1] "1.0 - 86.1 (45.2)"  "0.6 - 185.8 (35.6)"
[1] "hr="     "2.6e+07"
D41V2, binary
                cls
clus               0   1
  ING1 MUTATED     7   5
  ING1 WILD-TYPE 150  86
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING1 MUTATED      7    5
  ING1 WILD-TYPE  150   86
     clus
vv    ING1 MUTATED ING1 WILD-TYPE
  NO             7            150
  YES            5             86
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ING1 MUTATED                                        12
  ING1 WILD-TYPE                                     188
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  ING1 MUTATED                               0
  ING1 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  ING1 MUTATED                                   0
  ING1 WILD-TYPE                                44
D41V3, multiclass
                                         clus
vv                                        ING1 MUTATED ING1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           12            188
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ING1 MUTATED     9   0   0   0
  ING1 WILD-TYPE 163  10   7  18
D41V4, multiclass
    clus
vv   ING1 MUTATED ING1 WILD-TYPE
  R0            9            163
  R1            0             10
  R2            0              7
  RX            0             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"

Clustering(42) Variable = CCDC6 MUTATION ANALYSIS
D42V1, survival
                 sevent
clus2               0   1
  CCDC6 MUTATED     6   0
  CCDC6 WILD-TYPE 209  33
  CCDC6 MUTATED CCDC6 WILD-TYPE 
              6             242 
  CCDC6 MUTATED CCDC6 WILD-TYPE 
              0              33 
$`CCDC6 MUTATED`
TCGA-AP-A059 TCGA-BS-A0UF TCGA-D1-A15V TCGA-D1-A17B TCGA-D1-A17Q TCGA-FI-A2EX 
       48.03        85.84        39.48         7.00         1.78         9.34 

$`CCDC6 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        61.08        35.74        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       77.39        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       55.30        86.01        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        92.88       114.90        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       86.93        72.72        73.25        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W 
       28.67        23.93        22.55         1.74        21.99        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69        18.67         3.65        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       30.15        18.02         1.58         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2F8 
       59.01        30.67 

  CCDC6 MUTATED CCDC6 WILD-TYPE 
           1.78            0.56 
  CCDC6 MUTATED CCDC6 WILD-TYPE 
          85.84          185.79 
  CCDC6 MUTATED CCDC6 WILD-TYPE 
          24.41           35.90 
[1] "1.8 - 85.8 (24.4)"  "0.6 - 185.8 (35.9)"
[1] "hr="     "9100000"
D42V2, binary
                 cls
clus                0   1
  CCDC6 MUTATED     4   2
  CCDC6 WILD-TYPE 153  89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC6 MUTATED      4    2
  CCDC6 WILD-TYPE  153   89
     clus
vv    CCDC6 MUTATED CCDC6 WILD-TYPE
  NO              4             153
  YES             2              89
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CCDC6 MUTATED                                         4
  CCDC6 WILD-TYPE                                     196
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  CCDC6 MUTATED                               0
  CCDC6 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  CCDC6 MUTATED                                   2
  CCDC6 WILD-TYPE                                42
D42V3, multiclass
                                         clus
vv                                        CCDC6 MUTATED CCDC6 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             4             196
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   2              42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CCDC6 MUTATED     6   0   0   0
  CCDC6 WILD-TYPE 166  10   7  18
D42V4, multiclass
    clus
vv   CCDC6 MUTATED CCDC6 WILD-TYPE
  R0             6             166
  R1             0              10
  R2             0               7
  RX             0              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"

Clustering(43) Variable = ZNF781 MUTATION ANALYSIS
D43V1, survival
                  sevent
clus2                0   1
  ZNF781 MUTATED    10   0
  ZNF781 WILD-TYPE 205  33
  ZNF781 MUTATED ZNF781 WILD-TYPE 
              10              238 
  ZNF781 MUTATED ZNF781 WILD-TYPE 
               0               33 
$`ZNF781 MUTATED`
TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A11N TCGA-BS-A0UF 
       86.07        27.12        71.51        69.27        61.68        85.84 
TCGA-D1-A103 TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A17Q 
       21.99         3.65        17.49         1.78 

$`ZNF781 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O 
      113.36        88.34        75.72        54.44        44.78        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 
       82.39        81.57        86.93        72.72        73.25        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A174 
       31.07        33.63        10.65         0.69        18.67        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  ZNF781 MUTATED ZNF781 WILD-TYPE 
            1.78             0.56 
  ZNF781 MUTATED ZNF781 WILD-TYPE 
           86.07           185.79 
  ZNF781 MUTATED ZNF781 WILD-TYPE 
            44.4             35.9 
[1] "1.8 - 86.1 (44.4)"  "0.6 - 185.8 (35.9)"
[1] "hr="     "2.6e+07"
D43V2, binary
                  cls
clus                 0   1
  ZNF781 MUTATED     9   1
  ZNF781 WILD-TYPE 148  90
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF781 MUTATED      9    1
  ZNF781 WILD-TYPE  148   90
     clus
vv    ZNF781 MUTATED ZNF781 WILD-TYPE
  NO               9              148
  YES              1               90
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZNF781 MUTATED                                        10
  ZNF781 WILD-TYPE                                     190
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ZNF781 MUTATED                               0
  ZNF781 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZNF781 MUTATED                                   0
  ZNF781 WILD-TYPE                                44
D43V3, multiclass
                                         clus
vv                                        ZNF781 MUTATED ZNF781 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             10              190
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF781 MUTATED     6   1   0   1
  ZNF781 WILD-TYPE 166   9   7  17
D43V4, multiclass
    clus
vv   ZNF781 MUTATED ZNF781 WILD-TYPE
  R0              6              166
  R1              1                9
  R2              0                7
  RX              1               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"

Clustering(44) Variable = MKI67 MUTATION ANALYSIS
D44V1, survival
                 sevent
clus2               0   1
  MKI67 MUTATED    28   1
  MKI67 WILD-TYPE 187  32
  MKI67 MUTATED MKI67 WILD-TYPE 
             29             219 
  MKI67 MUTATED MKI67 WILD-TYPE 
              1              32 
$`MKI67 MUTATED`
TCGA-A5-A0GB TCGA-A5-A0GH TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       32.78        74.10       129.80        23.31        86.07        48.03 
TCGA-AP-A0LG TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A064 
       66.25        27.12        71.51        35.34        79.46        49.87 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-BG-A0M0 
       40.11        77.39        69.27        59.84        61.68        19.33 
TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A16E 
       85.55        85.84        82.39        73.25        21.99        36.79 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A17M TCGA-D1-A17Q 
        3.65        17.49        19.53        10.22         1.78 

$`MKI67 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GJ 
       37.02        83.51        17.85       112.54       105.37        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A05A 
       28.77        42.35        15.95        20.25        21.99        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89        23.87        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A062 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       45.99        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       86.01        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       57.76        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O 
      113.36        88.34        75.72        54.44        44.78        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       18.61        20.19        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0UM 
       30.74        97.41        92.88       114.90        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       22.55         1.74        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       37.32        36.36        37.51         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17N TCGA-D1-A17R 
        1.28        28.01        28.08        26.37         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  MKI67 MUTATED MKI67 WILD-TYPE 
           1.78            0.56 
  MKI67 MUTATED MKI67 WILD-TYPE 
         129.80          185.79 
  MKI67 MUTATED MKI67 WILD-TYPE 
          49.87           35.21 
[1] "1.8 - 129.8 (49.9)" "0.6 - 185.8 (35.2)"
[1] "hr=" "5"  
D44V2, binary
                 cls
clus                0   1
  MKI67 MUTATED    21   8
  MKI67 WILD-TYPE 136  83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED     21    8
  MKI67 WILD-TYPE  136   83
     clus
vv    MKI67 MUTATED MKI67 WILD-TYPE
  NO             21             136
  YES             8              83
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MKI67 MUTATED                                        29
  MKI67 WILD-TYPE                                     171
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  MKI67 MUTATED                               0
  MKI67 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  MKI67 MUTATED                                   0
  MKI67 WILD-TYPE                                44
D44V3, multiclass
                                         clus
vv                                        MKI67 MUTATED MKI67 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            29             171
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MKI67 MUTATED    21   3   0   1
  MKI67 WILD-TYPE 151   7   7  17
D44V4, multiclass
    clus
vv   MKI67 MUTATED MKI67 WILD-TYPE
  R0            21             151
  R1             3               7
  R2             0               7
  RX             1              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"

Clustering(45) Variable = EIF2S2 MUTATION ANALYSIS
D45V1, survival
                  sevent
clus2                0   1
  EIF2S2 MUTATED     9   0
  EIF2S2 WILD-TYPE 206  33
  EIF2S2 MUTATED EIF2S2 WILD-TYPE 
               9              239 
  EIF2S2 MUTATED EIF2S2 WILD-TYPE 
               0               33 
$`EIF2S2 MUTATED`
TCGA-AP-A059 TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11N TCGA-BG-A187 
       48.03        71.51        40.11        69.27        61.68        14.73 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-D1-A16Y 
       85.84        82.39        17.49 

$`EIF2S2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       88.24        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        61.08        35.74        37.78        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O 
      113.36        88.34        75.72        54.44        44.78        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UL 
       96.49        30.74        97.41        92.88       114.90        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       86.93        72.72        73.25        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A174 
       33.63        10.65         0.69        18.67         3.65        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.78        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  EIF2S2 MUTATED EIF2S2 WILD-TYPE 
           14.73             0.56 
  EIF2S2 MUTATED EIF2S2 WILD-TYPE 
           85.84           185.79 
  EIF2S2 MUTATED EIF2S2 WILD-TYPE 
           61.68            35.38 
[1] "14.7 - 85.8 (61.7)" "0.6 - 185.8 (35.4)"
[1] "hr="     "2.6e+07"
D45V2, binary
                  cls
clus                 0   1
  EIF2S2 MUTATED     7   2
  EIF2S2 WILD-TYPE 150  89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2S2 MUTATED      7    2
  EIF2S2 WILD-TYPE  150   89
     clus
vv    EIF2S2 MUTATED EIF2S2 WILD-TYPE
  NO               7              150
  YES              2               89
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  EIF2S2 MUTATED                                         9
  EIF2S2 WILD-TYPE                                     191
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  EIF2S2 MUTATED                               0
  EIF2S2 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  EIF2S2 MUTATED                                   0
  EIF2S2 WILD-TYPE                                44
D45V3, multiclass
                                         clus
vv                                        EIF2S2 MUTATED EIF2S2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              9              191
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  EIF2S2 MUTATED     5   1   0   1
  EIF2S2 WILD-TYPE 167   9   7  17
D45V4, multiclass
    clus
vv   EIF2S2 MUTATED EIF2S2 WILD-TYPE
  R0              5              167
  R1              1                9
  R2              0                7
  RX              1               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"

Clustering(46) Variable = BCOR MUTATION ANALYSIS
D46V1, survival
                sevent
clus2              0   1
  BCOR MUTATED    29   1
  BCOR WILD-TYPE 186  32
  BCOR MUTATED BCOR WILD-TYPE 
            30            218 
  BCOR MUTATED BCOR WILD-TYPE 
             1             32 
$`BCOR MUTATED`
TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LL TCGA-AX-A06H 
       42.35       129.80        86.07        48.03        83.97        27.39 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0K6 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11H 
       40.11        77.39        64.21        13.45        59.84        88.34 
TCGA-B5-A11N TCGA-BG-A0M4 TCGA-BG-A0MU TCGA-BG-A0VW TCGA-BS-A0TC TCGA-BS-A0TJ 
       61.68        71.24        20.28        52.01        85.55        67.99 
TCGA-BS-A0U8 TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A0ZN TCGA-D1-A0ZQ 
       97.41        85.84        82.39        73.25        16.83         8.55 
TCGA-D1-A103 TCGA-D1-A167 TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16X TCGA-D1-A17C 
       21.99        15.72        36.79         2.63         3.65         0.99 

$`BCOR WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       24.62        29.06        28.77        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       23.31        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        46.72        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       80.78        49.22        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       79.46        49.87        60.66        61.08        35.74        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       86.01        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A11F TCGA-B5-A11G 
       27.29        57.76        63.55        27.85       185.79       113.36 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       75.72        54.44        44.78        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       19.33        20.94        35.21        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0RY 
       48.56        23.47        43.04        59.74        21.17        15.42 
TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       51.06        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        24.33        78.21         4.80        77.95        61.87 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0UM 
       96.49        30.74        92.88       114.90        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZP 
       72.72        89.59        63.58        83.64        66.48        29.95 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        36.10        37.32        36.36        37.51 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
        0.69        18.67        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        1.58         7.00        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  BCOR MUTATED BCOR WILD-TYPE 
          0.99           0.56 
  BCOR MUTATED BCOR WILD-TYPE 
        129.80         185.79 
  BCOR MUTATED BCOR WILD-TYPE 
        55.925         35.145 
[1] "1.0 - 129.8 (55.9)" "0.6 - 185.8 (35.1)"
[1] "hr=" "5.2"
D46V2, binary
                cls
clus               0   1
  BCOR MUTATED    21   9
  BCOR WILD-TYPE 136  82
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     21    9
  BCOR WILD-TYPE  136   82
     clus
vv    BCOR MUTATED BCOR WILD-TYPE
  NO            21            136
  YES            9             82
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  BCOR MUTATED                                        30
  BCOR WILD-TYPE                                     170
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  BCOR MUTATED                               0
  BCOR WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  BCOR MUTATED                                   0
  BCOR WILD-TYPE                                44
D46V3, multiclass
                                         clus
vv                                        BCOR MUTATED BCOR WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           30            170
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BCOR MUTATED    23   1   0   0
  BCOR WILD-TYPE 149   9   7  18
D46V4, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  R0           23            149
  R1            1              9
  R2            0              7
  RX            0             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"

Clustering(47) Variable = RASA1 MUTATION ANALYSIS
D47V1, survival
                 sevent
clus2               0   1
  RASA1 MUTATED    21   0
  RASA1 WILD-TYPE 194  33
  RASA1 MUTATED RASA1 WILD-TYPE 
             21             227 
  RASA1 MUTATED RASA1 WILD-TYPE 
              0              33 
$`RASA1 MUTATED`
TCGA-A5-A0VQ TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z 
       15.95       129.80        86.07        48.03        27.12        71.51 
TCGA-AX-A0IU TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JR TCGA-B5-A0JY TCGA-B5-A11N 
       35.74        40.11        77.39        56.91        69.27        61.68 
TCGA-BG-A0VW TCGA-BK-A0C9 TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0UF TCGA-BS-A0UJ 
       52.01        35.90        85.55        78.21        85.84        82.39 
TCGA-D1-A15X TCGA-D1-A16Y TCGA-D1-A17Q 
       29.88        17.49         1.78 

$`RASA1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-AJ-A23M TCGA-AP-A052 
       24.62        29.06        28.77        42.35        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       23.31        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        46.72        83.97        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       80.78        49.22        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        80.55        88.24        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A1C7 
       49.87        27.39        60.66        61.08        37.78        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       25.51        71.24        86.37        55.30        86.01        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q 
       88.34        75.72        54.44        44.78        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ 
       21.17        20.28        15.42        51.06        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        15.45        23.70        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TE TCGA-BS-A0TG 
       31.00        24.99        46.95        24.33         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 
      114.90        81.57        86.93        72.72        73.25        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       21.99        39.48        30.08         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.51        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  RASA1 MUTATED RASA1 WILD-TYPE 
           1.78            0.56 
  RASA1 MUTATED RASA1 WILD-TYPE 
         129.80          185.79 
  RASA1 MUTATED RASA1 WILD-TYPE 
          56.91           35.08 
[1] "1.8 - 129.8 (56.9)" "0.6 - 185.8 (35.1)"
[1] "hr="   "8e+07"
D47V2, binary
                 cls
clus                0   1
  RASA1 MUTATED    16   5
  RASA1 WILD-TYPE 141  86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED     16    5
  RASA1 WILD-TYPE  141   86
     clus
vv    RASA1 MUTATED RASA1 WILD-TYPE
  NO             16             141
  YES             5              86
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  RASA1 MUTATED                                        19
  RASA1 WILD-TYPE                                     181
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  RASA1 MUTATED                               0
  RASA1 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  RASA1 MUTATED                                   2
  RASA1 WILD-TYPE                                42
D47V3, multiclass
                                         clus
vv                                        RASA1 MUTATED RASA1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            19             181
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   2              42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RASA1 MUTATED    16   1   0   1
  RASA1 WILD-TYPE 156   9   7  17
D47V4, multiclass
    clus
vv   RASA1 MUTATED RASA1 WILD-TYPE
  R0            16             156
  R1             1               9
  R2             0               7
  RX             1              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"

Clustering(48) Variable = DNER MUTATION ANALYSIS
D48V1, survival
                sevent
clus2              0   1
  DNER MUTATED    17   1
  DNER WILD-TYPE 198  32
  DNER MUTATED DNER WILD-TYPE 
            18            230 
  DNER MUTATED DNER WILD-TYPE 
             1             32 
$`DNER MUTATED`
TCGA-D1-A0ZO TCGA-A5-A0GA TCGA-A5-A0GW TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A05Z 
       19.79        17.85        23.21        86.07        27.12        71.51 
TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A11E TCGA-B5-A11R TCGA-B5-A11W 
       77.39        69.27        71.44        59.84        77.23        19.50 
TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A15X TCGA-D1-A16J TCGA-D1-A17Q 
       85.55        85.84        73.25        29.88        29.92         1.78 

$`DNER WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       51.55        12.56         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ 
       83.51        32.78       112.54       105.37        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX 
       60.53        46.55        73.87        28.27        54.02        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       37.91        17.59        19.59        24.62        29.06        28.77 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
       42.35        15.95        20.25       129.80        21.99        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       48.03        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        46.72        83.97        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       80.78        49.22        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        80.55        88.24        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       40.11        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       55.30        86.01        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       57.76        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        44.78        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11X 
       85.78        32.09        73.28        16.73        19.56        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        92.88       114.90        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        11.51        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       18.67         3.65        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  DNER MUTATED DNER WILD-TYPE 
          1.78           0.56 
  DNER MUTATED DNER WILD-TYPE 
         86.07         185.79 
  DNER MUTATED DNER WILD-TYPE 
        64.555         35.820 
[1] "1.8 - 86.1 (64.6)"  "0.6 - 185.8 (35.8)"
[1] "hr=" "2.8"
D48V2, binary
                cls
clus               0   1
  DNER MUTATED    11   7
  DNER WILD-TYPE 146  84
[1] "tbl2"
                cls
clus             [,1] [,2]
  DNER MUTATED     11    7
  DNER WILD-TYPE  146   84
     clus
vv    DNER MUTATED DNER WILD-TYPE
  NO            11            146
  YES            7             84
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DNER MUTATED                                        17
  DNER WILD-TYPE                                     183
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  DNER MUTATED                               0
  DNER WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DNER MUTATED                                   1
  DNER WILD-TYPE                                43
D48V3, multiclass
                                         clus
vv                                        DNER MUTATED DNER WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           17            183
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  1             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DNER MUTATED    12   1   0   0
  DNER WILD-TYPE 160   9   7  18
D48V4, multiclass
    clus
vv   DNER MUTATED DNER WILD-TYPE
  R0           12            160
  R1            1              9
  R2            0              7
  RX            0             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"

Clustering(49) Variable = C9ORF23 MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  C9ORF23 MUTATED     9   0
  C9ORF23 WILD-TYPE 206  33
  C9ORF23 MUTATED C9ORF23 WILD-TYPE 
                9               239 
  C9ORF23 MUTATED C9ORF23 WILD-TYPE 
                0                33 
$`C9ORF23 MUTATED`
TCGA-AP-A059 TCGA-AP-A0LE TCGA-AP-A0LM TCGA-B5-A11E TCGA-B5-A11N TCGA-D1-A103 
       48.03       110.37        27.12        59.84        61.68        21.99 
TCGA-D1-A16F TCGA-D1-A176 TCGA-D1-A17U 
        2.63        30.15        22.92 

$`C9ORF23 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       57.76        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O 
      113.36        88.34        75.72        54.44        44.78        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       85.84        82.39        81.57        86.93        72.72        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       17.49        19.53        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A1NU 
        1.51         1.78        11.15        24.30         2.33        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  C9ORF23 MUTATED C9ORF23 WILD-TYPE 
             2.63              0.56 
  C9ORF23 MUTATED C9ORF23 WILD-TYPE 
           110.37            185.79 
  C9ORF23 MUTATED C9ORF23 WILD-TYPE 
            30.15             35.90 
[1] "2.6 - 110.4 (30.1)" "0.6 - 185.8 (35.9)"
[1] "hr="     "2.6e+07"
D49V2, binary
                   cls
clus                  0   1
  C9ORF23 MUTATED     6   3
  C9ORF23 WILD-TYPE 151  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF23 MUTATED      6    3
  C9ORF23 WILD-TYPE  151   88
     clus
vv    C9ORF23 MUTATED C9ORF23 WILD-TYPE
  NO                6               151
  YES               3                88
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  C9ORF23 MUTATED                                         9
  C9ORF23 WILD-TYPE                                     191
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  C9ORF23 MUTATED                               0
  C9ORF23 WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  C9ORF23 MUTATED                                   0
  C9ORF23 WILD-TYPE                                44
D49V3, multiclass
                                         clus
vv                                        C9ORF23 MUTATED C9ORF23 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               9               191
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     0                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C9ORF23 MUTATED     7   0   0   0
  C9ORF23 WILD-TYPE 165  10   7  18
D49V4, multiclass
    clus
vv   C9ORF23 MUTATED C9ORF23 WILD-TYPE
  R0               7               165
  R1               0                10
  R2               0                 7
  RX               0                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"

Clustering(50) Variable = CUX1 MUTATION ANALYSIS
D50V1, survival
                sevent
clus2              0   1
  CUX1 MUTATED    20   1
  CUX1 WILD-TYPE 195  32
  CUX1 MUTATED CUX1 WILD-TYPE 
            21            227 
  CUX1 MUTATED CUX1 WILD-TYPE 
             1             32 
$`CUX1 MUTATED`
TCGA-A5-A0GI TCGA-A5-A0GP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N 
       88.18        46.55       129.80        86.07        48.03        23.87 
TCGA-AP-A0LM TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11J TCGA-BG-A18B 
       27.12        77.39        69.27        59.84        54.44        15.45 
TCGA-BS-A0TJ TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A15X TCGA-D1-A160 
       67.99        85.84        73.25        21.99        29.88         3.68 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A17Q 
       17.49        19.53         1.78 

$`CUX1 WILD-TYPE`
TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP 
       60.53       110.63        57.80        93.99        67.66        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       65.75        60.53        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 
       28.77        42.35        15.95        20.25        21.99        23.31 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       63.91        45.53        36.89        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37        66.25        36.36        97.71        46.72 
TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       83.97        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        61.08        35.74        37.78        40.11 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       86.01        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       57.76        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
      113.36        88.34        75.72        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.73        14.01        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0U5 
       85.55        78.21         4.80        77.95        61.87        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        92.88       114.90        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z 
       23.93        22.55         1.74        39.48        30.08         1.91 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        3.65        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.51        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  CUX1 MUTATED CUX1 WILD-TYPE 
          1.78           0.56 
  CUX1 MUTATED CUX1 WILD-TYPE 
        129.80         185.79 
  CUX1 MUTATED CUX1 WILD-TYPE 
         48.03          35.74 
[1] "1.8 - 129.8 (48.0)" "0.6 - 185.8 (35.7)"
[1] "hr=" "3.3"
D50V2, binary
                cls
clus               0   1
  CUX1 MUTATED    14   7
  CUX1 WILD-TYPE 143  84
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUX1 MUTATED     14    7
  CUX1 WILD-TYPE  143   84
     clus
vv    CUX1 MUTATED CUX1 WILD-TYPE
  NO            14            143
  YES            7             84
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CUX1 MUTATED                                        20
  CUX1 WILD-TYPE                                     180
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  CUX1 MUTATED                               0
  CUX1 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  CUX1 MUTATED                                   1
  CUX1 WILD-TYPE                                43
D50V3, multiclass
                                         clus
vv                                        CUX1 MUTATED CUX1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           20            180
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  1             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CUX1 MUTATED    16   0   0   2
  CUX1 WILD-TYPE 156  10   7  16
D50V4, multiclass
    clus
vv   CUX1 MUTATED CUX1 WILD-TYPE
  R0           16            156
  R1            0             10
  R2            0              7
  RX            2             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"

Clustering(51) Variable = CDK17 MUTATION ANALYSIS
D51V1, survival
                 sevent
clus2               0   1
  CDK17 MUTATED    13   1
  CDK17 WILD-TYPE 202  32
  CDK17 MUTATED CDK17 WILD-TYPE 
             14             234 
  CDK17 MUTATED CDK17 WILD-TYPE 
              1              32 
$`CDK17 MUTATED`
TCGA-A5-A0GP TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AX-A05Z TCGA-AX-A063 TCGA-B5-A0JR 
       46.55        36.36        97.71        71.51        79.46        56.91 
TCGA-B5-A11E TCGA-B5-A11G TCGA-BG-A0M0 TCGA-BS-A0UV TCGA-D1-A163 TCGA-D1-A16Y 
       59.84       113.36        19.33        73.25        32.58        17.49 
TCGA-D1-A17M TCGA-D1-A17Q 
       10.22         1.78 

$`CDK17 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
      110.37        66.25        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       45.99        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       37.78        40.11        77.39        34.65        25.51        71.24 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       86.37        55.30        86.01        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       27.85        13.45       185.79        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       44.78        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M2 
       16.57        50.89        11.87        18.61        20.19        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       92.88       114.90        85.84        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        1.91         3.68        29.33         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       18.67         3.65        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       26.37         1.51        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  CDK17 MUTATED CDK17 WILD-TYPE 
           1.78            0.56 
  CDK17 MUTATED CDK17 WILD-TYPE 
         113.36          185.79 
  CDK17 MUTATED CDK17 WILD-TYPE 
          51.73           35.56 
[1] "1.8 - 113.4 (51.7)" "0.6 - 185.8 (35.6)"
[1] "hr=" "2.3"
D51V2, binary
                 cls
clus                0   1
  CDK17 MUTATED    11   3
  CDK17 WILD-TYPE 146  88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK17 MUTATED     11    3
  CDK17 WILD-TYPE  146   88
     clus
vv    CDK17 MUTATED CDK17 WILD-TYPE
  NO             11             146
  YES             3              88
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CDK17 MUTATED                                        12
  CDK17 WILD-TYPE                                     188
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  CDK17 MUTATED                               1
  CDK17 WILD-TYPE                             3
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  CDK17 MUTATED                                   1
  CDK17 WILD-TYPE                                43
D51V3, multiclass
                                         clus
vv                                        CDK17 MUTATED CDK17 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            12             188
  MIXED SEROUS AND ENDOMETRIOID                       1               3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDK17 MUTATED     8   1   1   1
  CDK17 WILD-TYPE 164   9   6  17
D51V4, multiclass
    clus
vv   CDK17 MUTATED CDK17 WILD-TYPE
  R0             8             164
  R1             1               9
  R2             1               6
  RX             1              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"

Clustering(52) Variable = USP28 MUTATION ANALYSIS
D52V1, survival
                 sevent
clus2               0   1
  USP28 MUTATED    10   0
  USP28 WILD-TYPE 205  33
  USP28 MUTATED USP28 WILD-TYPE 
             10             238 
  USP28 MUTATED USP28 WILD-TYPE 
              0              33 
$`USP28 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11G TCGA-BS-A0UF 
      129.80        48.03        77.39        69.27       113.36        85.84 
TCGA-BS-A0UV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A17Q 
       73.25         1.74        21.99         1.78 

$`USP28 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        86.07        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       71.51        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 
       60.66        61.08        35.74        37.78        40.11        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 
       82.39        81.57        86.93        72.72        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A15W 
        4.87        28.67        23.93        22.55        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69        18.67         3.65        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  USP28 MUTATED USP28 WILD-TYPE 
           1.74            0.56 
  USP28 MUTATED USP28 WILD-TYPE 
         129.80          185.79 
  USP28 MUTATED USP28 WILD-TYPE 
          71.26           35.56 
[1] "1.7 - 129.8 (71.3)" "0.6 - 185.8 (35.6)"
[1] "hr="     "2.9e+07"
D52V2, binary
                 cls
clus                0   1
  USP28 MUTATED     8   2
  USP28 WILD-TYPE 149  89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      8    2
  USP28 WILD-TYPE  149   89
     clus
vv    USP28 MUTATED USP28 WILD-TYPE
  NO              8             149
  YES             2              89
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  USP28 MUTATED                                        10
  USP28 WILD-TYPE                                     190
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  USP28 MUTATED                               0
  USP28 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  USP28 MUTATED                                   0
  USP28 WILD-TYPE                                44
D52V3, multiclass
                                         clus
vv                                        USP28 MUTATED USP28 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            10             190
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  USP28 MUTATED     7   0   0   1
  USP28 WILD-TYPE 165  10   7  17
D52V4, multiclass
    clus
vv   USP28 MUTATED USP28 WILD-TYPE
  R0             7             165
  R1             0              10
  R2             0               7
  RX             1              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"

Clustering(53) Variable = MSH6 MUTATION ANALYSIS
D53V1, survival
                sevent
clus2              0   1
  MSH6 MUTATED    16   1
  MSH6 WILD-TYPE 199  32
  MSH6 MUTATED MSH6 WILD-TYPE 
            17            231 
  MSH6 MUTATED MSH6 WILD-TYPE 
             1             32 
$`MSH6 MUTATED`
TCGA-BG-A0M6 TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LE 
       22.06        42.35       129.80        86.07        48.03       110.37 
TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11R 
       27.12        71.51        40.11        69.27        59.84        77.23 
TCGA-BG-A0M4 TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A17Q 
       71.24        85.84        73.25        21.99         1.78 

$`MSH6 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       36.39        27.88        80.38        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 
       29.06        28.77        15.95        20.25        21.99        23.31 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       63.91        45.53        36.89        23.87        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      125.42       117.99        66.25        36.36        97.71        46.72 
TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       83.97        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       88.24        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        61.08        35.74        37.78        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       32.09        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0M9 
       20.19        19.33        20.94        35.21        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        92.88       114.90        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93        22.55         1.74        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  MSH6 MUTATED MSH6 WILD-TYPE 
          1.78           0.56 
  MSH6 MUTATED MSH6 WILD-TYPE 
        129.80         185.79 
  MSH6 MUTATED MSH6 WILD-TYPE 
         69.27          35.21 
[1] "1.8 - 129.8 (69.3)" "0.6 - 185.8 (35.2)"
[1] "hr=" "3.2"
D53V2, binary
                cls
clus               0   1
  MSH6 MUTATED    11   6
  MSH6 WILD-TYPE 146  85
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH6 MUTATED     11    6
  MSH6 WILD-TYPE  146   85
     clus
vv    MSH6 MUTATED MSH6 WILD-TYPE
  NO            11            146
  YES            6             85
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MSH6 MUTATED                                        16
  MSH6 WILD-TYPE                                     184
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  MSH6 MUTATED                               0
  MSH6 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  MSH6 MUTATED                                   1
  MSH6 WILD-TYPE                                43
D53V3, multiclass
                                         clus
vv                                        MSH6 MUTATED MSH6 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           16            184
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  1             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MSH6 MUTATED    13   1   0   0
  MSH6 WILD-TYPE 159   9   7  18
D53V4, multiclass
    clus
vv   MSH6 MUTATED MSH6 WILD-TYPE
  R0           13            159
  R1            1              9
  R2            0              7
  RX            0             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"

Clustering(54) Variable = WDR45 MUTATION ANALYSIS
D54V1, survival
                 sevent
clus2               0   1
  WDR45 MUTATED    10   1
  WDR45 WILD-TYPE 205  32
  WDR45 MUTATED WDR45 WILD-TYPE 
             11             237 
  WDR45 MUTATED WDR45 WILD-TYPE 
              1              32 
$`WDR45 MUTATED`
TCGA-AP-A051 TCGA-AP-A0LE TCGA-AP-A0LM TCGA-AX-A060 TCGA-B5-A0K3 TCGA-B5-A11E 
      129.80       110.37        27.12        35.34        27.29        59.84 
TCGA-B5-A11U TCGA-B5-A11Y TCGA-BS-A0TC TCGA-D1-A16X TCGA-D1-A17A 
       16.73        18.41        85.55         3.65         1.58 

$`WDR45 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.74        37.78        40.11        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       71.24        56.91        86.37        55.30        86.01        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 
       71.44        48.59        36.49        72.62        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        13.45       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z 
       77.23        73.28        19.56        19.50        19.59        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE 
       31.00        24.99        46.95        24.33        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       92.88       114.90        85.84        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       72.72        73.25        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
       10.65         0.69        18.67        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
       18.02         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  WDR45 MUTATED WDR45 WILD-TYPE 
           1.58            0.56 
  WDR45 MUTATED WDR45 WILD-TYPE 
         129.80          185.79 
  WDR45 MUTATED WDR45 WILD-TYPE 
          27.29           36.10 
[1] "1.6 - 129.8 (27.3)" "0.6 - 185.8 (36.1)"
[1] "hr=" "1.5"
D54V2, binary
                 cls
clus                0   1
  WDR45 MUTATED     7   4
  WDR45 WILD-TYPE 150  87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR45 MUTATED      7    4
  WDR45 WILD-TYPE  150   87
     clus
vv    WDR45 MUTATED WDR45 WILD-TYPE
  NO              7             150
  YES             4              87
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  WDR45 MUTATED                                        11
  WDR45 WILD-TYPE                                     189
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  WDR45 MUTATED                               0
  WDR45 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  WDR45 MUTATED                                   0
  WDR45 WILD-TYPE                                44
D54V3, multiclass
                                         clus
vv                                        WDR45 MUTATED WDR45 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            11             189
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WDR45 MUTATED     6   1   0   0
  WDR45 WILD-TYPE 166   9   7  18
D54V4, multiclass
    clus
vv   WDR45 MUTATED WDR45 WILD-TYPE
  R0             6             166
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(55) Variable = C14ORF166B MUTATION ANALYSIS
D55V1, survival
                      sevent
clus2                    0   1
  C14ORF166B MUTATED     9   0
  C14ORF166B WILD-TYPE 206  33
  C14ORF166B MUTATED C14ORF166B WILD-TYPE 
                   9                  239 
  C14ORF166B MUTATED C14ORF166B WILD-TYPE 
                   0                   33 
$`C14ORF166B MUTATED`
TCGA-AP-A056 TCGA-B5-A0JY TCGA-B5-A11N TCGA-BG-A0VW TCGA-BS-A0TC TCGA-BS-A0UF 
       86.07        69.27        61.68        52.01        85.55        85.84 
TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A17Q 
       73.25        21.99         1.78 

$`C14ORF166B WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        61.08        35.74        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       77.39        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       55.30        86.01        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       44.78        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       51.06        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        24.33        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 
       82.39        81.57        86.93        72.72        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V 
        4.87        28.67        23.93        22.55         1.74        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.51        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  C14ORF166B MUTATED C14ORF166B WILD-TYPE 
                1.78                 0.56 
  C14ORF166B MUTATED C14ORF166B WILD-TYPE 
               86.07               185.79 
  C14ORF166B MUTATED C14ORF166B WILD-TYPE 
               69.27                35.38 
[1] "1.8 - 86.1 (69.3)"  "0.6 - 185.8 (35.4)"
[1] "hr="     "2.6e+07"
D55V2, binary
                      cls
clus                     0   1
  C14ORF166B MUTATED     9   0
  C14ORF166B WILD-TYPE 148  91
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  C14ORF166B MUTATED      9    0
  C14ORF166B WILD-TYPE  148   91
     clus
vv    C14ORF166B MUTATED C14ORF166B WILD-TYPE
  NO                   9                  148
  YES                  0                   91
[1] 2 2
[1] FALSE
                      vv
clus                   ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  C14ORF166B MUTATED                                         9
  C14ORF166B WILD-TYPE                                     191
                      vv
clus                   MIXED SEROUS AND ENDOMETRIOID
  C14ORF166B MUTATED                               0
  C14ORF166B WILD-TYPE                             4
                      vv
clus                   SEROUS ENDOMETRIAL ADENOCARCINOMA
  C14ORF166B MUTATED                                   0
  C14ORF166B WILD-TYPE                                44
D55V3, multiclass
                                         clus
vv                                        C14ORF166B MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                  9
  MIXED SEROUS AND ENDOMETRIOID                            0
  SEROUS ENDOMETRIAL ADENOCARCINOMA                        0
                                         clus
vv                                        C14ORF166B WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                  191
  MIXED SEROUS AND ENDOMETRIOID                              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                         44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    R0  R1  R2  RX
  C14ORF166B MUTATED     7   0   0   0
  C14ORF166B WILD-TYPE 165  10   7  18
D55V4, multiclass
    clus
vv   C14ORF166B MUTATED C14ORF166B WILD-TYPE
  R0                  7                  165
  R1                  0                   10
  R2                  0                    7
  RX                  0                   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"

Clustering(56) Variable = ATM MUTATION ANALYSIS
D56V1, survival
               sevent
clus2             0   1
  ATM MUTATED    29   0
  ATM WILD-TYPE 186  33
  ATM MUTATED ATM WILD-TYPE 
           29           219 
  ATM MUTATED ATM WILD-TYPE 
            0            33 
$`ATM MUTATED`
TCGA-A5-A0GB TCGA-A5-A0GP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM 
       32.78        46.55       129.80        86.07        48.03        27.12 
TCGA-AP-A0LT TCGA-AX-A05Z TCGA-AX-A063 TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JR 
       49.22        71.51        79.46        40.11        77.39        56.91 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11G TCGA-B5-A11U TCGA-BG-A0M4 TCGA-BG-A0MT 
       69.27        59.84       113.36        16.73        71.24        21.17 
TCGA-BG-A2AE TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UM TCGA-BS-A0UV 
       23.70        85.55        85.84        82.39        86.93        73.25 
TCGA-D1-A15X TCGA-D1-A16F TCGA-D1-A16Y TCGA-D1-A17Q TCGA-D1-A17T 
       29.88         2.63        17.49         1.78         2.33 

$`ATM WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       37.02        83.51        17.85       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       65.75        60.53        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 
       28.77        42.35        15.95        20.25        21.99        23.31 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       63.91        45.53        36.89        23.87        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        82.52        33.40        61.64        80.78 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       88.24        35.34        45.99        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       61.08        35.74        37.78        34.65        25.51        71.24 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
       13.45       185.79        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V 
       61.68        85.78        32.09        77.23        73.28        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       59.74        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       14.01        15.45        15.45        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD 
       35.08        31.00        24.99        46.95        24.33        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V6 
       97.41        92.88       114.90        81.57        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       21.99        39.48        30.08         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A174 
       33.63        10.65         0.69        18.67         3.65        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       11.15        24.30        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  ATM MUTATED ATM WILD-TYPE 
         1.78          0.56 
  ATM MUTATED ATM WILD-TYPE 
       129.80        185.79 
  ATM MUTATED ATM WILD-TYPE 
        56.91         35.21 
[1] "1.8 - 129.8 (56.9)" "0.6 - 185.8 (35.2)"
[1] "hr="     "8.7e+07"
D56V2, binary
               cls
clus              0   1
  ATM MUTATED    21   8
  ATM WILD-TYPE 136  83
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     21    8
  ATM WILD-TYPE  136   83
     clus
vv    ATM MUTATED ATM WILD-TYPE
  NO           21           136
  YES           8            83
[1] 2 2
[1] FALSE
               vv
clus            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ATM MUTATED                                        28
  ATM WILD-TYPE                                     172
               vv
clus            MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  ATM MUTATED                               0                                 1
  ATM WILD-TYPE                             4                                43
D56V3, multiclass
                                         clus
vv                                        ATM MUTATED ATM WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA          28           172
  MIXED SEROUS AND ENDOMETRIOID                     0             4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                 1            43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  ATM MUTATED    21   1   0   1
  ATM WILD-TYPE 151   9   7  17
D56V4, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  R0          21           151
  R1           1             9
  R2           0             7
  RX           1            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"

Clustering(57) Variable = RAE1 MUTATION ANALYSIS
D57V1, survival
                sevent
clus2              0   1
  RAE1 MUTATED    11   0
  RAE1 WILD-TYPE 204  33
  RAE1 MUTATED RAE1 WILD-TYPE 
            11            237 
  RAE1 MUTATED RAE1 WILD-TYPE 
             0             33 
$`RAE1 MUTATED`
TCGA-A5-A0GH TCGA-AP-A056 TCGA-AX-A064 TCGA-AX-A0J1 TCGA-B5-A11E TCGA-B5-A11J 
       74.10        86.07        49.87        77.39        59.84        54.44 
TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A15V TCGA-D1-A160 TCGA-D1-A17Q 
       85.84        73.25        39.48         3.68         1.78 

$`RAE1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A06H TCGA-AX-A06L 
       71.51        35.34        45.99        79.46        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 
       61.08        35.74        37.78        40.11        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       71.24        56.91        86.37        55.30        86.01        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       88.34        75.72        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ 
       96.49        30.74        97.41        92.88       114.90        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        86.93        72.72        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W 
       28.67        23.93        22.55         1.74        21.99        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
       29.88         1.91        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  RAE1 MUTATED RAE1 WILD-TYPE 
          1.78           0.56 
  RAE1 MUTATED RAE1 WILD-TYPE 
         86.07         185.79 
  RAE1 MUTATED RAE1 WILD-TYPE 
         59.84          35.34 
[1] "1.8 - 86.1 (59.8)"  "0.6 - 185.8 (35.3)"
[1] "hr="     "2.7e+07"
D57V2, binary
                cls
clus               0   1
  RAE1 MUTATED    10   1
  RAE1 WILD-TYPE 147  90
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAE1 MUTATED     10    1
  RAE1 WILD-TYPE  147   90
     clus
vv    RAE1 MUTATED RAE1 WILD-TYPE
  NO            10            147
  YES            1             90
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  RAE1 MUTATED                                        10
  RAE1 WILD-TYPE                                     190
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  RAE1 MUTATED                               0
  RAE1 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  RAE1 MUTATED                                   1
  RAE1 WILD-TYPE                                43
D57V3, multiclass
                                         clus
vv                                        RAE1 MUTATED RAE1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           10            190
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  1             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RAE1 MUTATED     8   0   0   0
  RAE1 WILD-TYPE 164  10   7  18
D57V4, multiclass
    clus
vv   RAE1 MUTATED RAE1 WILD-TYPE
  R0            8            164
  R1            0             10
  R2            0              7
  RX            0             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"

Clustering(58) Variable = ZNF485 MUTATION ANALYSIS
D58V1, survival
                  sevent
clus2                0   1
  ZNF485 MUTATED     8   1
  ZNF485 WILD-TYPE 207  32
  ZNF485 MUTATED ZNF485 WILD-TYPE 
               9              239 
  ZNF485 MUTATED ZNF485 WILD-TYPE 
               1               32 
$`ZNF485 MUTATED`
TCGA-A5-A0GP TCGA-AP-A054 TCGA-AP-A059 TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY 
       46.55        23.31        48.03        71.51        40.11        69.27 
TCGA-BS-A0TC TCGA-D1-A103 TCGA-D1-A16Y 
       85.55        21.99        17.49 

$`ZNF485 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        86.07        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        55.30        86.01        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        92.88       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        86.93        72.72        73.25        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V 
        4.87        28.67        23.93        22.55         1.74        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A174 
       33.63        10.65         0.69        18.67         3.65        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.78        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  ZNF485 MUTATED ZNF485 WILD-TYPE 
           17.49             0.56 
  ZNF485 MUTATED ZNF485 WILD-TYPE 
           85.55           185.79 
  ZNF485 MUTATED ZNF485 WILD-TYPE 
           46.55            35.74 
[1] "17.5 - 85.5 (46.5)" "0.6 - 185.8 (35.7)"
[1] "hr=" "1.2"
D58V2, binary
                  cls
clus                 0   1
  ZNF485 MUTATED     8   1
  ZNF485 WILD-TYPE 149  90
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF485 MUTATED      8    1
  ZNF485 WILD-TYPE  149   90
     clus
vv    ZNF485 MUTATED ZNF485 WILD-TYPE
  NO               8              149
  YES              1               90
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZNF485 MUTATED                                         9
  ZNF485 WILD-TYPE                                     191
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ZNF485 MUTATED                               0
  ZNF485 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZNF485 MUTATED                                   0
  ZNF485 WILD-TYPE                                44
D58V3, multiclass
                                         clus
vv                                        ZNF485 MUTATED ZNF485 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              9              191
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF485 MUTATED     5   2   0   1
  ZNF485 WILD-TYPE 167   8   7  17
D58V4, multiclass
    clus
vv   ZNF485 MUTATED ZNF485 WILD-TYPE
  R0              5              167
  R1              2                8
  R2              0                7
  RX              1               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"

Clustering(59) Variable = POLE MUTATION ANALYSIS
D59V1, survival
                sevent
clus2              0   1
  POLE MUTATED    25   2
  POLE WILD-TYPE 190  31
  POLE MUTATED POLE WILD-TYPE 
            27            221 
  POLE MUTATED POLE WILD-TYPE 
             2             31 
$`POLE MUTATED`
TCGA-A5-A0GP TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       46.55        42.35       129.80        23.31        86.07        48.03 
TCGA-AP-A0LM TCGA-AP-A1DQ TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY 
       27.12        46.78        71.51        40.11        77.39        69.27 
TCGA-B5-A11E TCGA-B5-A11H TCGA-B5-A11N TCGA-B5-A11Y TCGA-BG-A0LX TCGA-BG-A0VX 
       59.84        88.34        61.68        18.41        20.19        34.29 
TCGA-BG-A18A TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UM TCGA-BS-A0UV TCGA-D1-A103 
       14.01        85.55        85.84        86.93        73.25        21.99 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A17Q 
        3.65        17.49         1.78 

$`POLE WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A05A 
       29.06        28.77        15.95        20.25        21.99        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89        23.87        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37        66.25        36.36        97.71        46.72 
TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       83.97        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       25.08        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       61.08        35.74        37.78        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        55.30        86.01        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J 
       27.85        13.45       185.79       113.36        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       44.78        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.56        19.50        19.59        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       11.87        18.61        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD 
       35.08        31.00        24.99        46.95        24.33        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        92.88       114.90        82.39        81.57        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.51        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  POLE MUTATED POLE WILD-TYPE 
          1.78           0.56 
  POLE MUTATED POLE WILD-TYPE 
        129.80         185.79 
  POLE MUTATED POLE WILD-TYPE 
         46.78          35.34 
[1] "1.8 - 129.8 (46.8)" "0.6 - 185.8 (35.3)"
[1] "hr=" "2.2"
D59V2, binary
                cls
clus               0   1
  POLE MUTATED    20   7
  POLE WILD-TYPE 137  84
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLE MUTATED     20    7
  POLE WILD-TYPE  137   84
     clus
vv    POLE MUTATED POLE WILD-TYPE
  NO            20            137
  YES            7             84
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  POLE MUTATED                                        26
  POLE WILD-TYPE                                     174
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  POLE MUTATED                               0
  POLE WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  POLE MUTATED                                   1
  POLE WILD-TYPE                                43
D59V3, multiclass
                                         clus
vv                                        POLE MUTATED POLE WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           26            174
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  1             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  POLE MUTATED    17   2   0   3
  POLE WILD-TYPE 155   8   7  15
D59V4, multiclass
    clus
vv   POLE MUTATED POLE WILD-TYPE
  R0           17            155
  R1            2              8
  R2            0              7
  RX            3             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"

Clustering(60) Variable = AHCYL1 MUTATION ANALYSIS
D60V1, survival
                  sevent
clus2                0   1
  AHCYL1 MUTATED     6   0
  AHCYL1 WILD-TYPE 209  33
  AHCYL1 MUTATED AHCYL1 WILD-TYPE 
               6              242 
  AHCYL1 MUTATED AHCYL1 WILD-TYPE 
               0               33 
$`AHCYL1 MUTATED`
TCGA-AP-A051 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-B5-A11Y TCGA-BS-A0UV TCGA-D1-A17Q 
      129.80        27.12        71.51        18.41        73.25         1.78 

$`AHCYL1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.56        19.50        19.59        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
      114.90        85.84        82.39        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       18.67         3.65        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  AHCYL1 MUTATED AHCYL1 WILD-TYPE 
            1.78             0.56 
  AHCYL1 MUTATED AHCYL1 WILD-TYPE 
          129.80           185.79 
  AHCYL1 MUTATED AHCYL1 WILD-TYPE 
          49.315           35.900 
[1] "1.8 - 129.8 (49.3)" "0.6 - 185.8 (35.9)"
[1] "hr="     "2.6e+07"
D60V2, binary
                  cls
clus                 0   1
  AHCYL1 MUTATED     4   2
  AHCYL1 WILD-TYPE 153  89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCYL1 MUTATED      4    2
  AHCYL1 WILD-TYPE  153   89
     clus
vv    AHCYL1 MUTATED AHCYL1 WILD-TYPE
  NO               4              153
  YES              2               89
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AHCYL1 MUTATED                                         6
  AHCYL1 WILD-TYPE                                     194
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  AHCYL1 MUTATED                               0
  AHCYL1 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  AHCYL1 MUTATED                                   0
  AHCYL1 WILD-TYPE                                44
D60V3, multiclass
                                         clus
vv                                        AHCYL1 MUTATED AHCYL1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              6              194
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  AHCYL1 MUTATED     4   1   0   0
  AHCYL1 WILD-TYPE 168   9   7  18
D60V4, multiclass
    clus
vv   AHCYL1 MUTATED AHCYL1 WILD-TYPE
  R0              4              168
  R1              1                9
  R2              0                7
  RX              0               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"

Clustering(61) Variable = ZNF334 MUTATION ANALYSIS
D61V1, survival
                  sevent
clus2                0   1
  ZNF334 MUTATED    16   1
  ZNF334 WILD-TYPE 199  32
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              17              231 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
               1               32 
$`ZNF334 MUTATED`
TCGA-A5-A0GP TCGA-A5-A0R9 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z 
       46.55        24.62        86.07        48.03        27.12        71.51 
TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-BS-A0UV TCGA-D1-A103 
       40.11        69.27        59.84        61.68        73.25        21.99 
TCGA-D1-A15X TCGA-D1-A16F TCGA-D1-A16I TCGA-D1-A16X TCGA-D1-A17Q 
       29.88         2.63        11.51         3.65         1.78 

$`ZNF334 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0RA 
       23.21        68.65        37.91        17.59        19.59        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 
       28.77        42.35        15.95        20.25       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       23.31        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        46.72        83.97        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       80.78        49.22        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        80.55        88.24        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       77.39        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       55.30        86.01        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
      114.90        85.84        82.39        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
        1.74        39.48        30.08         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        27.42        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
       10.65         0.69        18.67        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  ZNF334 MUTATED ZNF334 WILD-TYPE 
            1.78             0.56 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
           86.07           185.79 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
           40.11            35.90 
[1] "1.8 - 86.1 (40.1)"  "0.6 - 185.8 (35.9)"
[1] "hr=" "2.1"
D61V2, binary
                  cls
clus                 0   1
  ZNF334 MUTATED    12   5
  ZNF334 WILD-TYPE 145  86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED     12    5
  ZNF334 WILD-TYPE  145   86
     clus
vv    ZNF334 MUTATED ZNF334 WILD-TYPE
  NO              12              145
  YES              5               86
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZNF334 MUTATED                                        15
  ZNF334 WILD-TYPE                                     185
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ZNF334 MUTATED                               0
  ZNF334 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZNF334 MUTATED                                   2
  ZNF334 WILD-TYPE                                42
D61V3, multiclass
                                         clus
vv                                        ZNF334 MUTATED ZNF334 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             15              185
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    2               42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF334 MUTATED    13   1   0   0
  ZNF334 WILD-TYPE 159   9   7  18
D61V4, multiclass
    clus
vv   ZNF334 MUTATED ZNF334 WILD-TYPE
  R0             13              159
  R1              1                9
  R2              0                7
  RX              0               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"

Clustering(62) Variable = SACS MUTATION ANALYSIS
D62V1, survival
                sevent
clus2              0   1
  SACS MUTATED    25   1
  SACS WILD-TYPE 190  32
  SACS MUTATED SACS WILD-TYPE 
            26            222 
  SACS MUTATED SACS WILD-TYPE 
             1             32 
$`SACS MUTATED`
TCGA-D1-A0ZO TCGA-A5-A0GB TCGA-A5-A0GP TCGA-A5-A0VQ TCGA-AP-A051 TCGA-AP-A056 
       19.79        32.78        46.55        15.95       129.80        86.07 
TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 
       48.03        36.89        27.12        71.51        35.34        79.46 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JR TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N 
       40.11        77.39        56.91        69.27        59.84        61.68 
TCGA-BG-A0M4 TCGA-BG-A0VX TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UV 
       71.24        34.29        24.33        85.55        85.84        73.25 
TCGA-D1-A103 TCGA-D1-A16X 
       21.99         3.65 

$`SACS WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       51.55        12.56         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ 
       83.51        17.85       112.54       105.37        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       60.53        73.87        28.27        54.02        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       37.91        17.59        19.59        24.62        29.06        28.77 
TCGA-A5-A0VP TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H 
       42.35        20.25        21.99        23.31        63.91        45.53 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A062 
       13.58        33.21        29.69        80.55        88.24        45.99 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       34.65        25.51        71.24        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q 
       88.34        75.72        54.44        44.78        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0M9 
       20.19        19.33        20.94        35.21        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VZ TCGA-BG-A0W1 
       20.28        15.42        51.06        52.01        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       31.00        24.99        46.95        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
      114.90        82.39        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y 
       31.07        33.63        10.65         0.69        18.67        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  SACS MUTATED SACS WILD-TYPE 
          3.65           0.56 
  SACS MUTATED SACS WILD-TYPE 
        129.80         185.79 
  SACS MUTATED SACS WILD-TYPE 
        52.470         35.145 
[1] "3.6 - 129.8 (52.5)" "0.6 - 185.8 (35.1)"
[1] "hr=" "4.7"
D62V2, binary
                cls
clus               0   1
  SACS MUTATED    18   8
  SACS WILD-TYPE 139  83
[1] "tbl2"
                cls
clus             [,1] [,2]
  SACS MUTATED     18    8
  SACS WILD-TYPE  139   83
     clus
vv    SACS MUTATED SACS WILD-TYPE
  NO            18            139
  YES            8             83
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SACS MUTATED                                        25
  SACS WILD-TYPE                                     175
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  SACS MUTATED                               0
  SACS WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  SACS MUTATED                                   1
  SACS WILD-TYPE                                43
D62V3, multiclass
                                         clus
vv                                        SACS MUTATED SACS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           25            175
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  1             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SACS MUTATED    18   2   0   2
  SACS WILD-TYPE 154   8   7  16
D62V4, multiclass
    clus
vv   SACS MUTATED SACS WILD-TYPE
  R0           18            154
  R1            2              8
  R2            0              7
  RX            2             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"

Clustering(63) Variable = MSH4 MUTATION ANALYSIS
D63V1, survival
                sevent
clus2              0   1
  MSH4 MUTATED    15   0
  MSH4 WILD-TYPE 200  33
  MSH4 MUTATED MSH4 WILD-TYPE 
            15            233 
  MSH4 MUTATED MSH4 WILD-TYPE 
             0             33 
$`MSH4 MUTATED`
TCGA-A5-A0GI TCGA-A5-A0GP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM 
       88.18        46.55       129.80        86.07        48.03        27.12 
TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UV 
       71.51        69.27        59.84        85.55        85.84        73.25 
TCGA-D1-A103 TCGA-D1-A16X TCGA-D1-A17Q 
       21.99         3.65         1.78 

$`MSH4 WILD-TYPE`
TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP 
       60.53       110.63        57.80        93.99        67.66        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       65.75        60.53        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 
       28.77        42.35        15.95        20.25        21.99        23.31 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       63.91        45.53        36.89        23.87        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       49.22        25.08        46.78        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       80.55        88.24        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        61.08        35.74        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       77.39        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       55.30        86.01        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       24.99        46.95        24.33        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
      114.90        82.39        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y 
       31.07        33.63        10.65         0.69        18.67        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.51        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  MSH4 MUTATED MSH4 WILD-TYPE 
          1.78           0.56 
  MSH4 MUTATED MSH4 WILD-TYPE 
        129.80         185.79 
  MSH4 MUTATED MSH4 WILD-TYPE 
         69.27          35.34 
[1] "1.8 - 129.8 (69.3)" "0.6 - 185.8 (35.3)"
[1] "hr="     "7.6e+07"
D63V2, binary
                cls
clus               0   1
  MSH4 MUTATED    11   4
  MSH4 WILD-TYPE 146  87
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH4 MUTATED     11    4
  MSH4 WILD-TYPE  146   87
     clus
vv    MSH4 MUTATED MSH4 WILD-TYPE
  NO            11            146
  YES            4             87
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MSH4 MUTATED                                        15
  MSH4 WILD-TYPE                                     185
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  MSH4 MUTATED                               0
  MSH4 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  MSH4 MUTATED                                   0
  MSH4 WILD-TYPE                                44
D63V3, multiclass
                                         clus
vv                                        MSH4 MUTATED MSH4 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           15            185
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MSH4 MUTATED    12   1   0   0
  MSH4 WILD-TYPE 160   9   7  18
D63V4, multiclass
    clus
vv   MSH4 MUTATED MSH4 WILD-TYPE
  R0           12            160
  R1            1              9
  R2            0              7
  RX            0             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"

Clustering(64) Variable = SLC26A8 MUTATION ANALYSIS
D64V1, survival
                   sevent
clus2                 0   1
  SLC26A8 MUTATED    12   0
  SLC26A8 WILD-TYPE 203  33
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
               12               236 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
                0                33 
$`SLC26A8 MUTATED`
TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY 
       48.03        27.12        71.51        40.11        77.39        69.27 
TCGA-B5-A11E TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A167 TCGA-D1-A16X TCGA-D1-A17Q 
       59.84        85.84        73.25        15.72         3.65         1.78 

$`SLC26A8 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       61.08        35.74        37.78        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        55.30        86.01        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       27.85        13.45       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        92.88       114.90        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
        0.69        18.67        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
             1.78              0.56 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
            85.84            185.79 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
           53.935            35.560 
[1] "1.8 - 85.8 (53.9)"  "0.6 - 185.8 (35.6)"
[1] "hr="     "2.6e+07"
D64V2, binary
                   cls
clus                  0   1
  SLC26A8 MUTATED     9   3
  SLC26A8 WILD-TYPE 148  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A8 MUTATED      9    3
  SLC26A8 WILD-TYPE  148   88
     clus
vv    SLC26A8 MUTATED SLC26A8 WILD-TYPE
  NO                9               148
  YES               3                88
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SLC26A8 MUTATED                                        12
  SLC26A8 WILD-TYPE                                     188
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  SLC26A8 MUTATED                               0
  SLC26A8 WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  SLC26A8 MUTATED                                   0
  SLC26A8 WILD-TYPE                                44
D64V3, multiclass
                                         clus
vv                                        SLC26A8 MUTATED SLC26A8 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              12               188
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     0                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC26A8 MUTATED     9   1   0   0
  SLC26A8 WILD-TYPE 163   9   7  18
D64V4, multiclass
    clus
vv   SLC26A8 MUTATED SLC26A8 WILD-TYPE
  R0               9               163
  R1               1                 9
  R2               0                 7
  RX               0                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"

Clustering(65) Variable = KIF20B MUTATION ANALYSIS
D65V1, survival
                  sevent
clus2                0   1
  KIF20B MUTATED    20   1
  KIF20B WILD-TYPE 195  32
  KIF20B MUTATED KIF20B WILD-TYPE 
              21              227 
  KIF20B MUTATED KIF20B WILD-TYPE 
               1               32 
$`KIF20B MUTATED`
TCGA-A5-A0GP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z 
       46.55       129.80        86.07        48.03        27.12        71.51 
TCGA-AX-A063 TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11H 
       79.46        40.11        69.27        13.45        59.84        88.34 
TCGA-B5-A11N TCGA-B5-A11Y TCGA-BG-A186 TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A0ZS 
       61.68        18.41        13.78        85.84        73.25         4.87 
TCGA-D1-A103 TCGA-D1-A16X TCGA-D1-A17Q 
       21.99         3.65         1.78 

$`KIF20B WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       29.06        28.77        42.35        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       23.31        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        46.72        83.97        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       80.78        49.22        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A064 
       29.69        80.55        88.24        35.34        45.99        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        61.08        35.74        37.78        77.39 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       86.01        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A11F TCGA-B5-A11G 
       57.76        64.21        63.55        27.85       185.79       113.36 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       75.72        54.44        44.78        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        19.59        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       56.58        14.83        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       92.88       114.90        82.39        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        8.55         0.56        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y 
       31.07        33.63        10.65         0.69        18.67        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.51        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  KIF20B MUTATED KIF20B WILD-TYPE 
            1.78             0.56 
  KIF20B MUTATED KIF20B WILD-TYPE 
          129.80           185.79 
  KIF20B MUTATED KIF20B WILD-TYPE 
           48.03            35.38 
[1] "1.8 - 129.8 (48.0)" "0.6 - 185.8 (35.4)"
[1] "hr=" "3.3"
D65V2, binary
                  cls
clus                 0   1
  KIF20B MUTATED    15   6
  KIF20B WILD-TYPE 142  85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF20B MUTATED     15    6
  KIF20B WILD-TYPE  142   85
     clus
vv    KIF20B MUTATED KIF20B WILD-TYPE
  NO              15              142
  YES              6               85
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  KIF20B MUTATED                                        21
  KIF20B WILD-TYPE                                     179
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  KIF20B MUTATED                               0
  KIF20B WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  KIF20B MUTATED                                   0
  KIF20B WILD-TYPE                                44
D65V3, multiclass
                                         clus
vv                                        KIF20B MUTATED KIF20B WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             21              179
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KIF20B MUTATED    13   1   0   1
  KIF20B WILD-TYPE 159   9   7  17
D65V4, multiclass
    clus
vv   KIF20B MUTATED KIF20B WILD-TYPE
  R0             13              159
  R1              1                9
  R2              0                7
  RX              1               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"

Clustering(66) Variable = RRAS2 MUTATION ANALYSIS
D66V1, survival
                 sevent
clus2               0   1
  RRAS2 MUTATED     4   0
  RRAS2 WILD-TYPE 211  33
  RRAS2 MUTATED RRAS2 WILD-TYPE 
              4             244 
  RRAS2 MUTATED RRAS2 WILD-TYPE 
              0              33 
$`RRAS2 MUTATED`
TCGA-B5-A0K4 TCGA-BG-A0M4 TCGA-BG-A0YU TCGA-D1-A17U 
       57.76        71.24        14.83        22.92 

$`RRAS2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
      129.80        21.99        23.31        86.07        48.03        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89        23.87        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37        66.25        36.36        97.71        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       49.22        25.08        46.78        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       40.11        77.39        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       86.37        55.30        86.01        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       36.49        72.62        27.29        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       19.33        20.94        35.21        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       56.58        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       92.88       114.90        85.84        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       72.72        73.25        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69        18.67         3.65        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A1NU TCGA-D1-A1NX 
        1.78        11.15        24.30         2.33        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  RRAS2 MUTATED RRAS2 WILD-TYPE 
          14.83            0.56 
  RRAS2 MUTATED RRAS2 WILD-TYPE 
          71.24          185.79 
  RRAS2 MUTATED RRAS2 WILD-TYPE 
          40.34           35.90 
[1] "14.8 - 71.2 (40.3)" "0.6 - 185.8 (35.9)"
[1] "hr="     "9100000"
D66V2, binary
                 cls
clus                0   1
  RRAS2 MUTATED     2   2
  RRAS2 WILD-TYPE 155  89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRAS2 MUTATED      2    2
  RRAS2 WILD-TYPE  155   89
     clus
vv    RRAS2 MUTATED RRAS2 WILD-TYPE
  NO              2             155
  YES             2              89
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  RRAS2 MUTATED                                         4
  RRAS2 WILD-TYPE                                     196
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  RRAS2 MUTATED                               0
  RRAS2 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  RRAS2 MUTATED                                   0
  RRAS2 WILD-TYPE                                44
D66V3, multiclass
                                         clus
vv                                        RRAS2 MUTATED RRAS2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             4             196
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RRAS2 MUTATED     2   0   0   1
  RRAS2 WILD-TYPE 170  10   7  17
D66V4, multiclass
    clus
vv   RRAS2 MUTATED RRAS2 WILD-TYPE
  R0             2             170
  R1             0              10
  R2             0               7
  RX             1              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"

Clustering(67) Variable = CTNND1 MUTATION ANALYSIS
D67V1, survival
                  sevent
clus2                0   1
  CTNND1 MUTATED    17   2
  CTNND1 WILD-TYPE 198  31
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              19              229 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
               2               31 
$`CTNND1 MUTATED`
TCGA-A5-A0GA TCGA-A5-A0R8 TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM 
       17.85        19.59       129.80        86.07        48.03        27.12 
TCGA-AX-A05S TCGA-AX-A05T TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0TC TCGA-BS-A0UA 
       13.58        33.21        69.27        59.84        85.55       114.90 
TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A17Q TCGA-DI-A0WH 
       85.84        73.25         0.66        15.72         1.78        16.31 
TCGA-DI-A1NN 
       35.38 

$`CTNND1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       37.02        83.51        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        37.91        17.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 
       28.77        42.35        15.95        20.25        21.99        23.31 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       63.91        45.53        36.89        23.87        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       49.22        25.08        46.78        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       71.51        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        61.08        35.74        37.78        40.11        77.39 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       86.01        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       57.76        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        44.78        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        24.33        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UJ 
       67.99        96.49        30.74        97.41        92.88        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        86.93        72.72        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-E6-A1LZ 
       24.30         2.33        22.92        13.22        18.25        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  CTNND1 MUTATED CTNND1 WILD-TYPE 
            0.66             0.56 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
          129.80           185.79 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
           35.38            35.90 
[1] "0.7 - 129.8 (35.4)" "0.6 - 185.8 (35.9)"
[1] "hr=" "1.5"
D67V2, binary
                  cls
clus                 0   1
  CTNND1 MUTATED    12   7
  CTNND1 WILD-TYPE 145  84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED     12    7
  CTNND1 WILD-TYPE  145   84
     clus
vv    CTNND1 MUTATED CTNND1 WILD-TYPE
  NO              12              145
  YES              7               84
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CTNND1 MUTATED                                        18
  CTNND1 WILD-TYPE                                     182
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  CTNND1 MUTATED                               0
  CTNND1 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  CTNND1 MUTATED                                   1
  CTNND1 WILD-TYPE                                43
D67V3, multiclass
                                         clus
vv                                        CTNND1 MUTATED CTNND1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             18              182
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    1               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CTNND1 MUTATED    16   0   1   0
  CTNND1 WILD-TYPE 156  10   6  18
D67V4, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  R0             16              156
  R1              0               10
  R2              1                6
  RX              0               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"

Clustering(68) Variable = NFE2L3 MUTATION ANALYSIS
D68V1, survival
                  sevent
clus2                0   1
  NFE2L3 MUTATED    10   2
  NFE2L3 WILD-TYPE 205  31
  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
              12              236 
  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
               2               31 
$`NFE2L3 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-B5-A11I TCGA-BS-A0UV 
      129.80        86.07        48.03        27.12        75.72        73.25 
TCGA-D1-A103 TCGA-D1-A15X TCGA-D1-A17D TCGA-D1-A17Q TCGA-EY-A1GS TCGA-FI-A2D2 
       21.99        29.88        30.44         1.78        22.03        77.33 

$`NFE2L3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.74        37.78        40.11        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       71.24        56.91        86.37        55.30        86.01        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
      113.36        88.34        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       85.84        82.39        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       39.48        30.08         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-FI-A2EW 
       16.31        35.38        79.10        10.92        37.71        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
            1.78             0.56 
  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
          129.80           185.79 
  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
          39.235           35.900 
[1] "1.8 - 129.8 (39.2)" "0.6 - 185.8 (35.9)"
[1] "hr=" "1"  
D68V2, binary
                  cls
clus                 0   1
  NFE2L3 MUTATED     6   6
  NFE2L3 WILD-TYPE 151  85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L3 MUTATED      6    6
  NFE2L3 WILD-TYPE  151   85
     clus
vv    NFE2L3 MUTATED NFE2L3 WILD-TYPE
  NO               6              151
  YES              6               85
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  NFE2L3 MUTATED                                         9
  NFE2L3 WILD-TYPE                                     191
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  NFE2L3 MUTATED                               1
  NFE2L3 WILD-TYPE                             3
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  NFE2L3 MUTATED                                   2
  NFE2L3 WILD-TYPE                                42
D68V3, multiclass
                                         clus
vv                                        NFE2L3 MUTATED NFE2L3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              9              191
  MIXED SEROUS AND ENDOMETRIOID                        1                3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    2               42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NFE2L3 MUTATED    10   0   1   0
  NFE2L3 WILD-TYPE 162  10   6  18
D68V4, multiclass
    clus
vv   NFE2L3 MUTATED NFE2L3 WILD-TYPE
  R0             10              162
  R1              0               10
  R2              1                6
  RX              0               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"

Clustering(69) Variable = FAM65B MUTATION ANALYSIS
D69V1, survival
                  sevent
clus2                0   1
  FAM65B MUTATED    16   0
  FAM65B WILD-TYPE 199  33
  FAM65B MUTATED FAM65B WILD-TYPE 
              16              232 
  FAM65B MUTATED FAM65B WILD-TYPE 
               0               33 
$`FAM65B MUTATED`
TCGA-A5-A0VQ TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-B5-A0JY 
       15.95        86.07        48.03        27.12        40.11        69.27 
TCGA-B5-A11E TCGA-B5-A11N TCGA-B5-A11R TCGA-BS-A0TC TCGA-BS-A0UA TCGA-BS-A0UF 
       59.84        61.68        77.23        85.55       114.90        85.84 
TCGA-BS-A0UV TCGA-D1-A15X TCGA-D1-A17H TCGA-D1-A17Q 
       73.25        29.88        28.01         1.78 

$`FAM65B WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-AJ-A23M TCGA-AP-A051 
       24.62        29.06        28.77        42.35        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        55.30        86.01        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       27.85        13.45       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U 
       54.44        44.78        85.78        32.09        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       24.99        46.95        24.33        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 
       82.39        81.57        86.93        72.72        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       39.48        30.08         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
       30.44         1.28        28.08        26.37        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  FAM65B MUTATED FAM65B WILD-TYPE 
            1.78             0.56 
  FAM65B MUTATED FAM65B WILD-TYPE 
          114.90           185.79 
  FAM65B MUTATED FAM65B WILD-TYPE 
           60.76            35.36 
[1] "1.8 - 114.9 (60.8)" "0.6 - 185.8 (35.4)"
[1] "hr="     "7.6e+07"
D69V2, binary
                  cls
clus                 0   1
  FAM65B MUTATED    11   5
  FAM65B WILD-TYPE 146  86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65B MUTATED     11    5
  FAM65B WILD-TYPE  146   86
     clus
vv    FAM65B MUTATED FAM65B WILD-TYPE
  NO              11              146
  YES              5               86
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  FAM65B MUTATED                                        15
  FAM65B WILD-TYPE                                     185
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  FAM65B MUTATED                               0
  FAM65B WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  FAM65B MUTATED                                   1
  FAM65B WILD-TYPE                                43
D69V3, multiclass
                                         clus
vv                                        FAM65B MUTATED FAM65B WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             15              185
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    1               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FAM65B MUTATED    12   0   0   0
  FAM65B WILD-TYPE 160  10   7  18
D69V4, multiclass
    clus
vv   FAM65B MUTATED FAM65B WILD-TYPE
  R0             12              160
  R1              0               10
  R2              0                7
  RX              0               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"

Clustering(70) Variable = RNF43 MUTATION ANALYSIS
D70V1, survival
                 sevent
clus2               0   1
  RNF43 MUTATED    12   0
  RNF43 WILD-TYPE 203  33
  RNF43 MUTATED RNF43 WILD-TYPE 
             12             236 
  RNF43 MUTATED RNF43 WILD-TYPE 
              0              33 
$`RNF43 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AP-A0LT TCGA-AX-A060 TCGA-AX-A0J1 
      129.80        48.03        27.12        49.22        35.34        77.39 
TCGA-B5-A11E TCGA-B5-A11N TCGA-BG-A0LX TCGA-BG-A0M2 TCGA-BS-A0U8 TCGA-D1-A17M 
       59.84        61.68        20.19        20.94        97.41        10.22 

$`RNF43 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        86.07        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       33.40        61.64        80.78        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A062 
       33.21        29.69        80.55        88.24        71.51        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       37.78        40.11        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       86.37        55.30        86.01        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       27.85        13.45       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       54.44        44.78        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0M0 TCGA-BG-A0M3 
       16.57        50.89        11.87        18.61        19.33        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U9 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       85.84        82.39        81.57        86.93        72.72        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       18.67         3.65        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  RNF43 MUTATED RNF43 WILD-TYPE 
          10.22            0.56 
  RNF43 MUTATED RNF43 WILD-TYPE 
         129.80          185.79 
  RNF43 MUTATED RNF43 WILD-TYPE 
         48.625          35.820 
[1] "10.2 - 129.8 (48.6)" "0.6 - 185.8 (35.8)" 
[1] "hr="     "2.7e+07"
D70V2, binary
                 cls
clus                0   1
  RNF43 MUTATED     4   8
  RNF43 WILD-TYPE 153  83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      4    8
  RNF43 WILD-TYPE  153   83
     clus
vv    RNF43 MUTATED RNF43 WILD-TYPE
  NO              4             153
  YES             8              83
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  RNF43 MUTATED                                        12
  RNF43 WILD-TYPE                                     188
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  RNF43 MUTATED                               0
  RNF43 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  RNF43 MUTATED                                   0
  RNF43 WILD-TYPE                                44
D70V3, multiclass
                                         clus
vv                                        RNF43 MUTATED RNF43 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            12             188
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RNF43 MUTATED     8   1   0   0
  RNF43 WILD-TYPE 164   9   7  18
D70V4, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  R0             8             164
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(71) Variable = MRPL47 MUTATION ANALYSIS
D71V1, survival
                  sevent
clus2                0   1
  MRPL47 MUTATED     6   0
  MRPL47 WILD-TYPE 209  33
  MRPL47 MUTATED MRPL47 WILD-TYPE 
               6              242 
  MRPL47 MUTATED MRPL47 WILD-TYPE 
               0               33 
$`MRPL47 MUTATED`
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J TCGA-AX-A05Z TCGA-D1-A103 TCGA-D1-A17Q 
       86.07        48.03        36.89        71.51        21.99         1.78 

$`MRPL47 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05N 
      129.80        21.99        23.31        63.91        45.53        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.74        37.78        40.11        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       71.24        56.91        86.37        55.30        86.01        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        44.78        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
      114.90        85.84        82.39        81.57        86.93        72.72 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       73.25        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       22.55         1.74        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       18.67         3.65        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  MRPL47 MUTATED MRPL47 WILD-TYPE 
            1.78             0.56 
  MRPL47 MUTATED MRPL47 WILD-TYPE 
           86.07           185.79 
  MRPL47 MUTATED MRPL47 WILD-TYPE 
           42.46            35.82 
[1] "1.8 - 86.1 (42.5)"  "0.6 - 185.8 (35.8)"
[1] "hr="     "9300000"
D71V2, binary
                  cls
clus                 0   1
  MRPL47 MUTATED     5   1
  MRPL47 WILD-TYPE 152  90
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL47 MUTATED      5    1
  MRPL47 WILD-TYPE  152   90
     clus
vv    MRPL47 MUTATED MRPL47 WILD-TYPE
  NO               5              152
  YES              1               90
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MRPL47 MUTATED                                         5
  MRPL47 WILD-TYPE                                     195
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  MRPL47 MUTATED                               0
  MRPL47 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  MRPL47 MUTATED                                   1
  MRPL47 WILD-TYPE                                43
D71V3, multiclass
                                         clus
vv                                        MRPL47 MUTATED MRPL47 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              5              195
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    1               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MRPL47 MUTATED     5   1   0   0
  MRPL47 WILD-TYPE 167   9   7  18
D71V4, multiclass
    clus
vv   MRPL47 MUTATED MRPL47 WILD-TYPE
  R0              5              167
  R1              1                9
  R2              0                7
  RX              0               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"

Clustering(72) Variable = TIGD4 MUTATION ANALYSIS
D72V1, survival
                 sevent
clus2               0   1
  TIGD4 MUTATED    13   0
  TIGD4 WILD-TYPE 202  33
  TIGD4 MUTATED TIGD4 WILD-TYPE 
             13             235 
  TIGD4 MUTATED TIGD4 WILD-TYPE 
              0              33 
$`TIGD4 MUTATED`
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 
       86.07        48.03        27.12        71.51        40.11        77.39 
TCGA-B5-A0JY TCGA-BK-A0C9 TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A16N TCGA-D1-A16X 
       69.27        35.90        85.84        73.25        31.07         3.65 
TCGA-D1-A177 
       18.02 

$`TIGD4 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
      129.80        21.99        23.31        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       35.74        37.78        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        15.45        23.70        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       31.00        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       97.41        92.88       114.90        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        11.51        29.92        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A17A TCGA-D1-A17B 
       18.67        17.49        19.53        30.15         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  TIGD4 MUTATED TIGD4 WILD-TYPE 
           3.65            0.56 
  TIGD4 MUTATED TIGD4 WILD-TYPE 
          86.07          185.79 
  TIGD4 MUTATED TIGD4 WILD-TYPE 
          48.03           35.38 
[1] "3.6 - 86.1 (48.0)"  "0.6 - 185.8 (35.4)"
[1] "hr="     "2.7e+07"
D72V2, binary
                 cls
clus                0   1
  TIGD4 MUTATED     9   4
  TIGD4 WILD-TYPE 148  87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD4 MUTATED      9    4
  TIGD4 WILD-TYPE  148   87
     clus
vv    TIGD4 MUTATED TIGD4 WILD-TYPE
  NO              9             148
  YES             4              87
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  TIGD4 MUTATED                                        13
  TIGD4 WILD-TYPE                                     187
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  TIGD4 MUTATED                               0
  TIGD4 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  TIGD4 MUTATED                                   0
  TIGD4 WILD-TYPE                                44
D72V3, multiclass
                                         clus
vv                                        TIGD4 MUTATED TIGD4 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            13             187
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TIGD4 MUTATED    11   1   0   0
  TIGD4 WILD-TYPE 161   9   7  18
D72V4, multiclass
    clus
vv   TIGD4 MUTATED TIGD4 WILD-TYPE
  R0            11             161
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(73) Variable = FILIP1 MUTATION ANALYSIS
D73V1, survival
                  sevent
clus2                0   1
  FILIP1 MUTATED    16   0
  FILIP1 WILD-TYPE 199  33
  FILIP1 MUTATED FILIP1 WILD-TYPE 
              16              232 
  FILIP1 MUTATED FILIP1 WILD-TYPE 
               0               33 
$`FILIP1 MUTATED`
TCGA-AX-A06B TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A0LM TCGA-AP-A0LP 
       67.66        42.35       129.80        86.07        27.12        61.64 
TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11H TCGA-B5-A11R 
       71.51        40.11        69.27        59.84        88.34        77.23 
TCGA-BG-A0VW TCGA-BS-A0UF TCGA-D1-A103 TCGA-D1-A15X 
       52.01        85.84        21.99        29.88 

$`FILIP1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A1CP 
       88.18        60.53       110.63        57.80        93.99        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 
       29.06        28.77        15.95        20.25        21.99        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       48.03        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LQ 
       97.71        46.72        83.97        82.52        33.40        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       49.22        25.08        46.78        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       80.55        88.24        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        61.08        35.74        37.78        77.39 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       86.01        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       57.76        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
      113.36        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       32.09        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ 
       21.17        20.28        15.42        51.06        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        92.88       114.90        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       86.93        72.72        73.25        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W 
       28.67        23.93        22.55         1.74        39.48        30.08 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  FILIP1 MUTATED FILIP1 WILD-TYPE 
           21.99             0.56 
  FILIP1 MUTATED FILIP1 WILD-TYPE 
          129.80           185.79 
  FILIP1 MUTATED FILIP1 WILD-TYPE 
          64.650           35.145 
[1] "22.0 - 129.8 (64.7)" "0.6 - 185.8 (35.1)" 
[1] "hr="     "7.7e+07"
D73V2, binary
                  cls
clus                 0   1
  FILIP1 MUTATED    10   6
  FILIP1 WILD-TYPE 147  85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FILIP1 MUTATED     10    6
  FILIP1 WILD-TYPE  147   85
     clus
vv    FILIP1 MUTATED FILIP1 WILD-TYPE
  NO              10              147
  YES              6               85
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  FILIP1 MUTATED                                        15
  FILIP1 WILD-TYPE                                     185
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  FILIP1 MUTATED                               0
  FILIP1 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  FILIP1 MUTATED                                   1
  FILIP1 WILD-TYPE                                43
D73V3, multiclass
                                         clus
vv                                        FILIP1 MUTATED FILIP1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             15              185
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    1               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FILIP1 MUTATED    11   1   0   0
  FILIP1 WILD-TYPE 161   9   7  18
D73V4, multiclass
    clus
vv   FILIP1 MUTATED FILIP1 WILD-TYPE
  R0             11              161
  R1              1                9
  R2              0                7
  RX              0               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"

Clustering(74) Variable = SLC1A3 MUTATION ANALYSIS
D74V1, survival
                  sevent
clus2                0   1
  SLC1A3 MUTATED    11   1
  SLC1A3 WILD-TYPE 204  32
  SLC1A3 MUTATED SLC1A3 WILD-TYPE 
              12              236 
  SLC1A3 MUTATED SLC1A3 WILD-TYPE 
               1               32 
$`SLC1A3 MUTATED`
TCGA-B5-A0JN TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A0LM TCGA-B5-A0JY TCGA-B5-A11R 
       80.38        23.31        48.03        27.12        69.27        77.23 
TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A167 TCGA-D1-A17Q TCGA-FI-A2EW 
       85.55        85.84        73.25        15.72         1.78        59.01 

$`SLC1A3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       36.39        27.88        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        86.07        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.74        37.78        40.11        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       71.24        56.91        86.37        55.30        86.01        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       32.09        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        92.88       114.90        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  SLC1A3 MUTATED SLC1A3 WILD-TYPE 
            1.78             0.56 
  SLC1A3 MUTATED SLC1A3 WILD-TYPE 
           85.84           185.79 
  SLC1A3 MUTATED SLC1A3 WILD-TYPE 
           64.14            35.56 
[1] "1.8 - 85.8 (64.1)"  "0.6 - 185.8 (35.6)"
[1] "hr=" "1.9"
D74V2, binary
                  cls
clus                 0   1
  SLC1A3 MUTATED     8   4
  SLC1A3 WILD-TYPE 149  87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC1A3 MUTATED      8    4
  SLC1A3 WILD-TYPE  149   87
     clus
vv    SLC1A3 MUTATED SLC1A3 WILD-TYPE
  NO               8              149
  YES              4               87
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SLC1A3 MUTATED                                        10
  SLC1A3 WILD-TYPE                                     190
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  SLC1A3 MUTATED                               0
  SLC1A3 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  SLC1A3 MUTATED                                   2
  SLC1A3 WILD-TYPE                                42
D74V3, multiclass
                                         clus
vv                                        SLC1A3 MUTATED SLC1A3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             10              190
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    2               42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SLC1A3 MUTATED     8   1   0   0
  SLC1A3 WILD-TYPE 164   9   7  18
D74V4, multiclass
    clus
vv   SLC1A3 MUTATED SLC1A3 WILD-TYPE
  R0              8              164
  R1              1                9
  R2              0                7
  RX              0               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"

Clustering(75) Variable = UFSP2 MUTATION ANALYSIS
D75V1, survival
                 sevent
clus2               0   1
  UFSP2 MUTATED    11   0
  UFSP2 WILD-TYPE 204  33
  UFSP2 MUTATED UFSP2 WILD-TYPE 
             11             237 
  UFSP2 MUTATED UFSP2 WILD-TYPE 
              0              33 
$`UFSP2 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J1 
      129.80        86.07        48.03        27.12        71.51        77.39 
TCGA-B5-A11E TCGA-BS-A0UF TCGA-D1-A103 TCGA-D1-A168 TCGA-D1-A17Q 
       59.84        85.84        21.99        36.10         1.78 

$`UFSP2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        80.55        88.24        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       37.78        40.11        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       86.37        55.30        86.01        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       27.85        13.45       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        92.88       114.90        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       86.93        72.72        73.25        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W 
       28.67        23.93        22.55         1.74        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       15.72        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  UFSP2 MUTATED UFSP2 WILD-TYPE 
           1.78            0.56 
  UFSP2 MUTATED UFSP2 WILD-TYPE 
         129.80          185.79 
  UFSP2 MUTATED UFSP2 WILD-TYPE 
          59.84           35.38 
[1] "1.8 - 129.8 (59.8)" "0.6 - 185.8 (35.4)"
[1] "hr="     "2.7e+07"
D75V2, binary
                 cls
clus                0   1
  UFSP2 MUTATED     7   4
  UFSP2 WILD-TYPE 150  87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UFSP2 MUTATED      7    4
  UFSP2 WILD-TYPE  150   87
     clus
vv    UFSP2 MUTATED UFSP2 WILD-TYPE
  NO              7             150
  YES             4              87
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  UFSP2 MUTATED                                        11
  UFSP2 WILD-TYPE                                     189
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  UFSP2 MUTATED                               0
  UFSP2 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  UFSP2 MUTATED                                   0
  UFSP2 WILD-TYPE                                44
D75V3, multiclass
                                         clus
vv                                        UFSP2 MUTATED UFSP2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            11             189
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  UFSP2 MUTATED     9   1   0   0
  UFSP2 WILD-TYPE 163   9   7  18
D75V4, multiclass
    clus
vv   UFSP2 MUTATED UFSP2 WILD-TYPE
  R0             9             163
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(76) Variable = WBP4 MUTATION ANALYSIS
D76V1, survival
                sevent
clus2              0   1
  WBP4 MUTATED     8   0
  WBP4 WILD-TYPE 207  33
  WBP4 MUTATED WBP4 WILD-TYPE 
             8            240 
  WBP4 MUTATED WBP4 WILD-TYPE 
             0             33 
$`WBP4 MUTATED`
TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11E TCGA-D1-A103 
       86.07        27.12        40.11        69.27        59.84        21.99 
TCGA-D1-A160 TCGA-D1-A17Q 
        3.68         1.78 

$`WBP4 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       71.51        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        61.08        35.74        37.78        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       85.84        82.39        81.57        86.93        72.72        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A161 
        1.74        39.48        30.08        29.88         1.91        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       10.22         1.51        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  WBP4 MUTATED WBP4 WILD-TYPE 
          1.78           0.56 
  WBP4 MUTATED WBP4 WILD-TYPE 
         86.07         185.79 
  WBP4 MUTATED WBP4 WILD-TYPE 
        33.615         35.900 
[1] "1.8 - 86.1 (33.6)"  "0.6 - 185.8 (35.9)"
[1] "hr="     "2.5e+07"
D76V2, binary
                cls
clus               0   1
  WBP4 MUTATED     7   1
  WBP4 WILD-TYPE 150  90
[1] "tbl2"
                cls
clus             [,1] [,2]
  WBP4 MUTATED      7    1
  WBP4 WILD-TYPE  150   90
     clus
vv    WBP4 MUTATED WBP4 WILD-TYPE
  NO             7            150
  YES            1             90
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  WBP4 MUTATED                                         8
  WBP4 WILD-TYPE                                     192
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  WBP4 MUTATED                               0
  WBP4 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  WBP4 MUTATED                                   0
  WBP4 WILD-TYPE                                44
D76V3, multiclass
                                         clus
vv                                        WBP4 MUTATED WBP4 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            8            192
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  WBP4 MUTATED     6   0   0   0
  WBP4 WILD-TYPE 166  10   7  18
D76V4, multiclass
    clus
vv   WBP4 MUTATED WBP4 WILD-TYPE
  R0            6            166
  R1            0             10
  R2            0              7
  RX            0             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"

Clustering(77) Variable = TRIM59 MUTATION ANALYSIS
D77V1, survival
                  sevent
clus2                0   1
  TRIM59 MUTATED     9   0
  TRIM59 WILD-TYPE 206  33
  TRIM59 MUTATED TRIM59 WILD-TYPE 
               9              239 
  TRIM59 MUTATED TRIM59 WILD-TYPE 
               0               33 
$`TRIM59 MUTATED`
TCGA-A5-A0GP TCGA-AP-A056 TCGA-AP-A0LM TCGA-B5-A11N TCGA-BG-A0W1 TCGA-BS-A0TC 
       46.55        86.07        27.12        61.68        52.83        85.55 
TCGA-BS-A0UF TCGA-D1-A17Q TCGA-DI-A0WH 
       85.84         1.78        16.31 

$`TRIM59 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       52.01        34.29        52.64        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       24.33        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ 
       96.49        30.74        97.41        92.88       114.90        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        86.93        72.72        73.25        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       10.22         1.51        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       13.22        18.25        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  TRIM59 MUTATED TRIM59 WILD-TYPE 
            1.78             0.56 
  TRIM59 MUTATED TRIM59 WILD-TYPE 
           86.07           185.79 
  TRIM59 MUTATED TRIM59 WILD-TYPE 
           52.83            35.74 
[1] "1.8 - 86.1 (52.8)"  "0.6 - 185.8 (35.7)"
[1] "hr="     "2.6e+07"
D77V2, binary
                  cls
clus                 0   1
  TRIM59 MUTATED     7   2
  TRIM59 WILD-TYPE 150  89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM59 MUTATED      7    2
  TRIM59 WILD-TYPE  150   89
     clus
vv    TRIM59 MUTATED TRIM59 WILD-TYPE
  NO               7              150
  YES              2               89
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  TRIM59 MUTATED                                         9
  TRIM59 WILD-TYPE                                     191
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  TRIM59 MUTATED                               0
  TRIM59 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  TRIM59 MUTATED                                   0
  TRIM59 WILD-TYPE                                44
D77V3, multiclass
                                         clus
vv                                        TRIM59 MUTATED TRIM59 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              9              191
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIM59 MUTATED     8   0   0   0
  TRIM59 WILD-TYPE 164  10   7  18
D77V4, multiclass
    clus
vv   TRIM59 MUTATED TRIM59 WILD-TYPE
  R0              8              164
  R1              0               10
  R2              0                7
  RX              0               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"

Clustering(78) Variable = RSBN1L MUTATION ANALYSIS
D78V1, survival
                  sevent
clus2                0   1
  RSBN1L MUTATED    12   0
  RSBN1L WILD-TYPE 203  33
  RSBN1L MUTATED RSBN1L WILD-TYPE 
              12              236 
  RSBN1L MUTATED RSBN1L WILD-TYPE 
               0               33 
$`RSBN1L MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A0J0 TCGA-B5-A11E 
      129.80        86.07        71.51        35.34        40.11        59.84 
TCGA-BG-A0M0 TCGA-BS-A0TC TCGA-BS-A0U9 TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A15X 
       19.33        85.55        92.88        85.84        73.25        29.88 

$`RSBN1L WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        86.37        55.30        86.01        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        13.45       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       20.19        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD 
       35.08        31.00        24.99        46.95        24.33        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       97.41       114.90        82.39        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 
        1.74        21.99        39.48        30.08         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  RSBN1L MUTATED RSBN1L WILD-TYPE 
           19.33             0.56 
  RSBN1L MUTATED RSBN1L WILD-TYPE 
          129.80           185.79 
  RSBN1L MUTATED RSBN1L WILD-TYPE 
          72.380           35.295 
[1] "19.3 - 129.8 (72.4)" "0.6 - 185.8 (35.3)" 
[1] "hr="     "7.5e+07"
D78V2, binary
                  cls
clus                 0   1
  RSBN1L MUTATED     9   3
  RSBN1L WILD-TYPE 148  88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RSBN1L MUTATED      9    3
  RSBN1L WILD-TYPE  148   88
     clus
vv    RSBN1L MUTATED RSBN1L WILD-TYPE
  NO               9              148
  YES              3               88
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  RSBN1L MUTATED                                        11
  RSBN1L WILD-TYPE                                     189
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  RSBN1L MUTATED                               0
  RSBN1L WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  RSBN1L MUTATED                                   1
  RSBN1L WILD-TYPE                                43
D78V3, multiclass
                                         clus
vv                                        RSBN1L MUTATED RSBN1L WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             11              189
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    1               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RSBN1L MUTATED     8   2   0   1
  RSBN1L WILD-TYPE 164   8   7  17
D78V4, multiclass
    clus
vv   RSBN1L MUTATED RSBN1L WILD-TYPE
  R0              8              164
  R1              2                8
  R2              0                7
  RX              1               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"

Clustering(79) Variable = SERHL2 MUTATION ANALYSIS
D79V1, survival
                  sevent
clus2                0   1
  SERHL2 MUTATED     6   0
  SERHL2 WILD-TYPE 209  33
  SERHL2 MUTATED SERHL2 WILD-TYPE 
               6              242 
  SERHL2 MUTATED SERHL2 WILD-TYPE 
               0               33 
$`SERHL2 MUTATED`
TCGA-A5-A0GB TCGA-A5-A0GQ TCGA-AP-A056 TCGA-AP-A059 TCGA-B5-A11F TCGA-D1-A17D 
       32.78        73.87        86.07        48.03       185.79        30.44 

$`SERHL2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       37.02        83.51        17.85       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       65.75        60.53        46.55        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 
       28.77        42.35        15.95        20.25       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       23.31        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.74        37.78        40.11        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       71.24        56.91        86.37        55.30        86.01        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11G 
       64.21        63.55        27.85        13.45        59.84       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       85.84        82.39        81.57        86.93        72.72        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       18.67         3.65        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        1.58         7.00         0.99         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  SERHL2 MUTATED SERHL2 WILD-TYPE 
           30.44             0.56 
  SERHL2 MUTATED SERHL2 WILD-TYPE 
          185.79           129.80 
  SERHL2 MUTATED SERHL2 WILD-TYPE 
           60.95            35.82 
[1] "30.4 - 185.8 (61.0)" "0.6 - 129.8 (35.8)" 
[1] "hr="     "2.6e+07"
D79V2, binary
                  cls
clus                 0   1
  SERHL2 MUTATED     2   4
  SERHL2 WILD-TYPE 155  87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SERHL2 MUTATED      2    4
  SERHL2 WILD-TYPE  155   87
     clus
vv    SERHL2 MUTATED SERHL2 WILD-TYPE
  NO               2              155
  YES              4               87
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SERHL2 MUTATED                                         6
  SERHL2 WILD-TYPE                                     194
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  SERHL2 MUTATED                               0
  SERHL2 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  SERHL2 MUTATED                                   0
  SERHL2 WILD-TYPE                                44
D79V3, multiclass
                                         clus
vv                                        SERHL2 MUTATED SERHL2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              6              194
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SERHL2 MUTATED     5   0   0   0
  SERHL2 WILD-TYPE 167  10   7  18
D79V4, multiclass
    clus
vv   SERHL2 MUTATED SERHL2 WILD-TYPE
  R0              5              167
  R1              0               10
  R2              0                7
  RX              0               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"

Clustering(80) Variable = OR52I2 MUTATION ANALYSIS
D80V1, survival
                  sevent
clus2                0   1
  OR52I2 MUTATED     7   1
  OR52I2 WILD-TYPE 208  32
  OR52I2 MUTATED OR52I2 WILD-TYPE 
               8              240 
  OR52I2 MUTATED OR52I2 WILD-TYPE 
               1               32 
$`OR52I2 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A0L8 TCGA-AX-A0J0 TCGA-BK-A0CA TCGA-BS-A0UV 
      129.80        86.07        48.79        40.11        34.98        73.25 
TCGA-D1-A167 TCGA-D1-A17Q 
       15.72         1.78 

$`OR52I2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       23.87        20.91       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       61.08        35.74        37.78        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       71.24        56.91        86.37        55.30        86.01        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        44.78        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       35.90        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       85.84        82.39        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       29.33        32.58         0.66        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       10.22         1.51        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  OR52I2 MUTATED OR52I2 WILD-TYPE 
            1.78             0.56 
  OR52I2 MUTATED OR52I2 WILD-TYPE 
          129.80           185.79 
  OR52I2 MUTATED OR52I2 WILD-TYPE 
           44.45            35.82 
[1] "1.8 - 129.8 (44.5)" "0.6 - 185.8 (35.8)"
[1] "hr=" "1.4"
D80V2, binary
                  cls
clus                 0   1
  OR52I2 MUTATED     5   3
  OR52I2 WILD-TYPE 152  88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52I2 MUTATED      5    3
  OR52I2 WILD-TYPE  152   88
     clus
vv    OR52I2 MUTATED OR52I2 WILD-TYPE
  NO               5              152
  YES              3               88
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  OR52I2 MUTATED                                         6
  OR52I2 WILD-TYPE                                     194
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  OR52I2 MUTATED                               1
  OR52I2 WILD-TYPE                             3
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  OR52I2 MUTATED                                   1
  OR52I2 WILD-TYPE                                43
D80V3, multiclass
                                         clus
vv                                        OR52I2 MUTATED OR52I2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              6              194
  MIXED SEROUS AND ENDOMETRIOID                        1                3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    1               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR52I2 MUTATED     7   0   0   1
  OR52I2 WILD-TYPE 165  10   7  17
D80V4, multiclass
    clus
vv   OR52I2 MUTATED OR52I2 WILD-TYPE
  R0              7              165
  R1              0               10
  R2              0                7
  RX              1               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"

Clustering(81) Variable = SGK1 MUTATION ANALYSIS
D81V1, survival
                sevent
clus2              0   1
  SGK1 MUTATED    12   1
  SGK1 WILD-TYPE 203  32
  SGK1 MUTATED SGK1 WILD-TYPE 
            13            235 
  SGK1 MUTATED SGK1 WILD-TYPE 
             1             32 
$`SGK1 MUTATED`
TCGA-D1-A102 TCGA-A5-A0GV TCGA-A5-A0R8 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LI 
        4.44        54.02        19.59        86.07        48.03        97.71 
TCGA-AP-A0LL TCGA-AX-A05S TCGA-AX-A060 TCGA-B5-A0JY TCGA-B5-A11E TCGA-BG-A0M7 
       83.97        13.58        35.34        69.27        59.84        63.68 
TCGA-D1-A103 
       21.99 

$`SGK1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       51.55        12.56        19.79        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GW 
       65.75        60.53        46.55        73.87        28.27        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       68.65        37.91        17.59        24.62        29.06        28.77 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
       42.35        15.95        20.25       129.80        21.99        23.31 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       63.91        45.53        36.89        23.87        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      125.42       117.99       110.37        66.25        36.36        46.72 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       25.08        46.78        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       71.51        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        92.88       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 
       82.39        81.57        86.93        72.72        73.25        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  SGK1 MUTATED SGK1 WILD-TYPE 
          4.44           0.56 
  SGK1 MUTATED SGK1 WILD-TYPE 
         97.71         185.79 
  SGK1 MUTATED SGK1 WILD-TYPE 
         54.02          35.74 
[1] "4.4 - 97.7 (54.0)"  "0.6 - 185.8 (35.7)"
[1] "hr=" "1.9"
D81V2, binary
                cls
clus               0   1
  SGK1 MUTATED     8   5
  SGK1 WILD-TYPE 149  86
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK1 MUTATED      8    5
  SGK1 WILD-TYPE  149   86
     clus
vv    SGK1 MUTATED SGK1 WILD-TYPE
  NO             8            149
  YES            5             86
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SGK1 MUTATED                                        12
  SGK1 WILD-TYPE                                     188
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  SGK1 MUTATED                               0
  SGK1 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  SGK1 MUTATED                                   1
  SGK1 WILD-TYPE                                43
D81V3, multiclass
                                         clus
vv                                        SGK1 MUTATED SGK1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           12            188
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  1             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SGK1 MUTATED     7   1   2   1
  SGK1 WILD-TYPE 165   9   5  17
D81V4, multiclass
    clus
vv   SGK1 MUTATED SGK1 WILD-TYPE
  R0            7            165
  R1            1              9
  R2            2              5
  RX            1             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"

Clustering(82) Variable = LNX2 MUTATION ANALYSIS
D82V1, survival
                sevent
clus2              0   1
  LNX2 MUTATED    14   0
  LNX2 WILD-TYPE 201  33
  LNX2 MUTATED LNX2 WILD-TYPE 
            14            234 
  LNX2 MUTATED LNX2 WILD-TYPE 
             0             33 
$`LNX2 MUTATED`
TCGA-D1-A0ZO TCGA-AP-A051 TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY 
       19.79       129.80        71.51        40.11        77.39        69.27 
TCGA-B5-A11E TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A101 TCGA-D1-A103 
       59.84        85.84        82.39        73.25         1.74        21.99 
TCGA-D1-A160 TCGA-D1-A167 
        3.68        15.72 

$`LNX2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       51.55        12.56         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       29.06        28.77        42.35        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       61.08        35.74        37.78        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        55.30        86.01        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       27.85        13.45       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0UM 
       30.74        97.41        92.88       114.90        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A161 
       22.55        39.48        30.08        29.88         1.91        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  LNX2 MUTATED LNX2 WILD-TYPE 
          1.74           0.56 
  LNX2 MUTATED LNX2 WILD-TYPE 
        129.80         185.79 
  LNX2 MUTATED LNX2 WILD-TYPE 
        64.555         35.560 
[1] "1.7 - 129.8 (64.6)" "0.6 - 185.8 (35.6)"
[1] "hr="     "2.7e+07"
D82V2, binary
                cls
clus               0   1
  LNX2 MUTATED    12   2
  LNX2 WILD-TYPE 145  89
[1] "tbl2"
                cls
clus             [,1] [,2]
  LNX2 MUTATED     12    2
  LNX2 WILD-TYPE  145   89
     clus
vv    LNX2 MUTATED LNX2 WILD-TYPE
  NO            12            145
  YES            2             89
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  LNX2 MUTATED                                        14
  LNX2 WILD-TYPE                                     186
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  LNX2 MUTATED                               0
  LNX2 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  LNX2 MUTATED                                   0
  LNX2 WILD-TYPE                                44
D82V3, multiclass
                                         clus
vv                                        LNX2 MUTATED LNX2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           14            186
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LNX2 MUTATED    10   1   0   1
  LNX2 WILD-TYPE 162   9   7  17
D82V4, multiclass
    clus
vv   LNX2 MUTATED LNX2 WILD-TYPE
  R0           10            162
  R1            1              9
  R2            0              7
  RX            1             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"

Clustering(83) Variable = ALPK2 MUTATION ANALYSIS
D83V1, survival
                 sevent
clus2               0   1
  ALPK2 MUTATED    19   0
  ALPK2 WILD-TYPE 196  33
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             19             229 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
              0              33 
$`ALPK2 MUTATED`
TCGA-A5-A0GI TCGA-A5-A0GB TCGA-A5-A0GH TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LM 
       88.18        32.78        74.10       129.80        48.03        27.12 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11G TCGA-B5-A11J 
       71.51        35.34        40.11        69.27       113.36        54.44 
TCGA-B5-A11R TCGA-BS-A0U8 TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-D1-A103 TCGA-D1-A15X 
       77.23        97.41        85.84        82.39        21.99        29.88 
TCGA-D1-A17Q 
        1.78 

$`ALPK2 WILD-TYPE`
TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP 
       60.53       110.63        57.80        93.99        67.66        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GJ TCGA-A5-A0GN 
       83.51        17.85       112.54       105.37        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        73.87        28.27        54.02        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       37.91        17.59        19.59        24.62        29.06        28.77 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
       42.35        15.95        20.25        21.99        23.31        86.07 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       63.91        45.53        36.89        23.87        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       49.22        25.08        46.78        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       80.55        88.24        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        61.08        35.74        37.78        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       88.34        75.72        44.78        61.68        85.78        32.09 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       30.74        92.88       114.90        81.57        86.93        72.72 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       73.25        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 
       22.55         1.74        39.48        30.08         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       26.37        10.22         1.51        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  ALPK2 MUTATED ALPK2 WILD-TYPE 
           1.78            0.56 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
         129.80          185.79 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
          69.27           35.21 
[1] "1.8 - 129.8 (69.3)" "0.6 - 185.8 (35.2)"
[1] "hr="     "8.2e+07"
D83V2, binary
                 cls
clus                0   1
  ALPK2 MUTATED    10   9
  ALPK2 WILD-TYPE 147  82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     10    9
  ALPK2 WILD-TYPE  147   82
     clus
vv    ALPK2 MUTATED ALPK2 WILD-TYPE
  NO             10             147
  YES             9              82
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ALPK2 MUTATED                                        18
  ALPK2 WILD-TYPE                                     182
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  ALPK2 MUTATED                               0
  ALPK2 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  ALPK2 MUTATED                                   1
  ALPK2 WILD-TYPE                                43
D83V3, multiclass
                                         clus
vv                                        ALPK2 MUTATED ALPK2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            18             182
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ALPK2 MUTATED    12   2   0   0
  ALPK2 WILD-TYPE 160   8   7  18
D83V4, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  R0            12             160
  R1             2               8
  R2             0               7
  RX             0              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"

Clustering(84) Variable = REV3L MUTATION ANALYSIS
D84V1, survival
                 sevent
clus2               0   1
  REV3L MUTATED    20   0
  REV3L WILD-TYPE 195  33
  REV3L MUTATED REV3L WILD-TYPE 
             20             228 
  REV3L MUTATED REV3L WILD-TYPE 
              0              33 
$`REV3L MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
      129.80        86.07        48.03        27.12        71.51        40.11 
TCGA-B5-A0JY TCGA-B5-A11H TCGA-B5-A11N TCGA-B5-A11U TCGA-BG-A0VX TCGA-BS-A0TC 
       69.27        88.34        61.68        16.73        34.29        85.55 
TCGA-BS-A0UF TCGA-BS-A0UL TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A160 TCGA-D1-A16X 
       85.84        81.57        73.25        21.99         3.68         3.65 
TCGA-D1-A176 TCGA-D1-A17Q 
       30.15         1.78 

$`REV3L WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        80.55        88.24        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       37.78        77.39        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J 
       13.45        59.84       185.79       113.36        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V 
       44.78        85.78        32.09        77.23        73.28        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       52.01        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       24.33        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ 
       96.49        30.74        97.41        92.88       114.90        82.39 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93        22.55         1.74        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        1.91        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       18.67        17.49        19.53        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       10.22         1.51        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  REV3L MUTATED REV3L WILD-TYPE 
           1.78            0.56 
  REV3L MUTATED REV3L WILD-TYPE 
         129.80          185.79 
  REV3L MUTATED REV3L WILD-TYPE 
         54.855          35.560 
[1] "1.8 - 129.8 (54.9)" "0.6 - 185.8 (35.6)"
[1] "hr="     "7.8e+07"
D84V2, binary
                 cls
clus                0   1
  REV3L MUTATED    15   5
  REV3L WILD-TYPE 142  86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REV3L MUTATED     15    5
  REV3L WILD-TYPE  142   86
     clus
vv    REV3L MUTATED REV3L WILD-TYPE
  NO             15             142
  YES             5              86
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  REV3L MUTATED                                        20
  REV3L WILD-TYPE                                     180
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  REV3L MUTATED                               0
  REV3L WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  REV3L MUTATED                                   0
  REV3L WILD-TYPE                                44
D84V3, multiclass
                                         clus
vv                                        REV3L MUTATED REV3L WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            20             180
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  REV3L MUTATED    14   1   0   1
  REV3L WILD-TYPE 158   9   7  17
D84V4, multiclass
    clus
vv   REV3L MUTATED REV3L WILD-TYPE
  R0            14             158
  R1             1               9
  R2             0               7
  RX             1              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"

Clustering(85) Variable = CAB39L MUTATION ANALYSIS
D85V1, survival
                  sevent
clus2                0   1
  CAB39L MUTATED     8   0
  CAB39L WILD-TYPE 207  33
  CAB39L MUTATED CAB39L WILD-TYPE 
               8              240 
  CAB39L MUTATED CAB39L WILD-TYPE 
               0               33 
$`CAB39L MUTATED`
TCGA-A5-A0GP TCGA-AX-A05T TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-BG-A0M3 TCGA-BS-A0UF 
       46.55        33.21        40.11        69.27        35.21        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UV 
       82.39        73.25 

$`CAB39L WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       25.08        46.78        13.58        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       71.51        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        61.08        35.74        37.78        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        44.78        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 
       11.87        18.61        20.19        19.33        20.94        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        86.93        72.72        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  CAB39L MUTATED CAB39L WILD-TYPE 
           33.21             0.56 
  CAB39L MUTATED CAB39L WILD-TYPE 
           85.84           185.79 
  CAB39L MUTATED CAB39L WILD-TYPE 
           57.91            35.56 
[1] "33.2 - 85.8 (57.9)" "0.6 - 185.8 (35.6)"
[1] "hr="     "2.6e+07"
D85V2, binary
                  cls
clus                 0   1
  CAB39L MUTATED     7   1
  CAB39L WILD-TYPE 150  90
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      7    1
  CAB39L WILD-TYPE  150   90
     clus
vv    CAB39L MUTATED CAB39L WILD-TYPE
  NO               7              150
  YES              1               90
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CAB39L MUTATED                                         8
  CAB39L WILD-TYPE                                     192
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  CAB39L MUTATED                               0
  CAB39L WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  CAB39L MUTATED                                   0
  CAB39L WILD-TYPE                                44
D85V3, multiclass
                                         clus
vv                                        CAB39L MUTATED CAB39L WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              8              192
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CAB39L MUTATED     7   0   0   0
  CAB39L WILD-TYPE 165  10   7  18
D85V4, multiclass
    clus
vv   CAB39L MUTATED CAB39L WILD-TYPE
  R0              7              165
  R1              0               10
  R2              0                7
  RX              0               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"

Clustering(86) Variable = ERBB3 MUTATION ANALYSIS
D86V1, survival
                 sevent
clus2               0   1
  ERBB3 MUTATED    17   0
  ERBB3 WILD-TYPE 198  33
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             17             231 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
              0              33 
$`ERBB3 MUTATED`
TCGA-A5-A0VP TCGA-AP-A051 TCGA-AX-A060 TCGA-AX-A0J0 TCGA-B5-A11R TCGA-B5-A11V 
       42.35       129.80        35.34        40.11        77.23        19.56 
TCGA-BG-A0YU TCGA-BG-A18B TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A103 
       14.83        15.45        85.84        82.39        73.25        21.99 
TCGA-D1-A16J TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A17H TCGA-D1-A1NU 
       29.92        17.49        19.53        28.01        13.22 

$`ERBB3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       24.62        29.06        28.77        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       71.51        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       61.08        35.74        37.78        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       71.24        56.91        86.37        55.30        86.01        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        44.78        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11X 
       85.78        32.09        73.28        16.73        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.64        52.83        56.58        13.78        14.73        14.01 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       31.00        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       97.41        92.88       114.90        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NX TCGA-DI-A0WH 
       11.15        24.30         2.33        22.92        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  ERBB3 MUTATED ERBB3 WILD-TYPE 
          13.22            0.56 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
         129.80          185.79 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
          29.92           36.10 
[1] "13.2 - 129.8 (29.9)" "0.6 - 185.8 (36.1)" 
[1] "hr="     "2.7e+07"
D86V2, binary
                 cls
clus                0   1
  ERBB3 MUTATED    10   7
  ERBB3 WILD-TYPE 147  84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     10    7
  ERBB3 WILD-TYPE  147   84
     clus
vv    ERBB3 MUTATED ERBB3 WILD-TYPE
  NO             10             147
  YES             7              84
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ERBB3 MUTATED                                        16
  ERBB3 WILD-TYPE                                     184
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  ERBB3 MUTATED                               0
  ERBB3 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  ERBB3 MUTATED                                   1
  ERBB3 WILD-TYPE                                43
D86V3, multiclass
                                         clus
vv                                        ERBB3 MUTATED ERBB3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            16             184
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ERBB3 MUTATED    11   1   0   3
  ERBB3 WILD-TYPE 161   9   7  15
D86V4, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  R0            11             161
  R1             1               9
  R2             0               7
  RX             3              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"

Clustering(87) Variable = INPP4B MUTATION ANALYSIS
D87V1, survival
                  sevent
clus2                0   1
  INPP4B MUTATED    11   1
  INPP4B WILD-TYPE 204  32
  INPP4B MUTATED INPP4B WILD-TYPE 
              12              236 
  INPP4B MUTATED INPP4B WILD-TYPE 
               1               32 
$`INPP4B MUTATED`
TCGA-AP-A054 TCGA-AP-A056 TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JS 
       23.31        86.07        71.51        40.11        77.39        86.37 
TCGA-B5-A0JY TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UM TCGA-BS-A0UV TCGA-D1-A17Q 
       69.27        85.55        85.84        86.93        73.25         1.78 

$`INPP4B WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
      129.80        21.99        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       61.08        35.74        37.78        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       56.91        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD 
       35.08        31.00        24.99        46.95        24.33        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        92.88       114.90        82.39        81.57        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       18.67         3.65        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  INPP4B MUTATED INPP4B WILD-TYPE 
            1.78             0.56 
  INPP4B MUTATED INPP4B WILD-TYPE 
           86.93           185.79 
  INPP4B MUTATED INPP4B WILD-TYPE 
          75.320           35.275 
[1] "1.8 - 86.9 (75.3)"  "0.6 - 185.8 (35.3)"
[1] "hr=" "2.3"
D87V2, binary
                  cls
clus                 0   1
  INPP4B MUTATED    12   0
  INPP4B WILD-TYPE 145  91
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPP4B MUTATED     12    0
  INPP4B WILD-TYPE  145   91
     clus
vv    INPP4B MUTATED INPP4B WILD-TYPE
  NO              12              145
  YES              0               91
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  INPP4B MUTATED                                        12
  INPP4B WILD-TYPE                                     188
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  INPP4B MUTATED                               0
  INPP4B WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  INPP4B MUTATED                                   0
  INPP4B WILD-TYPE                                44
D87V3, multiclass
                                         clus
vv                                        INPP4B MUTATED INPP4B WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             12              188
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  INPP4B MUTATED     8   2   0   0
  INPP4B WILD-TYPE 164   8   7  18
D87V4, multiclass
    clus
vv   INPP4B MUTATED INPP4B WILD-TYPE
  R0              8              164
  R1              2                8
  R2              0                7
  RX              0               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"

Clustering(88) Variable = C1ORF100 MUTATION ANALYSIS
D88V1, survival
                    sevent
clus2                  0   1
  C1ORF100 MUTATED     9   0
  C1ORF100 WILD-TYPE 206  33
  C1ORF100 MUTATED C1ORF100 WILD-TYPE 
                 9                239 
  C1ORF100 MUTATED C1ORF100 WILD-TYPE 
                 0                 33 
$`C1ORF100 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LE TCGA-AX-A05Z TCGA-AX-A0J1 TCGA-B5-A0JY 
      129.80        48.03       110.37        71.51        77.39        69.27 
TCGA-B5-A11E TCGA-B5-A11R TCGA-BS-A0UV 
       59.84        77.23        73.25 

$`C1ORF100 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        86.07        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LG 
       23.87        20.91        48.79       125.42       117.99        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        40.11        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        55.30        86.01        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       27.85        13.45       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11S 
       54.44        44.78        61.68        85.78        32.09        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       31.00        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        92.88       114.90        85.84        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69        18.67         3.65        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.78        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  C1ORF100 MUTATED C1ORF100 WILD-TYPE 
             48.03               0.56 
  C1ORF100 MUTATED C1ORF100 WILD-TYPE 
            129.80             185.79 
  C1ORF100 MUTATED C1ORF100 WILD-TYPE 
             73.25              35.21 
[1] "48.0 - 129.8 (73.2)" "0.6 - 185.8 (35.2)" 
[1] "hr="     "2.7e+07"
D88V2, binary
                    cls
clus                   0   1
  C1ORF100 MUTATED     6   3
  C1ORF100 WILD-TYPE 151  88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF100 MUTATED      6    3
  C1ORF100 WILD-TYPE  151   88
     clus
vv    C1ORF100 MUTATED C1ORF100 WILD-TYPE
  NO                 6                151
  YES                3                 88
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  C1ORF100 MUTATED                                         9
  C1ORF100 WILD-TYPE                                     191
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  C1ORF100 MUTATED                               0
  C1ORF100 WILD-TYPE                             4
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  C1ORF100 MUTATED                                   0
  C1ORF100 WILD-TYPE                                44
D88V3, multiclass
                                         clus
vv                                        C1ORF100 MUTATED C1ORF100 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                9                191
  MIXED SEROUS AND ENDOMETRIOID                          0                  4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      0                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C1ORF100 MUTATED     5   1   0   0
  C1ORF100 WILD-TYPE 167   9   7  18
D88V4, multiclass
    clus
vv   C1ORF100 MUTATED C1ORF100 WILD-TYPE
  R0                5                167
  R1                1                  9
  R2                0                  7
  RX                0                 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"

Clustering(89) Variable = IL20 MUTATION ANALYSIS
D89V1, survival
                sevent
clus2              0   1
  IL20 MUTATED     7   0
  IL20 WILD-TYPE 208  33
  IL20 MUTATED IL20 WILD-TYPE 
             7            241 
  IL20 MUTATED IL20 WILD-TYPE 
             0             33 
$`IL20 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A060 TCGA-BS-A0UV 
      129.80        86.07        27.12        71.51        35.34        73.25 
TCGA-D1-A17N 
        1.51 

$`IL20 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A062 
       13.58        33.21        29.69        80.55        88.24        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       37.78        40.11        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        86.37        55.30        86.01        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       85.84        82.39        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       26.37        10.22         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  IL20 MUTATED IL20 WILD-TYPE 
          1.51           0.56 
  IL20 MUTATED IL20 WILD-TYPE 
        129.80         185.79 
  IL20 MUTATED IL20 WILD-TYPE 
         71.51          35.90 
[1] "1.5 - 129.8 (71.5)" "0.6 - 185.8 (35.9)"
[1] "hr="     "2.7e+07"
D89V2, binary
                cls
clus               0   1
  IL20 MUTATED     4   3
  IL20 WILD-TYPE 153  88
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL20 MUTATED      4    3
  IL20 WILD-TYPE  153   88
     clus
vv    IL20 MUTATED IL20 WILD-TYPE
  NO             4            153
  YES            3             88
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  IL20 MUTATED                                         7
  IL20 WILD-TYPE                                     193
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  IL20 MUTATED                               0
  IL20 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  IL20 MUTATED                                   0
  IL20 WILD-TYPE                                44
D89V3, multiclass
                                         clus
vv                                        IL20 MUTATED IL20 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            7            193
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IL20 MUTATED     5   2   0   0
  IL20 WILD-TYPE 167   8   7  18
D89V4, multiclass
    clus
vv   IL20 MUTATED IL20 WILD-TYPE
  R0            5            167
  R1            2              8
  R2            0              7
  RX            0             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"

Clustering(90) Variable = SLC44A3 MUTATION ANALYSIS
D90V1, survival
                   sevent
clus2                 0   1
  SLC44A3 MUTATED     6   0
  SLC44A3 WILD-TYPE 209  33
  SLC44A3 MUTATED SLC44A3 WILD-TYPE 
                6               242 
  SLC44A3 MUTATED SLC44A3 WILD-TYPE 
                0                33 
$`SLC44A3 MUTATED`
TCGA-AP-A051 TCGA-AP-A0LM TCGA-B5-A11E TCGA-BG-A0YU TCGA-BS-A0UF TCGA-D1-A16X 
      129.80        27.12        59.84        14.83        85.84         3.65 

$`SLC44A3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       71.51        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        61.08        35.74        37.78        40.11        77.39 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       86.01        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        82.39        81.57        86.93        72.72        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       18.67        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  SLC44A3 MUTATED SLC44A3 WILD-TYPE 
             3.65              0.56 
  SLC44A3 MUTATED SLC44A3 WILD-TYPE 
           129.80            185.79 
  SLC44A3 MUTATED SLC44A3 WILD-TYPE 
            43.48             35.90 
[1] "3.6 - 129.8 (43.5)" "0.6 - 185.8 (35.9)"
[1] "hr="     "2.6e+07"
D90V2, binary
                   cls
clus                  0   1
  SLC44A3 MUTATED     4   2
  SLC44A3 WILD-TYPE 153  89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A3 MUTATED      4    2
  SLC44A3 WILD-TYPE  153   89
     clus
vv    SLC44A3 MUTATED SLC44A3 WILD-TYPE
  NO                4               153
  YES               2                89
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SLC44A3 MUTATED                                         6
  SLC44A3 WILD-TYPE                                     194
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  SLC44A3 MUTATED                               0
  SLC44A3 WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  SLC44A3 MUTATED                                   0
  SLC44A3 WILD-TYPE                                44
D90V3, multiclass
                                         clus
vv                                        SLC44A3 MUTATED SLC44A3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               6               194
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     0                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC44A3 MUTATED     4   0   0   1
  SLC44A3 WILD-TYPE 168  10   7  17
D90V4, multiclass
    clus
vv   SLC44A3 MUTATED SLC44A3 WILD-TYPE
  R0               4               168
  R1               0                10
  R2               0                 7
  RX               1                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"

Clustering(91) Variable = TAP1 MUTATION ANALYSIS
D91V1, survival
                sevent
clus2              0   1
  TAP1 MUTATED     7   1
  TAP1 WILD-TYPE 208  32
  TAP1 MUTATED TAP1 WILD-TYPE 
             8            240 
  TAP1 MUTATED TAP1 WILD-TYPE 
             1             32 
$`TAP1 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0U7 
      129.80        86.07        48.03        69.27        59.84        30.74 
TCGA-BS-A0UV TCGA-D1-A103 
       73.25        21.99 

$`TAP1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        97.41        92.88       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 
       82.39        81.57        86.93        72.72        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V 
        4.87        28.67        23.93        22.55         1.74        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  TAP1 MUTATED TAP1 WILD-TYPE 
         21.99           0.56 
  TAP1 MUTATED TAP1 WILD-TYPE 
        129.80         185.79 
  TAP1 MUTATED TAP1 WILD-TYPE 
        64.555         35.560 
[1] "22.0 - 129.8 (64.6)" "0.6 - 185.8 (35.6)" 
[1] "hr=" "1.7"
D91V2, binary
                cls
clus               0   1
  TAP1 MUTATED     6   2
  TAP1 WILD-TYPE 151  89
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAP1 MUTATED      6    2
  TAP1 WILD-TYPE  151   89
     clus
vv    TAP1 MUTATED TAP1 WILD-TYPE
  NO             6            151
  YES            2             89
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  TAP1 MUTATED                                         8
  TAP1 WILD-TYPE                                     192
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  TAP1 MUTATED                               0
  TAP1 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  TAP1 MUTATED                                   0
  TAP1 WILD-TYPE                                44
D91V3, multiclass
                                         clus
vv                                        TAP1 MUTATED TAP1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            8            192
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TAP1 MUTATED     6   0   0   0
  TAP1 WILD-TYPE 166  10   7  18
D91V4, multiclass
    clus
vv   TAP1 MUTATED TAP1 WILD-TYPE
  R0            6            166
  R1            0             10
  R2            0              7
  RX            0             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"

Clustering(92) Variable = RHBDD3 MUTATION ANALYSIS
D92V1, survival
                  sevent
clus2                0   1
  RHBDD3 MUTATED     4   0
  RHBDD3 WILD-TYPE 211  33
  RHBDD3 MUTATED RHBDD3 WILD-TYPE 
               4              244 
  RHBDD3 MUTATED RHBDD3 WILD-TYPE 
               0               33 
$`RHBDD3 MUTATED`
TCGA-AP-A051 TCGA-D1-A103 TCGA-D1-A167 TCGA-D1-A17H 
      129.80        21.99        15.72        28.01 

$`RHBDD3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        61.08        35.74        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       77.39        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       55.30        86.01        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        92.88       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        86.93        72.72        73.25        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V 
        4.87        28.67        23.93        22.55         1.74        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69        18.67         3.65        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  RHBDD3 MUTATED RHBDD3 WILD-TYPE 
           15.72             0.56 
  RHBDD3 MUTATED RHBDD3 WILD-TYPE 
          129.80           185.79 
  RHBDD3 MUTATED RHBDD3 WILD-TYPE 
              25               36 
[1] "15.7 - 129.8 (25.0)" "0.6 - 185.8 (36.0)" 
[1] "hr="     "9900000"
D92V2, binary
                  cls
clus                 0   1
  RHBDD3 MUTATED     2   2
  RHBDD3 WILD-TYPE 155  89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RHBDD3 MUTATED      2    2
  RHBDD3 WILD-TYPE  155   89
     clus
vv    RHBDD3 MUTATED RHBDD3 WILD-TYPE
  NO               2              155
  YES              2               89
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  RHBDD3 MUTATED                                         4
  RHBDD3 WILD-TYPE                                     196
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  RHBDD3 MUTATED                               0
  RHBDD3 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  RHBDD3 MUTATED                                   0
  RHBDD3 WILD-TYPE                                44
D92V3, multiclass
                                         clus
vv                                        RHBDD3 MUTATED RHBDD3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              4              196
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RHBDD3 MUTATED     4   0   0   0
  RHBDD3 WILD-TYPE 168  10   7  18
D92V4, multiclass
    clus
vv   RHBDD3 MUTATED RHBDD3 WILD-TYPE
  R0              4              168
  R1              0               10
  R2              0                7
  RX              0               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"

Clustering(93) Variable = BRDT MUTATION ANALYSIS
D93V1, survival
                sevent
clus2              0   1
  BRDT MUTATED    14   0
  BRDT WILD-TYPE 201  33
  BRDT MUTATED BRDT WILD-TYPE 
            14            234 
  BRDT MUTATED BRDT WILD-TYPE 
             0             33 
$`BRDT MUTATED`
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY 
       86.07        48.03        27.12        71.51        40.11        69.27 
TCGA-B5-A11E TCGA-B5-A11N TCGA-BK-A0C9 TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UV 
       59.84        61.68        35.90        85.55        85.84        73.25 
TCGA-D1-A103 TCGA-D1-A17N 
       21.99         1.51 

$`BRDT WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
      129.80        21.99        23.31        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        55.30        86.01        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       27.85        13.45       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       54.44        44.78        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       15.45        23.70        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       24.99        46.95        24.33        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
      114.90        82.39        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       10.22         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  BRDT MUTATED BRDT WILD-TYPE 
          1.51           0.56 
  BRDT MUTATED BRDT WILD-TYPE 
         86.07         185.79 
  BRDT MUTATED BRDT WILD-TYPE 
        60.760         35.275 
[1] "1.5 - 86.1 (60.8)"  "0.6 - 185.8 (35.3)"
[1] "hr="     "2.7e+07"
D93V2, binary
                cls
clus               0   1
  BRDT MUTATED    12   2
  BRDT WILD-TYPE 145  89
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRDT MUTATED     12    2
  BRDT WILD-TYPE  145   89
     clus
vv    BRDT MUTATED BRDT WILD-TYPE
  NO            12            145
  YES            2             89
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  BRDT MUTATED                                        14
  BRDT WILD-TYPE                                     186
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  BRDT MUTATED                               0
  BRDT WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  BRDT MUTATED                                   0
  BRDT WILD-TYPE                                44
D93V3, multiclass
                                         clus
vv                                        BRDT MUTATED BRDT WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           14            186
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BRDT MUTATED    10   1   0   0
  BRDT WILD-TYPE 162   9   7  18
D93V4, multiclass
    clus
vv   BRDT MUTATED BRDT WILD-TYPE
  R0           10            162
  R1            1              9
  R2            0              7
  RX            0             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"

Clustering(94) Variable = RB1 MUTATION ANALYSIS
D94V1, survival
               sevent
clus2             0   1
  RB1 MUTATED    19   1
  RB1 WILD-TYPE 196  32
  RB1 MUTATED RB1 WILD-TYPE 
           20           228 
  RB1 MUTATED RB1 WILD-TYPE 
            1            32 
$`RB1 MUTATED`
TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05P TCGA-AP-A0LM 
       42.35       129.80        23.31        86.07        20.91        27.12 
TCGA-AX-A05Y TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-BG-A0VZ 
       88.24        40.11        77.39        69.27        59.84        52.64 
TCGA-BS-A0TC TCGA-BS-A0U9 TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A16N 
       85.55        92.88        85.84        73.25        21.99        31.07 
TCGA-D1-A16Y TCGA-D1-A17Q 
       17.49         1.78 

$`RB1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       24.62        29.06        28.77        15.95        20.25        21.99 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A0L8 
       48.03        63.91        45.53        36.89        23.87        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       49.22        25.08        46.78        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       80.55        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       27.39        60.66        61.08        35.74        37.78        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       34.29        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       30.74        97.41       114.90        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       22.55         1.74        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       11.51        29.92        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
        3.65        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       10.22         1.51        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  RB1 MUTATED RB1 WILD-TYPE 
         1.78          0.56 
  RB1 MUTATED RB1 WILD-TYPE 
       129.80        185.79 
  RB1 MUTATED RB1 WILD-TYPE 
        56.24         35.36 
[1] "1.8 - 129.8 (56.2)" "0.6 - 185.8 (35.4)"
[1] "hr=" "3.6"
D94V2, binary
               cls
clus              0   1
  RB1 MUTATED    16   4
  RB1 WILD-TYPE 141  87
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     16    4
  RB1 WILD-TYPE  141   87
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO           16           141
  YES           4            87
[1] 2 2
[1] FALSE
               vv
clus            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  RB1 MUTATED                                        20
  RB1 WILD-TYPE                                     180
               vv
clus            MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  RB1 MUTATED                               0                                 0
  RB1 WILD-TYPE                             4                                44
D94V3, multiclass
                                         clus
vv                                        RB1 MUTATED RB1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA          20           180
  MIXED SEROUS AND ENDOMETRIOID                     0             4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                 0            44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  RB1 MUTATED    15   1   0   2
  RB1 WILD-TYPE 157   9   7  16
D94V4, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  R0          15           157
  R1           1             9
  R2           0             7
  RX           2            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"

Clustering(95) Variable = MFAP5 MUTATION ANALYSIS
D95V1, survival
                 sevent
clus2               0   1
  MFAP5 MUTATED     9   0
  MFAP5 WILD-TYPE 206  33
  MFAP5 MUTATED MFAP5 WILD-TYPE 
              9             239 
  MFAP5 MUTATED MFAP5 WILD-TYPE 
              0              33 
$`MFAP5 MUTATED`
TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11Y 
       48.03        27.12        71.51        40.11        69.27        18.41 
TCGA-BG-A0M4 TCGA-BS-A0UF TCGA-D1-A15X 
       71.24        85.84        29.88 

$`MFAP5 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       61.08        35.74        37.78        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       71.24        56.91        86.37        55.30        86.01        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       19.59        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0M9 
       20.19        19.33        20.94        35.21        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        92.88       114.90        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       86.93        72.72        73.25        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       30.08         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69        18.67         3.65        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.78        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  MFAP5 MUTATED MFAP5 WILD-TYPE 
          18.41            0.56 
  MFAP5 MUTATED MFAP5 WILD-TYPE 
          85.84          185.79 
  MFAP5 MUTATED MFAP5 WILD-TYPE 
          48.03           35.74 
[1] "18.4 - 85.8 (48.0)" "0.6 - 185.8 (35.7)"
[1] "hr="     "2.6e+07"
D95V2, binary
                 cls
clus                0   1
  MFAP5 MUTATED     6   3
  MFAP5 WILD-TYPE 151  88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFAP5 MUTATED      6    3
  MFAP5 WILD-TYPE  151   88
     clus
vv    MFAP5 MUTATED MFAP5 WILD-TYPE
  NO              6             151
  YES             3              88
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MFAP5 MUTATED                                         8
  MFAP5 WILD-TYPE                                     192
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  MFAP5 MUTATED                               0
  MFAP5 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  MFAP5 MUTATED                                   1
  MFAP5 WILD-TYPE                                43
D95V3, multiclass
                                         clus
vv                                        MFAP5 MUTATED MFAP5 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             8             192
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MFAP5 MUTATED     6   1   0   0
  MFAP5 WILD-TYPE 166   9   7  18
D95V4, multiclass
    clus
vv   MFAP5 MUTATED MFAP5 WILD-TYPE
  R0             6             166
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(96) Variable = NAA15 MUTATION ANALYSIS
D96V1, survival
                 sevent
clus2               0   1
  NAA15 MUTATED    13   1
  NAA15 WILD-TYPE 202  32
  NAA15 MUTATED NAA15 WILD-TYPE 
             14             234 
  NAA15 MUTATED NAA15 WILD-TYPE 
              1              32 
$`NAA15 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J1 
      129.80        86.07        48.03        27.12        71.51        77.39 
TCGA-B5-A11E TCGA-B5-A121 TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A16G 
       59.84        16.57        85.55        85.84        73.25        27.42 
TCGA-D1-A16J TCGA-D1-A17K 
       29.92        28.08 

$`NAA15 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        80.55        88.24        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       37.78        40.11        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       86.37        55.30        86.01        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       27.85        13.45       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       17.36        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE 
       31.00        24.99        46.95        24.33        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       92.88       114.90        82.39        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16I 
       37.32        36.36        37.51        36.79         2.63        11.51 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M 
        0.99        30.44         1.28        28.01        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  NAA15 MUTATED NAA15 WILD-TYPE 
          16.57            0.56 
  NAA15 MUTATED NAA15 WILD-TYPE 
         129.80          185.79 
  NAA15 MUTATED NAA15 WILD-TYPE 
         65.675          35.560 
[1] "16.6 - 129.8 (65.7)" "0.6 - 185.8 (35.6)" 
[1] "hr=" "2.7"
D96V2, binary
                 cls
clus                0   1
  NAA15 MUTATED     8   6
  NAA15 WILD-TYPE 149  85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA15 MUTATED      8    6
  NAA15 WILD-TYPE  149   85
     clus
vv    NAA15 MUTATED NAA15 WILD-TYPE
  NO              8             149
  YES             6              85
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  NAA15 MUTATED                                        13
  NAA15 WILD-TYPE                                     187
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  NAA15 MUTATED                               0
  NAA15 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  NAA15 MUTATED                                   1
  NAA15 WILD-TYPE                                43
D96V3, multiclass
                                         clus
vv                                        NAA15 MUTATED NAA15 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            13             187
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NAA15 MUTATED    10   1   0   1
  NAA15 WILD-TYPE 162   9   7  17
D96V4, multiclass
    clus
vv   NAA15 MUTATED NAA15 WILD-TYPE
  R0            10             162
  R1             1               9
  R2             0               7
  RX             1              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"

Clustering(97) Variable = ZRANB3 MUTATION ANALYSIS
D97V1, survival
                  sevent
clus2                0   1
  ZRANB3 MUTATED     7   0
  ZRANB3 WILD-TYPE 208  33
  ZRANB3 MUTATED ZRANB3 WILD-TYPE 
               7              241 
  ZRANB3 MUTATED ZRANB3 WILD-TYPE 
               0               33 
$`ZRANB3 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-B5-A0JY TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A15X 
      129.80        86.07        69.27        85.84        73.25        29.88 
TCGA-D1-A177 
       18.02 

$`ZRANB3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       71.51        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        61.08        35.74        37.78        40.11        77.39 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       86.01        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       92.88       114.90        82.39        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 
        1.74        21.99        39.48        30.08         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A17A TCGA-D1-A17B 
        3.65        17.49        19.53        30.15         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  ZRANB3 MUTATED ZRANB3 WILD-TYPE 
           18.02             0.56 
  ZRANB3 MUTATED ZRANB3 WILD-TYPE 
          129.80           185.79 
  ZRANB3 MUTATED ZRANB3 WILD-TYPE 
           73.25            35.74 
[1] "18.0 - 129.8 (73.2)" "0.6 - 185.8 (35.7)" 
[1] "hr="     "2.7e+07"
D97V2, binary
                  cls
clus                 0   1
  ZRANB3 MUTATED     4   3
  ZRANB3 WILD-TYPE 153  88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZRANB3 MUTATED      4    3
  ZRANB3 WILD-TYPE  153   88
     clus
vv    ZRANB3 MUTATED ZRANB3 WILD-TYPE
  NO               4              153
  YES              3               88
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZRANB3 MUTATED                                         6
  ZRANB3 WILD-TYPE                                     194
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ZRANB3 MUTATED                               0
  ZRANB3 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZRANB3 MUTATED                                   1
  ZRANB3 WILD-TYPE                                43
D97V3, multiclass
                                         clus
vv                                        ZRANB3 MUTATED ZRANB3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              6              194
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    1               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZRANB3 MUTATED     6   0   0   0
  ZRANB3 WILD-TYPE 166  10   7  18
D97V4, multiclass
    clus
vv   ZRANB3 MUTATED ZRANB3 WILD-TYPE
  R0              6              166
  R1              0               10
  R2              0                7
  RX              0               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"

Clustering(98) Variable = SLC34A3 MUTATION ANALYSIS
D98V1, survival
                   sevent
clus2                 0   1
  SLC34A3 MUTATED     6   0
  SLC34A3 WILD-TYPE 209  33
  SLC34A3 MUTATED SLC34A3 WILD-TYPE 
                6               242 
  SLC34A3 MUTATED SLC34A3 WILD-TYPE 
                0                33 
$`SLC34A3 MUTATED`
TCGA-AP-A059 TCGA-AP-A0LM TCGA-B5-A11H TCGA-BS-A0UV TCGA-D1-A163 TCGA-D1-A17Q 
       48.03        27.12        88.34        73.25        32.58         1.78 

$`SLC34A3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       71.51        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        61.08        35.74        37.78        40.11        77.39 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       86.01        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
       59.84       185.79       113.36        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       92.88       114.90        85.84        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        1.91         3.68        29.33         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       18.67         3.65        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  SLC34A3 MUTATED SLC34A3 WILD-TYPE 
             1.78              0.56 
  SLC34A3 MUTATED SLC34A3 WILD-TYPE 
            88.34            185.79 
  SLC34A3 MUTATED SLC34A3 WILD-TYPE 
           40.305            35.900 
[1] "1.8 - 88.3 (40.3)"  "0.6 - 185.8 (35.9)"
[1] "hr="     "9300000"
D98V2, binary
                   cls
clus                  0   1
  SLC34A3 MUTATED     3   3
  SLC34A3 WILD-TYPE 154  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC34A3 MUTATED      3    3
  SLC34A3 WILD-TYPE  154   88
     clus
vv    SLC34A3 MUTATED SLC34A3 WILD-TYPE
  NO                3               154
  YES               3                88
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SLC34A3 MUTATED                                         6
  SLC34A3 WILD-TYPE                                     194
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  SLC34A3 MUTATED                               0
  SLC34A3 WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  SLC34A3 MUTATED                                   0
  SLC34A3 WILD-TYPE                                44
D98V3, multiclass
                                         clus
vv                                        SLC34A3 MUTATED SLC34A3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               6               194
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     0                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC34A3 MUTATED     5   0   0   0
  SLC34A3 WILD-TYPE 167  10   7  18
D98V4, multiclass
    clus
vv   SLC34A3 MUTATED SLC34A3 WILD-TYPE
  R0               5               167
  R1               0                10
  R2               0                 7
  RX               0                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"

Clustering(99) Variable = MLH3 MUTATION ANALYSIS
D99V1, survival
                sevent
clus2              0   1
  MLH3 MUTATED    16   1
  MLH3 WILD-TYPE 199  32
  MLH3 MUTATED MLH3 WILD-TYPE 
            17            231 
  MLH3 MUTATED MLH3 WILD-TYPE 
             1             32 
$`MLH3 MUTATED`
TCGA-A5-A0GP TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z 
       46.55        23.31        86.07        48.03        27.12        71.51 
TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A0K2 TCGA-B5-A11R TCGA-BS-A0UF TCGA-BS-A0UJ 
       40.11        69.27        72.62        77.23        85.84        82.39 
TCGA-D1-A103 TCGA-D1-A15X TCGA-D1-A16X TCGA-D1-A17Q TCGA-D1-A17U 
       21.99        29.88         3.65         1.78        22.92 

$`MLH3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       21.99        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        46.72        83.97        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       80.78        49.22        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        80.55        88.24        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       77.39        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K3 
       55.30        86.01        71.44        48.59        36.49        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       61.68        85.78        32.09        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 
      114.90        81.57        86.93        72.72        73.25        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       39.48        30.08         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 
       33.63        10.65         0.69        18.67        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       11.15        24.30         2.33        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  MLH3 MUTATED MLH3 WILD-TYPE 
          1.78           0.56 
  MLH3 MUTATED MLH3 WILD-TYPE 
         86.07         185.79 
  MLH3 MUTATED MLH3 WILD-TYPE 
         46.55          35.74 
[1] "1.8 - 86.1 (46.5)"  "0.6 - 185.8 (35.7)"
[1] "hr=" "2.4"
D99V2, binary
                cls
clus               0   1
  MLH3 MUTATED    12   5
  MLH3 WILD-TYPE 145  86
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH3 MUTATED     12    5
  MLH3 WILD-TYPE  145   86
     clus
vv    MLH3 MUTATED MLH3 WILD-TYPE
  NO            12            145
  YES            5             86
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MLH3 MUTATED                                        16
  MLH3 WILD-TYPE                                     184
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  MLH3 MUTATED                               0
  MLH3 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  MLH3 MUTATED                                   1
  MLH3 WILD-TYPE                                43
D99V3, multiclass
                                         clus
vv                                        MLH3 MUTATED MLH3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           16            184
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  1             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MLH3 MUTATED    12   2   0   0
  MLH3 WILD-TYPE 160   8   7  18
D99V4, multiclass
    clus
vv   MLH3 MUTATED MLH3 WILD-TYPE
  R0           12            160
  R1            2              8
  R2            0              7
  RX            0             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"

Clustering(100) Variable = CCDC147 MUTATION ANALYSIS
D100V1, survival
                   sevent
clus2                 0   1
  CCDC147 MUTATED    15   0
  CCDC147 WILD-TYPE 200  33
  CCDC147 MUTATED CCDC147 WILD-TYPE 
               15               233 
  CCDC147 MUTATED CCDC147 WILD-TYPE 
                0                33 
$`CCDC147 MUTATED`
TCGA-A5-A0GP TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AP-A0LT TCGA-AX-A05Z 
       46.55        86.07        48.03        27.12        49.22        71.51 
TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11N TCGA-B5-A11Y TCGA-BS-A0UF TCGA-BS-A0UV 
       40.11        69.27        61.68        18.41        85.84        73.25 
TCGA-D1-A103 TCGA-D1-A15X TCGA-D1-A17Q 
       21.99        29.88         1.78 

$`CCDC147 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       61.64        80.78        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        80.55        88.24        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       77.39        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       55.30        86.01        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       44.78        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.56        19.50        19.59        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
      114.90        82.39        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       39.48        30.08         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.51        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  CCDC147 MUTATED CCDC147 WILD-TYPE 
             1.78              0.56 
  CCDC147 MUTATED CCDC147 WILD-TYPE 
            86.07            185.79 
  CCDC147 MUTATED CCDC147 WILD-TYPE 
            48.03             35.38 
[1] "1.8 - 86.1 (48.0)"  "0.6 - 185.8 (35.4)"
[1] "hr="     "2.7e+07"
D100V2, binary
                   cls
clus                  0   1
  CCDC147 MUTATED    12   3
  CCDC147 WILD-TYPE 145  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC147 MUTATED     12    3
  CCDC147 WILD-TYPE  145   88
     clus
vv    CCDC147 MUTATED CCDC147 WILD-TYPE
  NO               12               145
  YES               3                88
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CCDC147 MUTATED                                        14
  CCDC147 WILD-TYPE                                     186
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  CCDC147 MUTATED                               0
  CCDC147 WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  CCDC147 MUTATED                                   1
  CCDC147 WILD-TYPE                                43
D100V3, multiclass
                                         clus
vv                                        CCDC147 MUTATED CCDC147 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              14               186
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     1                43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CCDC147 MUTATED    11   1   0   0
  CCDC147 WILD-TYPE 161   9   7  18
D100V4, multiclass
    clus
vv   CCDC147 MUTATED CCDC147 WILD-TYPE
  R0              11               161
  R1               1                 9
  R2               0                 7
  RX               0                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"

Clustering(101) Variable = ZNF662 MUTATION ANALYSIS
D101V1, survival
                  sevent
clus2                0   1
  ZNF662 MUTATED    13   0
  ZNF662 WILD-TYPE 202  33
  ZNF662 MUTATED ZNF662 WILD-TYPE 
              13              235 
  ZNF662 MUTATED ZNF662 WILD-TYPE 
               0               33 
$`ZNF662 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
      129.80        86.07        48.03        27.12        71.51        40.11 
TCGA-B5-A11E TCGA-B5-A11N TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A17Q 
       59.84        61.68        85.84        73.25        21.99         1.78 
TCGA-E6-A1LZ 
       79.10 

$`ZNF662 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        80.55        88.24        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       37.78        77.39        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       86.37        55.30        86.01        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       27.85        13.45       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       54.44        44.78        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       31.00        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       97.41        92.88       114.90        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       22.55         1.74        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       18.67         3.65        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  ZNF662 MUTATED ZNF662 WILD-TYPE 
            1.78             0.56 
  ZNF662 MUTATED ZNF662 WILD-TYPE 
          129.80           185.79 
  ZNF662 MUTATED ZNF662 WILD-TYPE 
           61.68            35.34 
[1] "1.8 - 129.8 (61.7)" "0.6 - 185.8 (35.3)"
[1] "hr="     "7.5e+07"
D101V2, binary
                  cls
clus                 0   1
  ZNF662 MUTATED     9   4
  ZNF662 WILD-TYPE 148  87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF662 MUTATED      9    4
  ZNF662 WILD-TYPE  148   87
     clus
vv    ZNF662 MUTATED ZNF662 WILD-TYPE
  NO               9              148
  YES              4               87
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZNF662 MUTATED                                        12
  ZNF662 WILD-TYPE                                     188
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ZNF662 MUTATED                               0
  ZNF662 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZNF662 MUTATED                                   1
  ZNF662 WILD-TYPE                                43
D101V3, multiclass
                                         clus
vv                                        ZNF662 MUTATED ZNF662 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             12              188
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    1               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF662 MUTATED    10   1   0   0
  ZNF662 WILD-TYPE 162   9   7  18
D101V4, multiclass
    clus
vv   ZNF662 MUTATED ZNF662 WILD-TYPE
  R0             10              162
  R1              1                9
  R2              0                7
  RX              0               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"

Clustering(102) Variable = PSMC4 MUTATION ANALYSIS
D102V1, survival
                 sevent
clus2               0   1
  PSMC4 MUTATED    11   0
  PSMC4 WILD-TYPE 204  33
  PSMC4 MUTATED PSMC4 WILD-TYPE 
             11             237 
  PSMC4 MUTATED PSMC4 WILD-TYPE 
              0              33 
$`PSMC4 MUTATED`
TCGA-A5-A0GP TCGA-A5-A0VP TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A0J0 
       46.55        42.35        86.07        48.03        27.12        40.11 
TCGA-BS-A0UF TCGA-BS-A0UM TCGA-BS-A0UV TCGA-D1-A167 TCGA-D1-A17F 
       85.84        86.93        73.25        15.72         1.28 

$`PSMC4 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 
       29.06        28.77        15.95        20.25       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       23.31        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        46.72        83.97        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       80.78        49.22        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       37.78        77.39        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       86.37        55.30        86.01        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ 
       96.49        30.74        97.41        92.88       114.90        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       81.57        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17H 
       18.02         1.58         7.00         0.99        30.44        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  PSMC4 MUTATED PSMC4 WILD-TYPE 
           1.28            0.56 
  PSMC4 MUTATED PSMC4 WILD-TYPE 
          86.93          185.79 
  PSMC4 MUTATED PSMC4 WILD-TYPE 
          46.55           35.38 
[1] "1.3 - 86.9 (46.5)"  "0.6 - 185.8 (35.4)"
[1] "hr="     "2.6e+07"
D102V2, binary
                 cls
clus                0   1
  PSMC4 MUTATED     7   4
  PSMC4 WILD-TYPE 150  87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMC4 MUTATED      7    4
  PSMC4 WILD-TYPE  150   87
     clus
vv    PSMC4 MUTATED PSMC4 WILD-TYPE
  NO              7             150
  YES             4              87
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PSMC4 MUTATED                                        11
  PSMC4 WILD-TYPE                                     189
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  PSMC4 MUTATED                               0
  PSMC4 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  PSMC4 MUTATED                                   0
  PSMC4 WILD-TYPE                                44
D102V3, multiclass
                                         clus
vv                                        PSMC4 MUTATED PSMC4 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            11             189
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PSMC4 MUTATED    11   0   0   0
  PSMC4 WILD-TYPE 161  10   7  18
D102V4, multiclass
    clus
vv   PSMC4 MUTATED PSMC4 WILD-TYPE
  R0            11             161
  R1             0              10
  R2             0               7
  RX             0              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"

Clustering(103) Variable = CCDC160 MUTATION ANALYSIS
D103V1, survival
                   sevent
clus2                 0   1
  CCDC160 MUTATED    11   0
  CCDC160 WILD-TYPE 204  33
  CCDC160 MUTATED CCDC160 WILD-TYPE 
               11               237 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
                0                33 
$`CCDC160 MUTATED`
TCGA-A5-A0GI TCGA-A5-A0GH TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A0LM TCGA-B5-A0JY 
       88.18        74.10       129.80        86.07        27.12        69.27 
TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A16X TCGA-D1-A17Q 
       85.84        73.25        21.99         3.65         1.78 

$`CCDC160 WILD-TYPE`
TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP 
       60.53       110.63        57.80        93.99        67.66        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GJ 
       83.51        17.85        32.78       112.54       105.37        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 
       28.77        42.35        15.95        20.25        21.99        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       48.03        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        46.72        83.97        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       80.78        49.22        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       37.78        40.11        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        55.30        86.01        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ 
       96.49        30.74        97.41        92.88       114.90        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        86.93        72.72        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W 
       28.67        23.93        22.55         1.74        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
       10.65         0.69        18.67        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  CCDC160 MUTATED CCDC160 WILD-TYPE 
             1.78              0.56 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
           129.80            185.79 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
            73.25             35.74 
[1] "1.8 - 129.8 (73.2)" "0.6 - 185.8 (35.7)"
[1] "hr="     "2.7e+07"
D103V2, binary
                   cls
clus                  0   1
  CCDC160 MUTATED     8   3
  CCDC160 WILD-TYPE 149  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC160 MUTATED      8    3
  CCDC160 WILD-TYPE  149   88
     clus
vv    CCDC160 MUTATED CCDC160 WILD-TYPE
  NO                8               149
  YES               3                88
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CCDC160 MUTATED                                        11
  CCDC160 WILD-TYPE                                     189
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  CCDC160 MUTATED                               0
  CCDC160 WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  CCDC160 MUTATED                                   0
  CCDC160 WILD-TYPE                                44
D103V3, multiclass
                                         clus
vv                                        CCDC160 MUTATED CCDC160 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              11               189
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     0                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CCDC160 MUTATED    10   0   0   0
  CCDC160 WILD-TYPE 162  10   7  18
D103V4, multiclass
    clus
vv   CCDC160 MUTATED CCDC160 WILD-TYPE
  R0              10               162
  R1               0                10
  R2               0                 7
  RX               0                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"

Clustering(104) Variable = PPIL4 MUTATION ANALYSIS
D104V1, survival
                 sevent
clus2               0   1
  PPIL4 MUTATED    11   0
  PPIL4 WILD-TYPE 204  33
  PPIL4 MUTATED PPIL4 WILD-TYPE 
             11             237 
  PPIL4 MUTATED PPIL4 WILD-TYPE 
              0              33 
$`PPIL4 MUTATED`
TCGA-BG-A0YV TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J1 
       12.56       129.80        48.03        27.12        71.51        77.39 
TCGA-B5-A11E TCGA-D1-A103 TCGA-D1-A167 TCGA-D1-A16Y TCGA-D1-A17Q 
       59.84        21.99        15.72        17.49         1.78 

$`PPIL4 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       51.55        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       29.06        28.77        42.35        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        80.55        88.24        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       37.78        40.11        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       86.37        55.30        86.01        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       27.85        13.45       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        92.88       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        86.93        72.72        73.25        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V 
        4.87        28.67        23.93        22.55         1.74        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A174 TCGA-D1-A176 
       10.65         0.69        18.67         3.65        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  PPIL4 MUTATED PPIL4 WILD-TYPE 
           1.78            0.56 
  PPIL4 MUTATED PPIL4 WILD-TYPE 
         129.80          185.79 
  PPIL4 MUTATED PPIL4 WILD-TYPE 
          27.12           35.90 
[1] "1.8 - 129.8 (27.1)" "0.6 - 185.8 (35.9)"
[1] "hr="     "2.7e+07"
D104V2, binary
                 cls
clus                0   1
  PPIL4 MUTATED     6   5
  PPIL4 WILD-TYPE 151  86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPIL4 MUTATED      6    5
  PPIL4 WILD-TYPE  151   86
     clus
vv    PPIL4 MUTATED PPIL4 WILD-TYPE
  NO              6             151
  YES             5              86
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PPIL4 MUTATED                                        10
  PPIL4 WILD-TYPE                                     190
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  PPIL4 MUTATED                               0
  PPIL4 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  PPIL4 MUTATED                                   1
  PPIL4 WILD-TYPE                                43
D104V3, multiclass
                                         clus
vv                                        PPIL4 MUTATED PPIL4 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            10             190
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PPIL4 MUTATED     8   1   0   1
  PPIL4 WILD-TYPE 164   9   7  17
D104V4, multiclass
    clus
vv   PPIL4 MUTATED PPIL4 WILD-TYPE
  R0             8             164
  R1             1               9
  R2             0               7
  RX             1              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"

Clustering(105) Variable = CCDC144A MUTATION ANALYSIS
D105V1, survival
                    sevent
clus2                  0   1
  CCDC144A MUTATED    17   1
  CCDC144A WILD-TYPE 198  32
  CCDC144A MUTATED CCDC144A WILD-TYPE 
                18                230 
  CCDC144A MUTATED CCDC144A WILD-TYPE 
                 1                 32 
$`CCDC144A MUTATED`
TCGA-A5-A0GP TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A0J0 
       46.55        86.07        27.12        71.51        35.34        40.11 
TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-B5-A11W TCGA-BS-A0UF 
       77.39        69.27        59.84        61.68        19.50        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A16G TCGA-D1-A16X TCGA-D1-A17Q TCGA-FI-A2EX 
       82.39        73.25        27.42         3.65         1.78         9.34 

$`CCDC144A WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A062 
       13.58        33.21        29.69        80.55        88.24        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       37.78        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       55.30        86.01        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        86.93        72.72        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79         2.63        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
       10.65         0.69        18.67        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2F8 
       59.01        30.67 

  CCDC144A MUTATED CCDC144A WILD-TYPE 
              1.78               0.56 
  CCDC144A MUTATED CCDC144A WILD-TYPE 
             86.07             185.79 
  CCDC144A MUTATED CCDC144A WILD-TYPE 
            53.195             35.560 
[1] "1.8 - 86.1 (53.2)"  "0.6 - 185.8 (35.6)"
[1] "hr=" "2.7"
D105V2, binary
                    cls
clus                   0   1
  CCDC144A MUTATED    14   4
  CCDC144A WILD-TYPE 143  87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CCDC144A MUTATED     14    4
  CCDC144A WILD-TYPE  143   87
     clus
vv    CCDC144A MUTATED CCDC144A WILD-TYPE
  NO                14                143
  YES                4                 87
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CCDC144A MUTATED                                        16
  CCDC144A WILD-TYPE                                     184
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  CCDC144A MUTATED                               0
  CCDC144A WILD-TYPE                             4
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  CCDC144A MUTATED                                   2
  CCDC144A WILD-TYPE                                42
D105V3, multiclass
                                         clus
vv                                        CCDC144A MUTATED CCDC144A WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               16                184
  MIXED SEROUS AND ENDOMETRIOID                          0                  4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      2                 42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  CCDC144A MUTATED    11   2   0   1
  CCDC144A WILD-TYPE 161   8   7  17
D105V4, multiclass
    clus
vv   CCDC144A MUTATED CCDC144A WILD-TYPE
  R0               11                161
  R1                2                  8
  R2                0                  7
  RX                1                 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"

Clustering(106) Variable = TUBGCP6 MUTATION ANALYSIS
D106V1, survival
                   sevent
clus2                 0   1
  TUBGCP6 MUTATED    19   1
  TUBGCP6 WILD-TYPE 196  32
  TUBGCP6 MUTATED TUBGCP6 WILD-TYPE 
               20               228 
  TUBGCP6 MUTATED TUBGCP6 WILD-TYPE 
                1                32 
$`TUBGCP6 MUTATED`
TCGA-D1-A0ZO TCGA-A5-A0R8 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A064 TCGA-AX-A0J0 
       19.79        19.59        48.03        27.12        49.87        40.11 
TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0TE TCGA-BS-A0TJ TCGA-BS-A0UF 
       77.39        69.27        59.84         4.80        67.99        85.84 
TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A167 TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A174 
       73.25        21.99        15.72         0.69         3.65        19.53 
TCGA-D1-A176 TCGA-D1-A17Q 
       30.15         1.78 

$`TUBGCP6 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       51.55        12.56         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        37.91        17.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 
       28.77        42.35        15.95        20.25       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       45.99        79.46        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       37.78        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       55.30        86.01        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG 
       24.99        46.95        24.33        85.55        78.21        77.95 
TCGA-BS-A0TI TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       61.87        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 
       82.39        81.57        86.93        72.72        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V 
        4.87        28.67        23.93        22.55         1.74        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       10.65        18.67        17.49        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       10.22         1.51        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  TUBGCP6 MUTATED TUBGCP6 WILD-TYPE 
             0.69              0.56 
  TUBGCP6 MUTATED TUBGCP6 WILD-TYPE 
            85.84            185.79 
  TUBGCP6 MUTATED TUBGCP6 WILD-TYPE 
           28.635            36.000 
[1] "0.7 - 85.8 (28.6)"  "0.6 - 185.8 (36.0)"
[1] "hr=" "2.2"
D106V2, binary
                   cls
clus                  0   1
  TUBGCP6 MUTATED    14   6
  TUBGCP6 WILD-TYPE 143  85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TUBGCP6 MUTATED     14    6
  TUBGCP6 WILD-TYPE  143   85
     clus
vv    TUBGCP6 MUTATED TUBGCP6 WILD-TYPE
  NO               14               143
  YES               6                85
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  TUBGCP6 MUTATED                                        20
  TUBGCP6 WILD-TYPE                                     180
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  TUBGCP6 MUTATED                               0
  TUBGCP6 WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  TUBGCP6 MUTATED                                   0
  TUBGCP6 WILD-TYPE                                44
D106V3, multiclass
                                         clus
vv                                        TUBGCP6 MUTATED TUBGCP6 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              20               180
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     0                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TUBGCP6 MUTATED    16   0   1   0
  TUBGCP6 WILD-TYPE 156  10   6  18
D106V4, multiclass
    clus
vv   TUBGCP6 MUTATED TUBGCP6 WILD-TYPE
  R0              16               156
  R1               0                10
  R2               1                 6
  RX               0                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"

Clustering(107) Variable = TTC39C MUTATION ANALYSIS
D107V1, survival
                  sevent
clus2                0   1
  TTC39C MUTATED     7   0
  TTC39C WILD-TYPE 208  33
  TTC39C MUTATED TTC39C WILD-TYPE 
               7              241 
  TTC39C MUTATED TTC39C WILD-TYPE 
               0               33 
$`TTC39C MUTATED`
TCGA-AP-A056 TCGA-AP-A0LT TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0UF 
       86.07        49.22        77.39        69.27        59.84        85.84 
TCGA-D1-A16X 
        3.65 

$`TTC39C WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LV 
       27.12        82.52        33.40        61.64        80.78        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       71.51        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 
       60.66        61.08        35.74        37.78        40.11        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 
       82.39        81.57        86.93        72.72        73.25        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  TTC39C MUTATED TTC39C WILD-TYPE 
            3.65             0.56 
  TTC39C MUTATED TTC39C WILD-TYPE 
           86.07           185.79 
  TTC39C MUTATED TTC39C WILD-TYPE 
           69.27            35.38 
[1] "3.6 - 86.1 (69.3)"  "0.6 - 185.8 (35.4)"
[1] "hr="     "2.6e+07"
D107V2, binary
                  cls
clus                 0   1
  TTC39C MUTATED     7   0
  TTC39C WILD-TYPE 150  91
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TTC39C MUTATED      7    0
  TTC39C WILD-TYPE  150   91
     clus
vv    TTC39C MUTATED TTC39C WILD-TYPE
  NO               7              150
  YES              0               91
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  TTC39C MUTATED                                         7
  TTC39C WILD-TYPE                                     193
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  TTC39C MUTATED                               0
  TTC39C WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  TTC39C MUTATED                                   0
  TTC39C WILD-TYPE                                44
D107V3, multiclass
                                         clus
vv                                        TTC39C MUTATED TTC39C WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              7              193
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TTC39C MUTATED     5   0   0   0
  TTC39C WILD-TYPE 167  10   7  18
D107V4, multiclass
    clus
vv   TTC39C MUTATED TTC39C WILD-TYPE
  R0              5              167
  R1              0               10
  R2              0                7
  RX              0               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"

Clustering(108) Variable = COL8A1 MUTATION ANALYSIS
D108V1, survival
                  sevent
clus2                0   1
  COL8A1 MUTATED     9   1
  COL8A1 WILD-TYPE 206  32
  COL8A1 MUTATED COL8A1 WILD-TYPE 
              10              238 
  COL8A1 MUTATED COL8A1 WILD-TYPE 
               1               32 
$`COL8A1 MUTATED`
TCGA-AP-A059 TCGA-AP-A0LG TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A064 TCGA-B5-A0K9 
       48.03        66.25        27.12        71.51        49.87        13.45 
TCGA-B5-A11E TCGA-B5-A11H TCGA-BS-A0UV TCGA-D1-A103 
       59.84        88.34        73.25        21.99 

$`COL8A1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
      110.37        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       45.99        79.46        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       37.78        40.11        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        86.37        55.30        86.01        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J 
       63.55        27.85       185.79       113.36        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       44.78        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       31.00        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        92.88       114.90        85.84        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93        22.55         1.74        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  COL8A1 MUTATED COL8A1 WILD-TYPE 
           13.45             0.56 
  COL8A1 MUTATED COL8A1 WILD-TYPE 
           88.34           185.79 
  COL8A1 MUTATED COL8A1 WILD-TYPE 
          54.855           35.560 
[1] "13.4 - 88.3 (54.9)" "0.6 - 185.8 (35.6)"
[1] "hr=" "1.5"
D108V2, binary
                  cls
clus                 0   1
  COL8A1 MUTATED     6   4
  COL8A1 WILD-TYPE 151  87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL8A1 MUTATED      6    4
  COL8A1 WILD-TYPE  151   87
     clus
vv    COL8A1 MUTATED COL8A1 WILD-TYPE
  NO               6              151
  YES              4               87
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  COL8A1 MUTATED                                        10
  COL8A1 WILD-TYPE                                     190
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  COL8A1 MUTATED                               0
  COL8A1 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  COL8A1 MUTATED                                   0
  COL8A1 WILD-TYPE                                44
D108V3, multiclass
                                         clus
vv                                        COL8A1 MUTATED COL8A1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             10              190
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  COL8A1 MUTATED     5   1   0   0
  COL8A1 WILD-TYPE 167   9   7  18
D108V4, multiclass
    clus
vv   COL8A1 MUTATED COL8A1 WILD-TYPE
  R0              5              167
  R1              1                9
  R2              0                7
  RX              0               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"

Clustering(109) Variable = PER3 MUTATION ANALYSIS
D109V1, survival
                sevent
clus2              0   1
  PER3 MUTATED    12   0
  PER3 WILD-TYPE 203  33
  PER3 MUTATED PER3 WILD-TYPE 
            12            236 
  PER3 MUTATED PER3 WILD-TYPE 
             0             33 
$`PER3 MUTATED`
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY 
       86.07        48.03        27.12        40.11        77.39        69.27 
TCGA-B5-A0K2 TCGA-B5-A11E TCGA-B5-A11N TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A167 
       72.62        59.84        61.68        73.25        21.99        15.72 

$`PER3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
      129.80        21.99        23.31        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       61.08        35.74        37.78        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        55.30        86.01        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       36.49        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       13.45       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       44.78        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       92.88       114.90        85.84        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       22.55         1.74        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 
        3.68        29.33        32.58         0.66        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  PER3 MUTATED PER3 WILD-TYPE 
         15.72           0.56 
  PER3 MUTATED PER3 WILD-TYPE 
         86.07         185.79 
  PER3 MUTATED PER3 WILD-TYPE 
         60.76          35.36 
[1] "15.7 - 86.1 (60.8)" "0.6 - 185.8 (35.4)"
[1] "hr="     "2.7e+07"
D109V2, binary
                cls
clus               0   1
  PER3 MUTATED     9   3
  PER3 WILD-TYPE 148  88
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED      9    3
  PER3 WILD-TYPE  148   88
     clus
vv    PER3 MUTATED PER3 WILD-TYPE
  NO             9            148
  YES            3             88
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PER3 MUTATED                                        12
  PER3 WILD-TYPE                                     188
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  PER3 MUTATED                               0
  PER3 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  PER3 MUTATED                                   0
  PER3 WILD-TYPE                                44
D109V3, multiclass
                                         clus
vv                                        PER3 MUTATED PER3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           12            188
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PER3 MUTATED     8   0   0   0
  PER3 WILD-TYPE 164  10   7  18
D109V4, multiclass
    clus
vv   PER3 MUTATED PER3 WILD-TYPE
  R0            8            164
  R1            0             10
  R2            0              7
  RX            0             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"

Clustering(110) Variable = MGA MUTATION ANALYSIS
D110V1, survival
               sevent
clus2             0   1
  MGA MUTATED    22   4
  MGA WILD-TYPE 193  29
  MGA MUTATED MGA WILD-TYPE 
           26           222 
  MGA MUTATED MGA WILD-TYPE 
            4            29 
$`MGA MUTATED`
TCGA-AP-A0LF TCGA-A5-A0VP TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 
       93.99        42.35        20.25       129.80        86.07        48.03 
TCGA-AP-A05N TCGA-AP-A0LD TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JR 
       23.87       117.99        27.12        71.51        40.11        56.91 
TCGA-B5-A0JY TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11N TCGA-B5-A11Y TCGA-BS-A0TC 
       69.27        13.45        59.84        61.68        18.41        85.55 
TCGA-BS-A0TE TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A15V TCGA-D1-A163 TCGA-D1-A167 
        4.80        85.84        73.25        39.48        32.58        15.72 
TCGA-D1-A16X TCGA-D1-A17C 
        3.65         0.99 

$`MGA WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A1CP 
       88.18        60.53       110.63        57.80        67.66        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A 
       29.06        28.77        15.95        21.99        23.31        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LE 
       45.53        36.89        20.91        48.79       125.42       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        77.39        34.65        25.51        71.24 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.50        19.59        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       24.33        78.21        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        92.88       114.90        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       23.93        22.55         1.74        21.99        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 
        1.91         3.68        29.33         0.66        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  MGA MUTATED MGA WILD-TYPE 
         0.99          0.56 
  MGA MUTATED MGA WILD-TYPE 
       129.80        185.79 
  MGA MUTATED MGA WILD-TYPE 
        45.19         35.36 
[1] "1.0 - 129.8 (45.2)" "0.6 - 185.8 (35.4)"
[1] "hr=" "1"  
D110V2, binary
               cls
clus              0   1
  MGA MUTATED    17   9
  MGA WILD-TYPE 140  82
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     17    9
  MGA WILD-TYPE  140   82
     clus
vv    MGA MUTATED MGA WILD-TYPE
  NO           17           140
  YES           9            82
[1] 2 2
[1] FALSE
               vv
clus            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MGA MUTATED                                        24
  MGA WILD-TYPE                                     176
               vv
clus            MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  MGA MUTATED                               0                                 2
  MGA WILD-TYPE                             4                                42
D110V3, multiclass
                                         clus
vv                                        MGA MUTATED MGA WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA          24           176
  MIXED SEROUS AND ENDOMETRIOID                     0             4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                 2            42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  MGA MUTATED    16   1   2   0
  MGA WILD-TYPE 156   9   5  18
D110V4, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  R0          16           156
  R1           1             9
  R2           2             5
  RX           0            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"

Clustering(111) Variable = GPRASP1 MUTATION ANALYSIS
D111V1, survival
                   sevent
clus2                 0   1
  GPRASP1 MUTATED    20   1
  GPRASP1 WILD-TYPE 195  32
  GPRASP1 MUTATED GPRASP1 WILD-TYPE 
               21               227 
  GPRASP1 MUTATED GPRASP1 WILD-TYPE 
                1                32 
$`GPRASP1 MUTATED`
TCGA-A5-A0GP TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM 
       46.55        20.25       129.80        86.07        48.03        27.12 
TCGA-AP-A0LQ TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A11E 
       80.78        71.51        40.11        69.27        71.44        59.84 
TCGA-BG-A0M3 TCGA-BG-A0MG TCGA-BG-A0VZ TCGA-BS-A0UF TCGA-D1-A103 TCGA-D1-A16X 
       35.21        48.56        52.64        85.84        21.99         3.65 
TCGA-D1-A17B TCGA-D1-A17D TCGA-D1-A17Q 
        7.00        30.44         1.78 

$`GPRASP1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AP-A052 TCGA-AP-A054 
       29.06        28.77        42.35        15.95        21.99        23.31 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       63.91        45.53        36.89        23.87        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LT 
       46.72        83.97        82.52        33.40        61.64        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       88.24        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        61.08        35.74        37.78        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        13.45       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       20.19        19.33        20.94        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       41.52        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0W1 TCGA-BG-A0W2 
       15.42        51.06        52.01        34.29        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       92.88       114.90        82.39        81.57        86.93        72.72 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       73.25        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       22.55         1.74        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       18.67        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17C TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
        0.99         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.51        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  GPRASP1 MUTATED GPRASP1 WILD-TYPE 
             1.78              0.56 
  GPRASP1 MUTATED GPRASP1 WILD-TYPE 
           129.80            185.79 
  GPRASP1 MUTATED GPRASP1 WILD-TYPE 
            48.03             35.38 
[1] "1.8 - 129.8 (48.0)" "0.6 - 185.8 (35.4)"
[1] "hr=" "3.4"
D111V2, binary
                   cls
clus                  0   1
  GPRASP1 MUTATED    14   7
  GPRASP1 WILD-TYPE 143  84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPRASP1 MUTATED     14    7
  GPRASP1 WILD-TYPE  143   84
     clus
vv    GPRASP1 MUTATED GPRASP1 WILD-TYPE
  NO               14               143
  YES               7                84
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  GPRASP1 MUTATED                                        20
  GPRASP1 WILD-TYPE                                     180
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  GPRASP1 MUTATED                               0
  GPRASP1 WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  GPRASP1 MUTATED                                   1
  GPRASP1 WILD-TYPE                                43
D111V3, multiclass
                                         clus
vv                                        GPRASP1 MUTATED GPRASP1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              20               180
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     1                43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  GPRASP1 MUTATED    16   1   0   0
  GPRASP1 WILD-TYPE 156   9   7  18
D111V4, multiclass
    clus
vv   GPRASP1 MUTATED GPRASP1 WILD-TYPE
  R0              16               156
  R1               1                 9
  R2               0                 7
  RX               0                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"

Clustering(112) Variable = PPM1D MUTATION ANALYSIS
D112V1, survival
                 sevent
clus2               0   1
  PPM1D MUTATED    11   0
  PPM1D WILD-TYPE 204  33
  PPM1D MUTATED PPM1D WILD-TYPE 
             11             237 
  PPM1D MUTATED PPM1D WILD-TYPE 
              0              33 
$`PPM1D MUTATED`
TCGA-AP-A056 TCGA-AX-A05Z TCGA-AX-A063 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11H 
       86.07        71.51        79.46        69.27        59.84        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-D1-A167 TCGA-D1-A16X TCGA-D1-A17H 
       85.84        82.39        15.72         3.65        28.01 

$`PPM1D WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       88.24        35.34        45.99        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UL 
       96.49        30.74        97.41        92.88       114.90        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       86.93        72.72        73.25        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
       10.65         0.69        18.67        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  PPM1D MUTATED PPM1D WILD-TYPE 
           3.65            0.56 
  PPM1D MUTATED PPM1D WILD-TYPE 
          88.34          185.79 
  PPM1D MUTATED PPM1D WILD-TYPE 
          71.51           35.38 
[1] "3.6 - 88.3 (71.5)"  "0.6 - 185.8 (35.4)"
[1] "hr="     "2.7e+07"
D112V2, binary
                 cls
clus                0   1
  PPM1D MUTATED    10   1
  PPM1D WILD-TYPE 147  90
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED     10    1
  PPM1D WILD-TYPE  147   90
     clus
vv    PPM1D MUTATED PPM1D WILD-TYPE
  NO             10             147
  YES             1              90
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PPM1D MUTATED                                        11
  PPM1D WILD-TYPE                                     189
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  PPM1D MUTATED                               0
  PPM1D WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  PPM1D MUTATED                                   0
  PPM1D WILD-TYPE                                44
D112V3, multiclass
                                         clus
vv                                        PPM1D MUTATED PPM1D WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            11             189
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PPM1D MUTATED     7   1   0   0
  PPM1D WILD-TYPE 165   9   7  18
D112V4, multiclass
    clus
vv   PPM1D MUTATED PPM1D WILD-TYPE
  R0             7             165
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(113) Variable = ZNF674 MUTATION ANALYSIS
D113V1, survival
                  sevent
clus2                0   1
  ZNF674 MUTATED    14   0
  ZNF674 WILD-TYPE 201  33
  ZNF674 MUTATED ZNF674 WILD-TYPE 
              14              234 
  ZNF674 MUTATED ZNF674 WILD-TYPE 
               0               33 
$`ZNF674 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LE TCGA-AP-A0LI TCGA-AP-A0LM 
      129.80        86.07        48.03       110.37        97.71        27.12 
TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11E TCGA-BG-A0VX TCGA-BS-A0TC TCGA-BS-A0UF 
       40.11        69.27        59.84        34.29        85.55        85.84 
TCGA-BS-A0UV TCGA-D1-A17Q 
       73.25         1.78 

$`ZNF674 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91        48.79       125.42       117.99        66.25        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       49.22        25.08        46.78        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       77.39        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       55.30        86.01        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       51.06        52.01        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        24.33        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 
       82.39        81.57        86.93        72.72        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       10.22         1.51        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  ZNF674 MUTATED ZNF674 WILD-TYPE 
            1.78             0.56 
  ZNF674 MUTATED ZNF674 WILD-TYPE 
          129.80           185.79 
  ZNF674 MUTATED ZNF674 WILD-TYPE 
          71.260           35.275 
[1] "1.8 - 129.8 (71.3)" "0.6 - 185.8 (35.3)"
[1] "hr="     "7.6e+07"
D113V2, binary
                  cls
clus                 0   1
  ZNF674 MUTATED    10   4
  ZNF674 WILD-TYPE 147  87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF674 MUTATED     10    4
  ZNF674 WILD-TYPE  147   87
     clus
vv    ZNF674 MUTATED ZNF674 WILD-TYPE
  NO              10              147
  YES              4               87
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZNF674 MUTATED                                        13
  ZNF674 WILD-TYPE                                     187
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ZNF674 MUTATED                               0
  ZNF674 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZNF674 MUTATED                                   1
  ZNF674 WILD-TYPE                                43
D113V3, multiclass
                                         clus
vv                                        ZNF674 MUTATED ZNF674 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             13              187
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    1               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF674 MUTATED    10   0   1   1
  ZNF674 WILD-TYPE 162  10   6  17
D113V4, multiclass
    clus
vv   ZNF674 MUTATED ZNF674 WILD-TYPE
  R0             10              162
  R1              0               10
  R2              1                6
  RX              1               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"

Clustering(114) Variable = LIMK2 MUTATION ANALYSIS
D114V1, survival
                 sevent
clus2               0   1
  LIMK2 MUTATED    12   0
  LIMK2 WILD-TYPE 203  33
  LIMK2 MUTATED LIMK2 WILD-TYPE 
             12             236 
  LIMK2 MUTATED LIMK2 WILD-TYPE 
              0              33 
$`LIMK2 MUTATED`
TCGA-AP-A059 TCGA-AP-A0LP TCGA-AP-A0LT TCGA-AX-A05Z TCGA-B5-A0K1 TCGA-B5-A11Y 
       48.03        61.64        49.22        71.51        36.49        18.41 
TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A17B TCGA-D1-A17D 
       85.84        73.25        18.67         3.65         7.00        30.44 

$`LIMK2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LQ TCGA-AP-A0LV TCGA-AP-A1DQ 
       27.12        82.52        33.40        80.78        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.74        37.78        40.11        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       71.24        56.91        86.37        55.30        86.01        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       71.44        48.59        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       19.59        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ 
       96.49        30.74        97.41        92.88       114.90        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        86.93        72.72        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
       33.63        10.65         0.69        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17C TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
       18.02         1.58         0.99         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  LIMK2 MUTATED LIMK2 WILD-TYPE 
           3.65            0.56 
  LIMK2 MUTATED LIMK2 WILD-TYPE 
          85.84          185.79 
  LIMK2 MUTATED LIMK2 WILD-TYPE 
          42.26           35.82 
[1] "3.6 - 85.8 (42.3)"  "0.6 - 185.8 (35.8)"
[1] "hr="     "2.6e+07"
D114V2, binary
                 cls
clus                0   1
  LIMK2 MUTATED     9   3
  LIMK2 WILD-TYPE 148  88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LIMK2 MUTATED      9    3
  LIMK2 WILD-TYPE  148   88
     clus
vv    LIMK2 MUTATED LIMK2 WILD-TYPE
  NO              9             148
  YES             3              88
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  LIMK2 MUTATED                                        11
  LIMK2 WILD-TYPE                                     189
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  LIMK2 MUTATED                               0
  LIMK2 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  LIMK2 MUTATED                                   1
  LIMK2 WILD-TYPE                                43
D114V3, multiclass
                                         clus
vv                                        LIMK2 MUTATED LIMK2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            11             189
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LIMK2 MUTATED     9   1   0   0
  LIMK2 WILD-TYPE 163   9   7  18
D114V4, multiclass
    clus
vv   LIMK2 MUTATED LIMK2 WILD-TYPE
  R0             9             163
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(115) Variable = ZNF606 MUTATION ANALYSIS
D115V1, survival
                  sevent
clus2                0   1
  ZNF606 MUTATED    15   1
  ZNF606 WILD-TYPE 200  32
  ZNF606 MUTATED ZNF606 WILD-TYPE 
              16              232 
  ZNF606 MUTATED ZNF606 WILD-TYPE 
               1               32 
$`ZNF606 MUTATED`
TCGA-D1-A0ZO TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A05Z TCGA-AX-A063 
       19.79       129.80        86.07        48.03        71.51        79.46 
TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-BG-A0MG TCGA-BS-A0TA 
       40.11        69.27        59.84        61.68        48.56        24.33 
TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A16Y TCGA-D1-A17Q 
       73.25        21.99        17.49         1.78 

$`ZNF606 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       51.55        12.56         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       29.06        28.77        42.35        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       23.31        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        80.55        88.24        35.34        45.99 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       77.39        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       55.30        86.01        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MO 
       71.24        63.68        74.63        41.52        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        92.88       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 
       82.39        81.57        86.93        72.72        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V 
        4.87        28.67        23.93        22.55         1.74        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A174 
       33.63        10.65         0.69        18.67         3.65        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  ZNF606 MUTATED ZNF606 WILD-TYPE 
            1.78             0.56 
  ZNF606 MUTATED ZNF606 WILD-TYPE 
          129.80           185.79 
  ZNF606 MUTATED ZNF606 WILD-TYPE 
           54.20            35.36 
[1] "1.8 - 129.8 (54.2)" "0.6 - 185.8 (35.4)"
[1] "hr=" "2.7"
D115V2, binary
                  cls
clus                 0   1
  ZNF606 MUTATED    13   3
  ZNF606 WILD-TYPE 144  88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF606 MUTATED     13    3
  ZNF606 WILD-TYPE  144   88
     clus
vv    ZNF606 MUTATED ZNF606 WILD-TYPE
  NO              13              144
  YES              3               88
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZNF606 MUTATED                                        16
  ZNF606 WILD-TYPE                                     184
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ZNF606 MUTATED                               0
  ZNF606 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZNF606 MUTATED                                   0
  ZNF606 WILD-TYPE                                44
D115V3, multiclass
                                         clus
vv                                        ZNF606 MUTATED ZNF606 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             16              184
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF606 MUTATED    10   1   0   2
  ZNF606 WILD-TYPE 162   9   7  16
D115V4, multiclass
    clus
vv   ZNF606 MUTATED ZNF606 WILD-TYPE
  R0             10              162
  R1              1                9
  R2              0                7
  RX              2               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"

Clustering(116) Variable = SFRP4 MUTATION ANALYSIS
D116V1, survival
                 sevent
clus2               0   1
  SFRP4 MUTATED     8   0
  SFRP4 WILD-TYPE 207  33
  SFRP4 MUTATED SFRP4 WILD-TYPE 
              8             240 
  SFRP4 MUTATED SFRP4 WILD-TYPE 
              0              33 
$`SFRP4 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AX-A05Z TCGA-B5-A11E TCGA-BG-A0VZ TCGA-BS-A0UV 
      129.80        86.07        71.51        59.84        52.64        73.25 
TCGA-D1-A16Y TCGA-DI-A0WH 
       17.49        16.31 

$`SFRP4 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       57.76        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        44.78        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       52.01        34.29        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       85.84        82.39        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
        3.65        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       22.92        13.22        18.25        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  SFRP4 MUTATED SFRP4 WILD-TYPE 
          16.31            0.56 
  SFRP4 MUTATED SFRP4 WILD-TYPE 
         129.80          185.79 
  SFRP4 MUTATED SFRP4 WILD-TYPE 
         65.675          35.560 
[1] "16.3 - 129.8 (65.7)" "0.6 - 185.8 (35.6)" 
[1] "hr="     "2.7e+07"
D116V2, binary
                 cls
clus                0   1
  SFRP4 MUTATED     6   2
  SFRP4 WILD-TYPE 151  89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRP4 MUTATED      6    2
  SFRP4 WILD-TYPE  151   89
     clus
vv    SFRP4 MUTATED SFRP4 WILD-TYPE
  NO              6             151
  YES             2              89
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SFRP4 MUTATED                                         8
  SFRP4 WILD-TYPE                                     192
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  SFRP4 MUTATED                               0
  SFRP4 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  SFRP4 MUTATED                                   0
  SFRP4 WILD-TYPE                                44
D116V3, multiclass
                                         clus
vv                                        SFRP4 MUTATED SFRP4 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             8             192
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SFRP4 MUTATED     5   1   0   1
  SFRP4 WILD-TYPE 167   9   7  17
D116V4, multiclass
    clus
vv   SFRP4 MUTATED SFRP4 WILD-TYPE
  R0             5             167
  R1             1               9
  R2             0               7
  RX             1              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"

Clustering(117) Variable = TXNRD1 MUTATION ANALYSIS
D117V1, survival
                  sevent
clus2                0   1
  TXNRD1 MUTATED     8   0
  TXNRD1 WILD-TYPE 207  33
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
               8              240 
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
               0               33 
$`TXNRD1 MUTATED`
TCGA-AP-A0LF TCGA-AP-A051 TCGA-AP-A0LD TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY 
       93.99       129.80       117.99        40.11        77.39        69.27 
TCGA-B5-A11E TCGA-D1-A17Q 
       59.84         1.78 

$`TXNRD1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A1CP 
       88.18        60.53       110.63        57.80        67.66        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       29.06        28.77        42.35        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LE TCGA-AP-A0LG 
       23.87        20.91        48.79       125.42       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       61.08        35.74        37.78        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        55.30        86.01        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       27.85        13.45       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        92.88       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        86.93        72.72        73.25        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       10.22         1.51        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
            1.78             0.56 
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
          129.80           185.79 
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
           73.33            35.36 
[1] "1.8 - 129.8 (73.3)" "0.6 - 185.8 (35.4)"
[1] "hr="     "2.9e+07"
D117V2, binary
                  cls
clus                 0   1
  TXNRD1 MUTATED     7   1
  TXNRD1 WILD-TYPE 150  90
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNRD1 MUTATED      7    1
  TXNRD1 WILD-TYPE  150   90
     clus
vv    TXNRD1 MUTATED TXNRD1 WILD-TYPE
  NO               7              150
  YES              1               90
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  TXNRD1 MUTATED                                         8
  TXNRD1 WILD-TYPE                                     192
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  TXNRD1 MUTATED                               0
  TXNRD1 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  TXNRD1 MUTATED                                   0
  TXNRD1 WILD-TYPE                                44
D117V3, multiclass
                                         clus
vv                                        TXNRD1 MUTATED TXNRD1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              8              192
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TXNRD1 MUTATED     5   0   1   0
  TXNRD1 WILD-TYPE 167  10   6  18
D117V4, multiclass
    clus
vv   TXNRD1 MUTATED TXNRD1 WILD-TYPE
  R0              5              167
  R1              0               10
  R2              1                6
  RX              0               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"

Clustering(118) Variable = LETMD1 MUTATION ANALYSIS
D118V1, survival
                  sevent
clus2                0   1
  LETMD1 MUTATED     6   0
  LETMD1 WILD-TYPE 209  33
  LETMD1 MUTATED LETMD1 WILD-TYPE 
               6              242 
  LETMD1 MUTATED LETMD1 WILD-TYPE 
               0               33 
$`LETMD1 MUTATED`
TCGA-AP-A051 TCGA-AX-A05Z TCGA-AX-A0J1 TCGA-B5-A11E TCGA-BS-A0UF TCGA-BS-A0V8 
      129.80        71.51        77.39        59.84        85.84        83.64 

$`LETMD1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       88.24        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 
       60.66        61.08        35.74        37.78        40.11        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       57.76        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        44.78        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        82.39        81.57        86.93        72.72        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       89.59        63.58        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  LETMD1 MUTATED LETMD1 WILD-TYPE 
           59.84             0.56 
  LETMD1 MUTATED LETMD1 WILD-TYPE 
          129.80           185.79 
  LETMD1 MUTATED LETMD1 WILD-TYPE 
          80.515           35.360 
[1] "59.8 - 129.8 (80.5)" "0.6 - 185.8 (35.4)" 
[1] "hr="     "2.7e+07"
D118V2, binary
                  cls
clus                 0   1
  LETMD1 MUTATED     4   2
  LETMD1 WILD-TYPE 153  89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LETMD1 MUTATED      4    2
  LETMD1 WILD-TYPE  153   89
     clus
vv    LETMD1 MUTATED LETMD1 WILD-TYPE
  NO               4              153
  YES              2               89
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  LETMD1 MUTATED                                         6
  LETMD1 WILD-TYPE                                     194
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  LETMD1 MUTATED                               0
  LETMD1 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  LETMD1 MUTATED                                   0
  LETMD1 WILD-TYPE                                44
D118V3, multiclass
                                         clus
vv                                        LETMD1 MUTATED LETMD1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              6              194
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LETMD1 MUTATED     3   2   0   0
  LETMD1 WILD-TYPE 169   8   7  18
D118V4, multiclass
    clus
vv   LETMD1 MUTATED LETMD1 WILD-TYPE
  R0              3              169
  R1              2                8
  R2              0                7
  RX              0               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"

Clustering(119) Variable = ZNF721 MUTATION ANALYSIS
D119V1, survival
                  sevent
clus2                0   1
  ZNF721 MUTATED    13   0
  ZNF721 WILD-TYPE 202  33
  ZNF721 MUTATED ZNF721 WILD-TYPE 
              13              235 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
               0               33 
$`ZNF721 MUTATED`
TCGA-A5-A0GP TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       46.55        86.07        48.03        27.12        71.51        40.11 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-BG-A187 TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 
       69.27        59.84        14.73        85.84        73.25        21.99 
TCGA-D1-A16X 
        3.65 

$`ZNF721 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        80.55        88.24        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       37.78        77.39        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       13.45       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       44.78        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       56.58        14.83        13.78        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       92.88       114.90        82.39        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  ZNF721 MUTATED ZNF721 WILD-TYPE 
            3.65             0.56 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
           86.07           185.79 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
           48.03            35.38 
[1] "3.6 - 86.1 (48.0)"  "0.6 - 185.8 (35.4)"
[1] "hr="     "2.7e+07"
D119V2, binary
                  cls
clus                 0   1
  ZNF721 MUTATED    10   3
  ZNF721 WILD-TYPE 147  88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF721 MUTATED     10    3
  ZNF721 WILD-TYPE  147   88
     clus
vv    ZNF721 MUTATED ZNF721 WILD-TYPE
  NO              10              147
  YES              3               88
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZNF721 MUTATED                                        13
  ZNF721 WILD-TYPE                                     187
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ZNF721 MUTATED                               0
  ZNF721 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZNF721 MUTATED                                   0
  ZNF721 WILD-TYPE                                44
D119V3, multiclass
                                         clus
vv                                        ZNF721 MUTATED ZNF721 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             13              187
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF721 MUTATED    10   1   0   0
  ZNF721 WILD-TYPE 162   9   7  18
D119V4, multiclass
    clus
vv   ZNF721 MUTATED ZNF721 WILD-TYPE
  R0             10              162
  R1              1                9
  R2              0                7
  RX              0               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"

Clustering(120) Variable = RASSF9 MUTATION ANALYSIS
D120V1, survival
                  sevent
clus2                0   1
  RASSF9 MUTATED     9   0
  RASSF9 WILD-TYPE 206  33
  RASSF9 MUTATED RASSF9 WILD-TYPE 
               9              239 
  RASSF9 MUTATED RASSF9 WILD-TYPE 
               0               33 
$`RASSF9 MUTATED`
TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-BS-A0UJ 
       86.07        27.12        71.51        40.11        69.27        82.39 
TCGA-BS-A0UM TCGA-BS-A0UV TCGA-D1-A17Q 
       86.93        73.25         1.78 

$`RASSF9 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       61.08        35.74        37.78        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       71.24        56.91        86.37        55.30        86.01        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       85.84        81.57        72.72        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.51        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  RASSF9 MUTATED RASSF9 WILD-TYPE 
            1.78             0.56 
  RASSF9 MUTATED RASSF9 WILD-TYPE 
           86.93           185.79 
  RASSF9 MUTATED RASSF9 WILD-TYPE 
           71.51            35.38 
[1] "1.8 - 86.9 (71.5)"  "0.6 - 185.8 (35.4)"
[1] "hr="     "2.6e+07"
D120V2, binary
                  cls
clus                 0   1
  RASSF9 MUTATED     8   1
  RASSF9 WILD-TYPE 149  90
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASSF9 MUTATED      8    1
  RASSF9 WILD-TYPE  149   90
     clus
vv    RASSF9 MUTATED RASSF9 WILD-TYPE
  NO               8              149
  YES              1               90
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  RASSF9 MUTATED                                         9
  RASSF9 WILD-TYPE                                     191
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  RASSF9 MUTATED                               0
  RASSF9 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  RASSF9 MUTATED                                   0
  RASSF9 WILD-TYPE                                44
D120V3, multiclass
                                         clus
vv                                        RASSF9 MUTATED RASSF9 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              9              191
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RASSF9 MUTATED     7   1   0   0
  RASSF9 WILD-TYPE 165   9   7  18
D120V4, multiclass
    clus
vv   RASSF9 MUTATED RASSF9 WILD-TYPE
  R0              7              165
  R1              1                9
  R2              0                7
  RX              0               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"

Clustering(121) Variable = AGXT2 MUTATION ANALYSIS
D121V1, survival
                 sevent
clus2               0   1
  AGXT2 MUTATED     9   2
  AGXT2 WILD-TYPE 206  31
  AGXT2 MUTATED AGXT2 WILD-TYPE 
             11             237 
  AGXT2 MUTATED AGXT2 WILD-TYPE 
              2              31 
$`AGXT2 MUTATED`
TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A05N TCGA-AP-A0LM TCGA-AX-A05Z 
       42.35       129.80        86.07        23.87        27.12        71.51 
TCGA-AX-A0J0 TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A16X TCGA-D1-A17R 
       40.11        73.25        21.99         3.65        11.15 

$`AGXT2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       24.62        29.06        28.77        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05P 
       23.31        48.03        63.91        45.53        36.89        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        46.72        83.97        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       80.78        49.22        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        80.55        88.24        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       77.39        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       55.30        86.01        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        92.88       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        86.93        72.72        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W 
       28.67        23.93        22.55         1.74        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
       10.65         0.69        18.67        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  AGXT2 MUTATED AGXT2 WILD-TYPE 
           3.65            0.56 
  AGXT2 MUTATED AGXT2 WILD-TYPE 
         129.80          185.79 
  AGXT2 MUTATED AGXT2 WILD-TYPE 
          40.11           35.90 
[1] "3.6 - 129.8 (40.1)" "0.6 - 185.8 (35.9)"
[1] "hr=" "1.2"
D121V2, binary
                 cls
clus                0   1
  AGXT2 MUTATED     8   3
  AGXT2 WILD-TYPE 149  88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGXT2 MUTATED      8    3
  AGXT2 WILD-TYPE  149   88
     clus
vv    AGXT2 MUTATED AGXT2 WILD-TYPE
  NO              8             149
  YES             3              88
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AGXT2 MUTATED                                        11
  AGXT2 WILD-TYPE                                     189
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  AGXT2 MUTATED                               0
  AGXT2 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  AGXT2 MUTATED                                   0
  AGXT2 WILD-TYPE                                44
D121V3, multiclass
                                         clus
vv                                        AGXT2 MUTATED AGXT2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            11             189
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AGXT2 MUTATED    10   1   0   0
  AGXT2 WILD-TYPE 162   9   7  18
D121V4, multiclass
    clus
vv   AGXT2 MUTATED AGXT2 WILD-TYPE
  R0            10             162
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(122) Variable = MECOM MUTATION ANALYSIS
D122V1, survival
                 sevent
clus2               0   1
  MECOM MUTATED    12   0
  MECOM WILD-TYPE 203  33
  MECOM MUTATED MECOM WILD-TYPE 
             12             236 
  MECOM MUTATED MECOM WILD-TYPE 
              0              33 
$`MECOM MUTATED`
TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A0J1 TCGA-B5-A0JR 
       42.35       129.80        86.07        48.03        77.39        56.91 
TCGA-B5-A11G TCGA-B5-A11V TCGA-BG-A0VV TCGA-D1-A103 TCGA-D1-A161 TCGA-D1-A165 
      113.36        19.56        51.06        21.99        29.33         0.66 

$`MECOM WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       24.62        29.06        28.77        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       23.31        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        40.11        34.65        25.51        71.24 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       86.37        55.30        86.01        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11I 
       27.85        13.45        59.84       185.79        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        16.73        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       15.42        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       92.88       114.90        85.84        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       72.72        73.25        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93        22.55         1.74        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
        1.91         3.68        32.58        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  MECOM MUTATED MECOM WILD-TYPE 
           0.66            0.56 
  MECOM MUTATED MECOM WILD-TYPE 
         129.80          185.79 
  MECOM MUTATED MECOM WILD-TYPE 
         49.545          35.560 
[1] "0.7 - 129.8 (49.5)" "0.6 - 185.8 (35.6)"
[1] "hr="     "2.9e+07"
D122V2, binary
                 cls
clus                0   1
  MECOM MUTATED     9   3
  MECOM WILD-TYPE 148  88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MECOM MUTATED      9    3
  MECOM WILD-TYPE  148   88
     clus
vv    MECOM MUTATED MECOM WILD-TYPE
  NO              9             148
  YES             3              88
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MECOM MUTATED                                        12
  MECOM WILD-TYPE                                     188
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  MECOM MUTATED                               0
  MECOM WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  MECOM MUTATED                                   0
  MECOM WILD-TYPE                                44
D122V3, multiclass
                                         clus
vv                                        MECOM MUTATED MECOM WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            12             188
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MECOM MUTATED     9   0   0   0
  MECOM WILD-TYPE 163  10   7  18
D122V4, multiclass
    clus
vv   MECOM MUTATED MECOM WILD-TYPE
  R0             9             163
  R1             0              10
  R2             0               7
  RX             0              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"

Clustering(123) Variable = ATP6V1C2 MUTATION ANALYSIS
D123V1, survival
                    sevent
clus2                  0   1
  ATP6V1C2 MUTATED    12   0
  ATP6V1C2 WILD-TYPE 203  33
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
                12                236 
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
                 0                 33 
$`ATP6V1C2 MUTATED`
TCGA-AP-A051 TCGA-AP-A0LG TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11J 
      129.80        66.25        27.12        40.11        69.27        54.44 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A17M TCGA-D1-A17Q TCGA-D1-A17S 
       85.84        82.39        73.25        10.22         1.78        24.30 

$`ATP6V1C2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
      110.37        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       61.08        35.74        37.78        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       71.24        56.91        86.37        55.30        86.01        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       88.34        75.72        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UL 
       96.49        30.74        97.41        92.88       114.90        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69        18.67         3.65        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17N TCGA-D1-A17R 
        1.28        28.01        28.08        26.37         1.51        11.15 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
              1.78               0.56 
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
            129.80             185.79 
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
            60.345             35.560 
[1] "1.8 - 129.8 (60.3)" "0.6 - 185.8 (35.6)"
[1] "hr="     "2.7e+07"
D123V2, binary
                    cls
clus                   0   1
  ATP6V1C2 MUTATED     8   4
  ATP6V1C2 WILD-TYPE 149  87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1C2 MUTATED      8    4
  ATP6V1C2 WILD-TYPE  149   87
     clus
vv    ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  NO                 8                149
  YES                4                 87
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ATP6V1C2 MUTATED                                        12
  ATP6V1C2 WILD-TYPE                                     188
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  ATP6V1C2 MUTATED                               0
  ATP6V1C2 WILD-TYPE                             4
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  ATP6V1C2 MUTATED                                   0
  ATP6V1C2 WILD-TYPE                                44
D123V3, multiclass
                                         clus
vv                                        ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               12                188
  MIXED SEROUS AND ENDOMETRIOID                          0                  4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      0                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ATP6V1C2 MUTATED    10   0   0   0
  ATP6V1C2 WILD-TYPE 162  10   7  18
D123V4, multiclass
    clus
vv   ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  R0               10                162
  R1                0                 10
  R2                0                  7
  RX                0                 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"

Clustering(124) Variable = DYM MUTATION ANALYSIS
D124V1, survival
               sevent
clus2             0   1
  DYM MUTATED     9   1
  DYM WILD-TYPE 206  32
  DYM MUTATED DYM WILD-TYPE 
           10           238 
  DYM MUTATED DYM WILD-TYPE 
            1            32 
$`DYM MUTATED`
TCGA-A5-A0GP TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A0K9 
       46.55        86.07        48.03        40.11        69.27        13.45 
TCGA-B5-A11N TCGA-D1-A103 TCGA-D1-A15X TCGA-D1-A17Q 
       61.68        21.99        29.88         1.78 

$`DYM WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       61.08        35.74        37.78        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       71.24        56.91        86.37        55.30        86.01        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        59.84       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       75.72        54.44        44.78        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        92.88       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        86.93        72.72        73.25        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V 
        4.87        28.67        23.93        22.55         1.74        39.48 
TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       30.08         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69        18.67         3.65        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  DYM MUTATED DYM WILD-TYPE 
         1.78          0.56 
  DYM MUTATED DYM WILD-TYPE 
        86.07        185.79 
  DYM MUTATED DYM WILD-TYPE 
        43.33         35.82 
[1] "1.8 - 86.1 (43.3)"  "0.6 - 185.8 (35.8)"
[1] "hr=" "1.2"
D124V2, binary
               cls
clus              0   1
  DYM MUTATED     7   3
  DYM WILD-TYPE 150  88
[1] "tbl2"
               cls
clus            [,1] [,2]
  DYM MUTATED      7    3
  DYM WILD-TYPE  150   88
     clus
vv    DYM MUTATED DYM WILD-TYPE
  NO            7           150
  YES           3            88
[1] 2 2
[1] FALSE
               vv
clus            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DYM MUTATED                                         9
  DYM WILD-TYPE                                     191
               vv
clus            MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  DYM MUTATED                               0                                 1
  DYM WILD-TYPE                             4                                43
D124V3, multiclass
                                         clus
vv                                        DYM MUTATED DYM WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           9           191
  MIXED SEROUS AND ENDOMETRIOID                     0             4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                 1            43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  DYM MUTATED     7   0   0   0
  DYM WILD-TYPE 165  10   7  18
D124V4, multiclass
    clus
vv   DYM MUTATED DYM WILD-TYPE
  R0           7           165
  R1           0            10
  R2           0             7
  RX           0            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"

Clustering(125) Variable = TAB3 MUTATION ANALYSIS
D125V1, survival
                sevent
clus2              0   1
  TAB3 MUTATED    18   0
  TAB3 WILD-TYPE 197  33
  TAB3 MUTATED TAB3 WILD-TYPE 
            18            230 
  TAB3 MUTATED TAB3 WILD-TYPE 
             0             33 
$`TAB3 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A063 TCGA-AX-A06H 
      129.80        48.03        27.12        71.51        79.46        27.39 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-BS-A0UF TCGA-BS-A0UL TCGA-BS-A0UV 
       40.11        77.39        69.27        85.84        81.57        73.25 
TCGA-BS-A0WQ TCGA-D1-A0ZV TCGA-D1-A103 TCGA-D1-A174 TCGA-D1-A17D TCGA-D1-A17Q 
       66.48        23.93        21.99        19.53        30.44         1.78 

$`TAB3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        86.07        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       45.99        49.87        60.66        61.08        35.74        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       86.01        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       92.88       114.90        82.39        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       63.58        83.64        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W 
        4.87        28.67        22.55         1.74        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A176 
       10.65         0.69        18.67         3.65        17.49        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17F TCGA-D1-A17H 
       18.02         1.58         7.00         0.99         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  TAB3 MUTATED TAB3 WILD-TYPE 
          1.78           0.56 
  TAB3 MUTATED TAB3 WILD-TYPE 
        129.80         185.79 
  TAB3 MUTATED TAB3 WILD-TYPE 
        57.255         35.560 
[1] "1.8 - 129.8 (57.3)" "0.6 - 185.8 (35.6)"
[1] "hr="     "7.7e+07"
D125V2, binary
                cls
clus               0   1
  TAB3 MUTATED    13   5
  TAB3 WILD-TYPE 144  86
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB3 MUTATED     13    5
  TAB3 WILD-TYPE  144   86
     clus
vv    TAB3 MUTATED TAB3 WILD-TYPE
  NO            13            144
  YES            5             86
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  TAB3 MUTATED                                        18
  TAB3 WILD-TYPE                                     182
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  TAB3 MUTATED                               0
  TAB3 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  TAB3 MUTATED                                   0
  TAB3 WILD-TYPE                                44
D125V3, multiclass
                                         clus
vv                                        TAB3 MUTATED TAB3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           18            182
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TAB3 MUTATED    15   2   0   0
  TAB3 WILD-TYPE 157   8   7  18
D125V4, multiclass
    clus
vv   TAB3 MUTATED TAB3 WILD-TYPE
  R0           15            157
  R1            2              8
  R2            0              7
  RX            0             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"

Clustering(126) Variable = ZNF649 MUTATION ANALYSIS
D126V1, survival
                  sevent
clus2                0   1
  ZNF649 MUTATED    14   0
  ZNF649 WILD-TYPE 201  33
  ZNF649 MUTATED ZNF649 WILD-TYPE 
              14              234 
  ZNF649 MUTATED ZNF649 WILD-TYPE 
               0               33 
$`ZNF649 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
      129.80        86.07        48.03        27.12        71.51        40.11 
TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A0K2 TCGA-BS-A0TC TCGA-D1-A103 TCGA-D1-A16X 
       77.39        69.27        72.62        85.55        21.99         3.65 
TCGA-D1-A16Y TCGA-D1-A17Q 
       17.49         1.78 

$`ZNF649 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        80.55        88.24        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       37.78        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K3 
       55.30        86.01        71.44        48.59        36.49        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       24.99        46.95        24.33        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
      114.90        85.84        82.39        81.57        86.93        72.72 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       73.25        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       22.55         1.74        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       18.67        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       10.22         1.51        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  ZNF649 MUTATED ZNF649 WILD-TYPE 
            1.78             0.56 
  ZNF649 MUTATED ZNF649 WILD-TYPE 
          129.80           185.79 
  ZNF649 MUTATED ZNF649 WILD-TYPE 
           58.65            35.56 
[1] "1.8 - 129.8 (58.6)" "0.6 - 185.8 (35.6)"
[1] "hr="     "2.7e+07"
D126V2, binary
                  cls
clus                 0   1
  ZNF649 MUTATED    11   3
  ZNF649 WILD-TYPE 146  88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF649 MUTATED     11    3
  ZNF649 WILD-TYPE  146   88
     clus
vv    ZNF649 MUTATED ZNF649 WILD-TYPE
  NO              11              146
  YES              3               88
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZNF649 MUTATED                                        14
  ZNF649 WILD-TYPE                                     186
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ZNF649 MUTATED                               0
  ZNF649 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZNF649 MUTATED                                   0
  ZNF649 WILD-TYPE                                44
D126V3, multiclass
                                         clus
vv                                        ZNF649 MUTATED ZNF649 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             14              186
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF649 MUTATED    10   1   0   1
  ZNF649 WILD-TYPE 162   9   7  17
D126V4, multiclass
    clus
vv   ZNF649 MUTATED ZNF649 WILD-TYPE
  R0             10              162
  R1              1                9
  R2              0                7
  RX              1               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"

Clustering(127) Variable = FN1 MUTATION ANALYSIS
D127V1, survival
               sevent
clus2             0   1
  FN1 MUTATED    23   1
  FN1 WILD-TYPE 192  32
  FN1 MUTATED FN1 WILD-TYPE 
           24           224 
  FN1 MUTATED FN1 WILD-TYPE 
            1            32 
$`FN1 MUTATED`
TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM 
       42.35       129.80        23.31        86.07        48.03        27.12 
TCGA-AX-A05Z TCGA-AX-A0J1 TCGA-B5-A0JR TCGA-B5-A0JY TCGA-B5-A11N TCGA-BG-A0M4 
       71.51        77.39        56.91        69.27        61.68        71.24 
TCGA-BG-A0MQ TCGA-BG-A0VW TCGA-BG-A18C TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A101 
       59.74        52.01        15.45        85.84        73.25         1.74 
TCGA-D1-A103 TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A17D TCGA-D1-A17Q TCGA-DI-A0WH 
       21.99        17.49        19.53        30.44         1.78        16.31 

$`FN1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       24.62        29.06        28.77        15.95        20.25        21.99 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       63.91        45.53        36.89        23.87        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       49.22        25.08        46.78        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       80.55        88.24        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        61.08        35.74        37.78        40.11 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       34.65        25.51        71.24        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O 
      113.36        88.34        75.72        54.44        44.78        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M7 
       18.61        20.19        19.33        20.94        35.21        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MT 
       74.63        41.52        48.56        23.47        43.04        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       20.28        15.42        51.06        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       92.88       114.90        82.39        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17F 
       30.15        18.02         1.58         7.00         0.99         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A1NN 
       24.30         2.33        22.92        13.22        18.25        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  FN1 MUTATED FN1 WILD-TYPE 
         1.74          0.56 
  FN1 MUTATED FN1 WILD-TYPE 
       129.80        185.79 
  FN1 MUTATED FN1 WILD-TYPE 
        50.02         35.56 
[1] "1.7 - 129.8 (50.0)" "0.6 - 185.8 (35.6)"
[1] "hr=" "3.8"
D127V2, binary
               cls
clus              0   1
  FN1 MUTATED    16   8
  FN1 WILD-TYPE 141  83
[1] "tbl2"
               cls
clus            [,1] [,2]
  FN1 MUTATED     16    8
  FN1 WILD-TYPE  141   83
     clus
vv    FN1 MUTATED FN1 WILD-TYPE
  NO           16           141
  YES           8            83
[1] 2 2
[1] FALSE
               vv
clus            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  FN1 MUTATED                                        24
  FN1 WILD-TYPE                                     176
               vv
clus            MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  FN1 MUTATED                               0                                 0
  FN1 WILD-TYPE                             4                                44
D127V3, multiclass
                                         clus
vv                                        FN1 MUTATED FN1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA          24           176
  MIXED SEROUS AND ENDOMETRIOID                     0             4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                 0            44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  FN1 MUTATED    16   2   0   3
  FN1 WILD-TYPE 156   8   7  15
D127V4, multiclass
    clus
vv   FN1 MUTATED FN1 WILD-TYPE
  R0          16           156
  R1           2             8
  R2           0             7
  RX           3            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"

Clustering(128) Variable = CCDC150 MUTATION ANALYSIS
D128V1, survival
                   sevent
clus2                 0   1
  CCDC150 MUTATED    11   0
  CCDC150 WILD-TYPE 204  33
  CCDC150 MUTATED CCDC150 WILD-TYPE 
               11               237 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
                0                33 
$`CCDC150 MUTATED`
TCGA-A5-A0GQ TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-BG-A0M9 TCGA-BS-A0UF 
       73.87        86.07        27.12        40.11        74.63        85.84 
TCGA-D1-A103 TCGA-D1-A15X TCGA-D1-A16F TCGA-D1-A177 TCGA-D1-A17Q 
       21.99        29.88         2.63        18.02         1.78 

$`CCDC150 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        46.55        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       61.08        35.74        37.78        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       71.24        56.91        86.37        55.30        86.01        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        44.78        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       71.24        63.68        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 
       82.39        81.57        86.93        72.72        73.25        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       39.48        30.08         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69        18.67         3.65        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       30.15         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  CCDC150 MUTATED CCDC150 WILD-TYPE 
             1.78              0.56 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
            86.07            185.79 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
            29.88             35.90 
[1] "1.8 - 86.1 (29.9)"  "0.6 - 185.8 (35.9)"
[1] "hr="     "2.6e+07"
D128V2, binary
                   cls
clus                  0   1
  CCDC150 MUTATED     8   3
  CCDC150 WILD-TYPE 149  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      8    3
  CCDC150 WILD-TYPE  149   88
     clus
vv    CCDC150 MUTATED CCDC150 WILD-TYPE
  NO                8               149
  YES               3                88
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CCDC150 MUTATED                                        10
  CCDC150 WILD-TYPE                                     190
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  CCDC150 MUTATED                               0
  CCDC150 WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  CCDC150 MUTATED                                   1
  CCDC150 WILD-TYPE                                43
D128V3, multiclass
                                         clus
vv                                        CCDC150 MUTATED CCDC150 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              10               190
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     1                43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CCDC150 MUTATED    11   0   0   0
  CCDC150 WILD-TYPE 161  10   7  18
D128V4, multiclass
    clus
vv   CCDC150 MUTATED CCDC150 WILD-TYPE
  R0              11               161
  R1               0                10
  R2               0                 7
  RX               0                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"

Clustering(129) Variable = KIF21A MUTATION ANALYSIS
D129V1, survival
                  sevent
clus2                0   1
  KIF21A MUTATED    15   0
  KIF21A WILD-TYPE 200  33
  KIF21A MUTATED KIF21A WILD-TYPE 
              15              233 
  KIF21A MUTATED KIF21A WILD-TYPE 
               0               33 
$`KIF21A MUTATED`
TCGA-A5-A0VP TCGA-AP-A056 TCGA-AP-A0LD TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY 
       42.35        86.07       117.99        71.51        40.11        69.27 
TCGA-B5-A11E TCGA-B5-A11N TCGA-BG-A0M0 TCGA-BS-A0UF TCGA-BS-A0UL TCGA-D1-A103 
       59.84        61.68        19.33        85.84        81.57        21.99 
TCGA-D1-A167 TCGA-D1-A16X TCGA-D1-A17Q 
       15.72         3.65         1.78 

$`KIF21A WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       24.62        29.06        28.77        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LE TCGA-AP-A0LG 
       23.87        20.91        48.79       125.42       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        55.30        86.01        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       27.85        13.45       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       54.44        44.78        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M2 
       16.57        50.89        11.87        18.61        20.19        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       92.88       114.90        82.39        86.93        72.72        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       29.33        32.58         0.66        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y 
       31.07        33.63        10.65         0.69        18.67        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.51        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  KIF21A MUTATED KIF21A WILD-TYPE 
            1.78             0.56 
  KIF21A MUTATED KIF21A WILD-TYPE 
          117.99           185.79 
  KIF21A MUTATED KIF21A WILD-TYPE 
           59.84            35.38 
[1] "1.8 - 118.0 (59.8)" "0.6 - 185.8 (35.4)"
[1] "hr="     "7.5e+07"
D129V2, binary
                  cls
clus                 0   1
  KIF21A MUTATED    13   2
  KIF21A WILD-TYPE 144  89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED     13    2
  KIF21A WILD-TYPE  144   89
     clus
vv    KIF21A MUTATED KIF21A WILD-TYPE
  NO              13              144
  YES              2               89
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  KIF21A MUTATED                                        15
  KIF21A WILD-TYPE                                     185
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  KIF21A MUTATED                               0
  KIF21A WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  KIF21A MUTATED                                   0
  KIF21A WILD-TYPE                                44
D129V3, multiclass
                                         clus
vv                                        KIF21A MUTATED KIF21A WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             15              185
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KIF21A MUTATED    11   1   0   0
  KIF21A WILD-TYPE 161   9   7  18
D129V4, multiclass
    clus
vv   KIF21A MUTATED KIF21A WILD-TYPE
  R0             11              161
  R1              1                9
  R2              0                7
  RX              0               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"

Clustering(130) Variable = BHLHB9 MUTATION ANALYSIS
D130V1, survival
                  sevent
clus2                0   1
  BHLHB9 MUTATED     8   0
  BHLHB9 WILD-TYPE 207  33
  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
               8              240 
  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
               0               33 
$`BHLHB9 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-BG-A0LX TCGA-BS-A0UV 
      129.80        48.03        40.11        69.27        20.19        73.25 
TCGA-D1-A103 TCGA-D1-A16Y 
       21.99        17.49 

$`BHLHB9 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        86.07        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       71.51        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        61.08        35.74        37.78        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        44.78        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       11.87        18.61        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       85.84        82.39        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
           17.49             0.56 
  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
          129.80           185.79 
  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
           44.07            35.82 
[1] "17.5 - 129.8 (44.1)" "0.6 - 185.8 (35.8)" 
[1] "hr="     "2.6e+07"
D130V2, binary
                  cls
clus                 0   1
  BHLHB9 MUTATED     5   3
  BHLHB9 WILD-TYPE 152  88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BHLHB9 MUTATED      5    3
  BHLHB9 WILD-TYPE  152   88
     clus
vv    BHLHB9 MUTATED BHLHB9 WILD-TYPE
  NO               5              152
  YES              3               88
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  BHLHB9 MUTATED                                         8
  BHLHB9 WILD-TYPE                                     192
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  BHLHB9 MUTATED                               0
  BHLHB9 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  BHLHB9 MUTATED                                   0
  BHLHB9 WILD-TYPE                                44
D130V3, multiclass
                                         clus
vv                                        BHLHB9 MUTATED BHLHB9 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              8              192
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  BHLHB9 MUTATED     6   0   0   1
  BHLHB9 WILD-TYPE 166  10   7  17
D130V4, multiclass
    clus
vv   BHLHB9 MUTATED BHLHB9 WILD-TYPE
  R0              6              166
  R1              0               10
  R2              0                7
  RX              1               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"

Clustering(131) Variable = EXOSC9 MUTATION ANALYSIS
D131V1, survival
                  sevent
clus2                0   1
  EXOSC9 MUTATED     9   1
  EXOSC9 WILD-TYPE 206  32
  EXOSC9 MUTATED EXOSC9 WILD-TYPE 
              10              238 
  EXOSC9 MUTATED EXOSC9 WILD-TYPE 
               1               32 
$`EXOSC9 MUTATED`
TCGA-D1-A0ZO TCGA-A5-A0VP TCGA-AP-A056 TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 
       19.79        42.35        86.07        71.51        40.11        77.39 
TCGA-B5-A0JY TCGA-B5-A0K9 TCGA-BS-A0UV TCGA-D1-A17Q 
       69.27        13.45        73.25         1.78 

$`EXOSC9 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       51.55        12.56         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 
       29.06        28.77        15.95        20.25       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        48.03        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       35.74        37.78        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       44.78        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       31.00        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        92.88       114.90        85.84        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69        18.67         3.65        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  EXOSC9 MUTATED EXOSC9 WILD-TYPE 
            1.78             0.56 
  EXOSC9 MUTATED EXOSC9 WILD-TYPE 
           86.07           185.79 
  EXOSC9 MUTATED EXOSC9 WILD-TYPE 
           55.81            35.56 
[1] "1.8 - 86.1 (55.8)"  "0.6 - 185.8 (35.6)"
[1] "hr=" "1.4"
D131V2, binary
                  cls
clus                 0   1
  EXOSC9 MUTATED     8   2
  EXOSC9 WILD-TYPE 149  89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EXOSC9 MUTATED      8    2
  EXOSC9 WILD-TYPE  149   89
     clus
vv    EXOSC9 MUTATED EXOSC9 WILD-TYPE
  NO               8              149
  YES              2               89
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  EXOSC9 MUTATED                                        10
  EXOSC9 WILD-TYPE                                     190
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  EXOSC9 MUTATED                               0
  EXOSC9 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  EXOSC9 MUTATED                                   0
  EXOSC9 WILD-TYPE                                44
D131V3, multiclass
                                         clus
vv                                        EXOSC9 MUTATED EXOSC9 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             10              190
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  EXOSC9 MUTATED     7   1   0   0
  EXOSC9 WILD-TYPE 165   9   7  18
D131V4, multiclass
    clus
vv   EXOSC9 MUTATED EXOSC9 WILD-TYPE
  R0              7              165
  R1              1                9
  R2              0                7
  RX              0               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"

Clustering(132) Variable = ZKSCAN1 MUTATION ANALYSIS
D132V1, survival
                   sevent
clus2                 0   1
  ZKSCAN1 MUTATED     7   0
  ZKSCAN1 WILD-TYPE 208  33
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                7               241 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                0                33 
$`ZKSCAN1 MUTATED`
TCGA-AP-A059 TCGA-AX-A0J1 TCGA-BG-A18B TCGA-BS-A0UF TCGA-D1-A103 TCGA-D1-A15X 
       48.03        77.39        15.45        85.84        21.99        29.88 
TCGA-D1-A163 
       32.58 

$`ZKSCAN1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        61.08        35.74        37.78        40.11 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       86.01        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       44.78        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18C 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       92.88       114.90        82.39        81.57        86.93        72.72 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       73.25        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 
       22.55         1.74        39.48        30.08         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       29.33         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
            15.45              0.56 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
            85.84            185.79 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
            32.58             35.90 
[1] "15.4 - 85.8 (32.6)" "0.6 - 185.8 (35.9)"
[1] "hr="     "2.5e+07"
D132V2, binary
                   cls
clus                  0   1
  ZKSCAN1 MUTATED     4   3
  ZKSCAN1 WILD-TYPE 153  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN1 MUTATED      4    3
  ZKSCAN1 WILD-TYPE  153   88
     clus
vv    ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  NO                4               153
  YES               3                88
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZKSCAN1 MUTATED                                         6
  ZKSCAN1 WILD-TYPE                                     194
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  ZKSCAN1 MUTATED                               0
  ZKSCAN1 WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZKSCAN1 MUTATED                                   1
  ZKSCAN1 WILD-TYPE                                43
D132V3, multiclass
                                         clus
vv                                        ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               6               194
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     1                43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZKSCAN1 MUTATED     6   0   0   1
  ZKSCAN1 WILD-TYPE 166  10   7  17
D132V4, multiclass
    clus
vv   ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  R0               6               166
  R1               0                10
  R2               0                 7
  RX               1                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"

Clustering(133) Variable = OR8B8 MUTATION ANALYSIS
D133V1, survival
                 sevent
clus2               0   1
  OR8B8 MUTATED     7   0
  OR8B8 WILD-TYPE 208  33
  OR8B8 MUTATED OR8B8 WILD-TYPE 
              7             241 
  OR8B8 MUTATED OR8B8 WILD-TYPE 
              0              33 
$`OR8B8 MUTATED`
TCGA-A5-A0GH TCGA-AP-A059 TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0UV 
       74.10        48.03        71.51        69.27        59.84        73.25 
TCGA-D1-A17Q 
        1.78 

$`OR8B8 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        86.07        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       85.84        82.39        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       26.37        10.22         1.51        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  OR8B8 MUTATED OR8B8 WILD-TYPE 
           1.78            0.56 
  OR8B8 MUTATED OR8B8 WILD-TYPE 
          74.10          185.79 
  OR8B8 MUTATED OR8B8 WILD-TYPE 
          69.27           35.38 
[1] "1.8 - 74.1 (69.3)"  "0.6 - 185.8 (35.4)"
[1] "hr="     "2.6e+07"
D133V2, binary
                 cls
clus                0   1
  OR8B8 MUTATED     6   1
  OR8B8 WILD-TYPE 151  90
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8B8 MUTATED      6    1
  OR8B8 WILD-TYPE  151   90
     clus
vv    OR8B8 MUTATED OR8B8 WILD-TYPE
  NO              6             151
  YES             1              90
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  OR8B8 MUTATED                                         7
  OR8B8 WILD-TYPE                                     193
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  OR8B8 MUTATED                               0
  OR8B8 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  OR8B8 MUTATED                                   0
  OR8B8 WILD-TYPE                                44
D133V3, multiclass
                                         clus
vv                                        OR8B8 MUTATED OR8B8 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             7             193
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR8B8 MUTATED     4   1   0   0
  OR8B8 WILD-TYPE 168   9   7  18
D133V4, multiclass
    clus
vv   OR8B8 MUTATED OR8B8 WILD-TYPE
  R0             4             168
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(134) Variable = SENP7 MUTATION ANALYSIS
D134V1, survival
                 sevent
clus2               0   1
  SENP7 MUTATED    11   1
  SENP7 WILD-TYPE 204  32
  SENP7 MUTATED SENP7 WILD-TYPE 
             12             236 
  SENP7 MUTATED SENP7 WILD-TYPE 
              1              32 
$`SENP7 MUTATED`
TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A063 
      129.80        23.31        86.07        48.03        27.12        79.46 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0UV TCGA-D1-A103 
       40.11        77.39        69.27        59.84        73.25        21.99 

$`SENP7 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       21.99        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        46.72        83.97        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       80.78        49.22        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       86.01        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       57.76        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        44.78        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
      114.90        85.84        82.39        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  SENP7 MUTATED SENP7 WILD-TYPE 
          21.99            0.56 
  SENP7 MUTATED SENP7 WILD-TYPE 
         129.80          185.79 
  SENP7 MUTATED SENP7 WILD-TYPE 
         64.555          35.360 
[1] "22.0 - 129.8 (64.6)" "0.6 - 185.8 (35.4)" 
[1] "hr=" "2.4"
D134V2, binary
                 cls
clus                0   1
  SENP7 MUTATED     9   3
  SENP7 WILD-TYPE 148  88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP7 MUTATED      9    3
  SENP7 WILD-TYPE  148   88
     clus
vv    SENP7 MUTATED SENP7 WILD-TYPE
  NO              9             148
  YES             3              88
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SENP7 MUTATED                                        12
  SENP7 WILD-TYPE                                     188
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  SENP7 MUTATED                               0
  SENP7 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  SENP7 MUTATED                                   0
  SENP7 WILD-TYPE                                44
D134V3, multiclass
                                         clus
vv                                        SENP7 MUTATED SENP7 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            12             188
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SENP7 MUTATED     9   1   0   0
  SENP7 WILD-TYPE 163   9   7  18
D134V4, multiclass
    clus
vv   SENP7 MUTATED SENP7 WILD-TYPE
  R0             9             163
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(135) Variable = WDR65 MUTATION ANALYSIS
D135V1, survival
                 sevent
clus2               0   1
  WDR65 MUTATED     6   0
  WDR65 WILD-TYPE 209  33
  WDR65 MUTATED WDR65 WILD-TYPE 
              6             242 
  WDR65 MUTATED WDR65 WILD-TYPE 
              0              33 
$`WDR65 MUTATED`
TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11E TCGA-D1-A16X TCGA-D1-A17Q 
       27.12        40.11        69.27        59.84         3.65         1.78 

$`WDR65 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
      129.80        21.99        23.31        86.07        48.03        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89        23.87        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37        66.25        36.36        97.71        46.72 
TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       83.97        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        61.08        35.74        37.78        77.39 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       86.01        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       57.76        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        44.78        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
      114.90        85.84        82.39        81.57        86.93        72.72 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       73.25        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
        0.69        18.67        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  WDR65 MUTATED WDR65 WILD-TYPE 
           1.78            0.56 
  WDR65 MUTATED WDR65 WILD-TYPE 
          69.27          185.79 
  WDR65 MUTATED WDR65 WILD-TYPE 
         33.615          35.900 
[1] "1.8 - 69.3 (33.6)"  "0.6 - 185.8 (35.9)"
[1] "hr="     "9200000"
D135V2, binary
                 cls
clus                0   1
  WDR65 MUTATED     5   1
  WDR65 WILD-TYPE 152  90
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED      5    1
  WDR65 WILD-TYPE  152   90
     clus
vv    WDR65 MUTATED WDR65 WILD-TYPE
  NO              5             152
  YES             1              90
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  WDR65 MUTATED                                         6
  WDR65 WILD-TYPE                                     194
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  WDR65 MUTATED                               0
  WDR65 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  WDR65 MUTATED                                   0
  WDR65 WILD-TYPE                                44
D135V3, multiclass
                                         clus
vv                                        WDR65 MUTATED WDR65 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             6             194
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WDR65 MUTATED     4   0   0   0
  WDR65 WILD-TYPE 168  10   7  18
D135V4, multiclass
    clus
vv   WDR65 MUTATED WDR65 WILD-TYPE
  R0             4             168
  R1             0              10
  R2             0               7
  RX             0              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"

Clustering(136) Variable = NRIP1 MUTATION ANALYSIS
D136V1, survival
                 sevent
clus2               0   1
  NRIP1 MUTATED    12   1
  NRIP1 WILD-TYPE 203  32
  NRIP1 MUTATED NRIP1 WILD-TYPE 
             13             235 
  NRIP1 MUTATED NRIP1 WILD-TYPE 
              1              32 
$`NRIP1 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AP-A0LT TCGA-AX-A0J0 TCGA-AX-A0J1 
      129.80        48.03        27.12        49.22        40.11        77.39 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A16X TCGA-D1-A17Q 
       69.27        59.84        85.84        73.25         3.65         1.78 
TCGA-EY-A1GS 
       22.03 

$`NRIP1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        86.07        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       33.40        61.64        80.78        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       35.74        37.78        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       13.45       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       44.78        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       31.00        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       97.41        92.88       114.90        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
        0.69        18.67        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       79.10        10.92        37.71        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  NRIP1 MUTATED NRIP1 WILD-TYPE 
           1.78            0.56 
  NRIP1 MUTATED NRIP1 WILD-TYPE 
         129.80          185.79 
  NRIP1 MUTATED NRIP1 WILD-TYPE 
          49.22           35.38 
[1] "1.8 - 129.8 (49.2)" "0.6 - 185.8 (35.4)"
[1] "hr=" "2.2"
D136V2, binary
                 cls
clus                0   1
  NRIP1 MUTATED    10   3
  NRIP1 WILD-TYPE 147  88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NRIP1 MUTATED     10    3
  NRIP1 WILD-TYPE  147   88
     clus
vv    NRIP1 MUTATED NRIP1 WILD-TYPE
  NO             10             147
  YES             3              88
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  NRIP1 MUTATED                                        12
  NRIP1 WILD-TYPE                                     188
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  NRIP1 MUTATED                               0
  NRIP1 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  NRIP1 MUTATED                                   1
  NRIP1 WILD-TYPE                                43
D136V3, multiclass
                                         clus
vv                                        NRIP1 MUTATED NRIP1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            12             188
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NRIP1 MUTATED    10   0   1   0
  NRIP1 WILD-TYPE 162  10   6  18
D136V4, multiclass
    clus
vv   NRIP1 MUTATED NRIP1 WILD-TYPE
  R0            10             162
  R1             0              10
  R2             1               6
  RX             0              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"

Clustering(137) Variable = MCTP1 MUTATION ANALYSIS
D137V1, survival
                 sevent
clus2               0   1
  MCTP1 MUTATED    13   0
  MCTP1 WILD-TYPE 202  33
  MCTP1 MUTATED MCTP1 WILD-TYPE 
             13             235 
  MCTP1 MUTATED MCTP1 WILD-TYPE 
              0              33 
$`MCTP1 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
      129.80        48.03        36.89        27.12        71.51        40.11 
TCGA-B5-A0JY TCGA-BS-A0TC TCGA-BS-A0U8 TCGA-BS-A0UV TCGA-D1-A0ZR TCGA-D1-A0ZS 
       69.27        85.55        97.41        73.25         0.56         4.87 
TCGA-D1-A17Q 
        1.78 

$`MCTP1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05N 
       21.99        23.31        86.07        63.91        45.53        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        80.55        88.24        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       37.78        77.39        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD 
       35.08        31.00        24.99        46.95        24.33        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       92.88       114.90        85.84        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
       29.95         8.55        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       26.37        10.22         1.51        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  MCTP1 MUTATED MCTP1 WILD-TYPE 
           0.56            0.66 
  MCTP1 MUTATED MCTP1 WILD-TYPE 
         129.80          185.79 
  MCTP1 MUTATED MCTP1 WILD-TYPE 
          48.03           35.38 
[1] "0.6 - 129.8 (48.0)" "0.7 - 185.8 (35.4)"
[1] "hr="     "2.7e+07"
D137V2, binary
                 cls
clus                0   1
  MCTP1 MUTATED     8   5
  MCTP1 WILD-TYPE 149  86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCTP1 MUTATED      8    5
  MCTP1 WILD-TYPE  149   86
     clus
vv    MCTP1 MUTATED MCTP1 WILD-TYPE
  NO              8             149
  YES             5              86
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MCTP1 MUTATED                                        12
  MCTP1 WILD-TYPE                                     188
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  MCTP1 MUTATED                               0
  MCTP1 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  MCTP1 MUTATED                                   1
  MCTP1 WILD-TYPE                                43
D137V3, multiclass
                                         clus
vv                                        MCTP1 MUTATED MCTP1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            12             188
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MCTP1 MUTATED    10   1   0   0
  MCTP1 WILD-TYPE 162   9   7  18
D137V4, multiclass
    clus
vv   MCTP1 MUTATED MCTP1 WILD-TYPE
  R0            10             162
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(138) Variable = CCDC146 MUTATION ANALYSIS
D138V1, survival
                   sevent
clus2                 0   1
  CCDC146 MUTATED    14   0
  CCDC146 WILD-TYPE 201  33
  CCDC146 MUTATED CCDC146 WILD-TYPE 
               14               234 
  CCDC146 MUTATED CCDC146 WILD-TYPE 
                0                33 
$`CCDC146 MUTATED`
TCGA-A5-A0GP TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       46.55        86.07        48.03        27.12        71.51        40.11 
TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-BS-A0UF TCGA-BS-A0UV 
       77.39        69.27        59.84        61.68        85.84        73.25 
TCGA-D1-A16X TCGA-D1-A17Q 
        3.65         1.78 

$`CCDC146 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        80.55        88.24        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       37.78        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       55.30        86.01        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
      114.90        82.39        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       10.22         1.51        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  CCDC146 MUTATED CCDC146 WILD-TYPE 
             1.78              0.56 
  CCDC146 MUTATED CCDC146 WILD-TYPE 
            86.07            185.79 
  CCDC146 MUTATED CCDC146 WILD-TYPE 
           60.760            35.275 
[1] "1.8 - 86.1 (60.8)"  "0.6 - 185.8 (35.3)"
[1] "hr="     "2.7e+07"
D138V2, binary
                   cls
clus                  0   1
  CCDC146 MUTATED    12   2
  CCDC146 WILD-TYPE 145  89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC146 MUTATED     12    2
  CCDC146 WILD-TYPE  145   89
     clus
vv    CCDC146 MUTATED CCDC146 WILD-TYPE
  NO               12               145
  YES               2                89
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CCDC146 MUTATED                                        14
  CCDC146 WILD-TYPE                                     186
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  CCDC146 MUTATED                               0
  CCDC146 WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  CCDC146 MUTATED                                   0
  CCDC146 WILD-TYPE                                44
D138V3, multiclass
                                         clus
vv                                        CCDC146 MUTATED CCDC146 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              14               186
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     0                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CCDC146 MUTATED    10   1   0   0
  CCDC146 WILD-TYPE 162   9   7  18
D138V4, multiclass
    clus
vv   CCDC146 MUTATED CCDC146 WILD-TYPE
  R0              10               162
  R1               1                 9
  R2               0                 7
  RX               0                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"

Clustering(139) Variable = ZNF620 MUTATION ANALYSIS
D139V1, survival
                  sevent
clus2                0   1
  ZNF620 MUTATED     9   0
  ZNF620 WILD-TYPE 206  33
  ZNF620 MUTATED ZNF620 WILD-TYPE 
               9              239 
  ZNF620 MUTATED ZNF620 WILD-TYPE 
               0               33 
$`ZNF620 MUTATED`
TCGA-A5-A0GJ TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-B5-A0JY TCGA-B5-A11E 
       65.75        86.07        48.03        27.12        69.27        59.84 
TCGA-BS-A0UF TCGA-D1-A16Y TCGA-D1-A17Q 
       85.84        17.49         1.78 

$`ZNF620 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.74        37.78        40.11        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       71.24        56.91        86.37        55.30        86.01        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        13.45       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ 
       96.49        30.74        97.41        92.88       114.90        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        86.93        72.72        73.25        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.51        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  ZNF620 MUTATED ZNF620 WILD-TYPE 
            1.78             0.56 
  ZNF620 MUTATED ZNF620 WILD-TYPE 
           86.07           185.79 
  ZNF620 MUTATED ZNF620 WILD-TYPE 
           59.84            35.74 
[1] "1.8 - 86.1 (59.8)"  "0.6 - 185.8 (35.7)"
[1] "hr="     "2.6e+07"
D139V2, binary
                  cls
clus                 0   1
  ZNF620 MUTATED     7   2
  ZNF620 WILD-TYPE 150  89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF620 MUTATED      7    2
  ZNF620 WILD-TYPE  150   89
     clus
vv    ZNF620 MUTATED ZNF620 WILD-TYPE
  NO               7              150
  YES              2               89
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZNF620 MUTATED                                         9
  ZNF620 WILD-TYPE                                     191
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ZNF620 MUTATED                               0
  ZNF620 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZNF620 MUTATED                                   0
  ZNF620 WILD-TYPE                                44
D139V3, multiclass
                                         clus
vv                                        ZNF620 MUTATED ZNF620 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              9              191
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF620 MUTATED     6   0   0   1
  ZNF620 WILD-TYPE 166  10   7  17
D139V4, multiclass
    clus
vv   ZNF620 MUTATED ZNF620 WILD-TYPE
  R0              6              166
  R1              0               10
  R2              0                7
  RX              1               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"

Clustering(140) Variable = PTPN12 MUTATION ANALYSIS
D140V1, survival
                  sevent
clus2                0   1
  PTPN12 MUTATED     9   1
  PTPN12 WILD-TYPE 206  32
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              10              238 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
               1               32 
$`PTPN12 MUTATED`
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-AP-A059 TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A11E 
       17.85        32.78        48.03        71.51        69.27        59.84 
TCGA-BK-A0C9 TCGA-BS-A0TC TCGA-BS-A0UF TCGA-D1-A103 
       35.90        85.55        85.84        21.99 

$`PTPN12 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ 
       37.02        83.51       112.54       105.37        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 
       28.77        42.35        15.95        20.25       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.74        37.78        40.11        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       71.24        56.91        86.37        55.30        86.01        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        13.45       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0CA TCGA-BK-A0CB 
       14.01        15.45        15.45        23.70        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD 
       35.08        31.00        24.99        46.95        24.33        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       97.41        92.88       114.90        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       72.72        73.25        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93        22.55         1.74        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  PTPN12 MUTATED PTPN12 WILD-TYPE 
           17.85             0.56 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
           85.84           185.79 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
          53.935           35.560 
[1] "17.9 - 85.8 (53.9)" "0.6 - 185.8 (35.6)"
[1] "hr=" "1.6"
D140V2, binary
                  cls
clus                 0   1
  PTPN12 MUTATED     8   2
  PTPN12 WILD-TYPE 149  89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED      8    2
  PTPN12 WILD-TYPE  149   89
     clus
vv    PTPN12 MUTATED PTPN12 WILD-TYPE
  NO               8              149
  YES              2               89
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PTPN12 MUTATED                                        10
  PTPN12 WILD-TYPE                                     190
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  PTPN12 MUTATED                               0
  PTPN12 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  PTPN12 MUTATED                                   0
  PTPN12 WILD-TYPE                                44
D140V3, multiclass
                                         clus
vv                                        PTPN12 MUTATED PTPN12 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             10              190
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PTPN12 MUTATED     7   1   0   0
  PTPN12 WILD-TYPE 165   9   7  18
D140V4, multiclass
    clus
vv   PTPN12 MUTATED PTPN12 WILD-TYPE
  R0              7              165
  R1              1                9
  R2              0                7
  RX              0               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"

Clustering(141) Variable = RIOK3 MUTATION ANALYSIS
D141V1, survival
                 sevent
clus2               0   1
  RIOK3 MUTATED     9   0
  RIOK3 WILD-TYPE 206  33
  RIOK3 MUTATED RIOK3 WILD-TYPE 
              9             239 
  RIOK3 MUTATED RIOK3 WILD-TYPE 
              0              33 
$`RIOK3 MUTATED`
TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A11E TCGA-B5-A11N 
       86.07        48.03        40.11        77.39        59.84        61.68 
TCGA-BS-A0UV TCGA-D1-A16X TCGA-D1-A17Q 
       73.25         3.65         1.78 

$`RIOK3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
      129.80        21.99        23.31        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       71.51        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 
       60.66        61.08        35.74        37.78        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       71.24        56.91        86.37        55.30        86.01        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q 
       88.34        75.72        54.44        44.78        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        92.88       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 
       82.39        81.57        86.93        72.72        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y 
       31.07        33.63        10.65         0.69        18.67        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.51        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  RIOK3 MUTATED RIOK3 WILD-TYPE 
           1.78            0.56 
  RIOK3 MUTATED RIOK3 WILD-TYPE 
          86.07          185.79 
  RIOK3 MUTATED RIOK3 WILD-TYPE 
          59.84           35.38 
[1] "1.8 - 86.1 (59.8)"  "0.6 - 185.8 (35.4)"
[1] "hr="     "2.6e+07"
D141V2, binary
                 cls
clus                0   1
  RIOK3 MUTATED     8   1
  RIOK3 WILD-TYPE 149  90
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIOK3 MUTATED      8    1
  RIOK3 WILD-TYPE  149   90
     clus
vv    RIOK3 MUTATED RIOK3 WILD-TYPE
  NO              8             149
  YES             1              90
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  RIOK3 MUTATED                                         9
  RIOK3 WILD-TYPE                                     191
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  RIOK3 MUTATED                               0
  RIOK3 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  RIOK3 MUTATED                                   0
  RIOK3 WILD-TYPE                                44
D141V3, multiclass
                                         clus
vv                                        RIOK3 MUTATED RIOK3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             9             191
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RIOK3 MUTATED     7   0   0   0
  RIOK3 WILD-TYPE 165  10   7  18
D141V4, multiclass
    clus
vv   RIOK3 MUTATED RIOK3 WILD-TYPE
  R0             7             165
  R1             0              10
  R2             0               7
  RX             0              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"

Clustering(142) Variable = CASP8 MUTATION ANALYSIS
D142V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED    15   2
  CASP8 WILD-TYPE 200  31
  CASP8 MUTATED CASP8 WILD-TYPE 
             17             231 
  CASP8 MUTATED CASP8 WILD-TYPE 
              2              31 
$`CASP8 MUTATED`
TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A05S TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A11E 
       86.07        48.03        13.58        71.51        40.11        59.84 
TCGA-B5-A11N TCGA-BS-A0TA TCGA-BS-A0TJ TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UV 
       61.68        24.33        67.99        85.84        82.39        73.25 
TCGA-D1-A161 TCGA-D1-A167 TCGA-D1-A16X TCGA-D1-A17Q TCGA-FI-A2EW 
       29.33        15.72         3.65         1.78        59.01 

$`CASP8 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
      129.80        21.99        23.31        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       46.78        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        86.37        55.30        86.01        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        13.45       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       75.72        54.44        44.78        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TC TCGA-BS-A0TD 
       35.08        31.00        24.99        46.95        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
        4.80        77.95        61.87        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       92.88       114.90        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 
       33.63        10.65         0.69        18.67        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33         9.34        30.67 

  CASP8 MUTATED CASP8 WILD-TYPE 
           1.78            0.56 
  CASP8 MUTATED CASP8 WILD-TYPE 
          86.07          185.79 
  CASP8 MUTATED CASP8 WILD-TYPE 
          59.01           35.38 
[1] "1.8 - 86.1 (59.0)"  "0.6 - 185.8 (35.4)"
[1] "hr=" "1.2"
D142V2, binary
                 cls
clus                0   1
  CASP8 MUTATED    12   5
  CASP8 WILD-TYPE 145  86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     12    5
  CASP8 WILD-TYPE  145   86
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO             12             145
  YES             5              86
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CASP8 MUTATED                                        16
  CASP8 WILD-TYPE                                     184
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  CASP8 MUTATED                               0
  CASP8 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  CASP8 MUTATED                                   1
  CASP8 WILD-TYPE                                43
D142V3, multiclass
                                         clus
vv                                        CASP8 MUTATED CASP8 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            16             184
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CASP8 MUTATED    12   1   1   1
  CASP8 WILD-TYPE 160   9   6  17
D142V4, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  R0            12             160
  R1             1               9
  R2             1               6
  RX             1              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"

Clustering(143) Variable = GFAP MUTATION ANALYSIS
D143V1, survival
                sevent
clus2              0   1
  GFAP MUTATED     6   0
  GFAP WILD-TYPE 209  33
  GFAP MUTATED GFAP WILD-TYPE 
             6            242 
  GFAP MUTATED GFAP WILD-TYPE 
             0             33 
$`GFAP MUTATED`
TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A11E TCGA-D1-A103 
       48.03        27.12        71.51        69.27        59.84        21.99 

$`GFAP WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       85.84        82.39        81.57        86.93        72.72        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  GFAP MUTATED GFAP WILD-TYPE 
         21.99           0.56 
  GFAP MUTATED GFAP WILD-TYPE 
         71.51         185.79 
  GFAP MUTATED GFAP WILD-TYPE 
        53.935         35.820 
[1] "22.0 - 71.5 (53.9)" "0.6 - 185.8 (35.8)"
[1] "hr="     "2.5e+07"
D143V2, binary
                cls
clus               0   1
  GFAP MUTATED     4   2
  GFAP WILD-TYPE 153  89
[1] "tbl2"
                cls
clus             [,1] [,2]
  GFAP MUTATED      4    2
  GFAP WILD-TYPE  153   89
     clus
vv    GFAP MUTATED GFAP WILD-TYPE
  NO             4            153
  YES            2             89
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  GFAP MUTATED                                         6
  GFAP WILD-TYPE                                     194
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  GFAP MUTATED                               0
  GFAP WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  GFAP MUTATED                                   0
  GFAP WILD-TYPE                                44
D143V3, multiclass
                                         clus
vv                                        GFAP MUTATED GFAP WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            6            194
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GFAP MUTATED     3   1   0   0
  GFAP WILD-TYPE 169   9   7  18
D143V4, multiclass
    clus
vv   GFAP MUTATED GFAP WILD-TYPE
  R0            3            169
  R1            1              9
  R2            0              7
  RX            0             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"

Clustering(144) Variable = OMA1 MUTATION ANALYSIS
D144V1, survival
                sevent
clus2              0   1
  OMA1 MUTATED    10   0
  OMA1 WILD-TYPE 205  33
  OMA1 MUTATED OMA1 WILD-TYPE 
            10            238 
  OMA1 MUTATED OMA1 WILD-TYPE 
             0             33 
$`OMA1 MUTATED`
TCGA-AP-A0LM TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-BS-A0TC 
       27.12        71.51        69.27        59.84        61.68        85.55 
TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A16F TCGA-D1-A16X 
       73.25        21.99         2.63         3.65 

$`OMA1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
      129.80        21.99        23.31        86.07        48.03        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89        23.87        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37        66.25        36.36        97.71        46.72 
TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       83.97        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       88.24        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        61.08        35.74        37.78        40.11        77.39 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       86.01        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       57.76        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O 
      113.36        88.34        75.72        54.44        44.78        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       24.33        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        92.88       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 
       82.39        81.57        86.93        72.72        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V 
        4.87        28.67        23.93        22.55         1.74        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
       10.65         0.69        18.67        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  OMA1 MUTATED OMA1 WILD-TYPE 
          2.63           0.56 
  OMA1 MUTATED OMA1 WILD-TYPE 
         85.55         185.79 
  OMA1 MUTATED OMA1 WILD-TYPE 
         60.76          35.82 
[1] "2.6 - 85.5 (60.8)"  "0.6 - 185.8 (35.8)"
[1] "hr="     "2.6e+07"
D144V2, binary
                cls
clus               0   1
  OMA1 MUTATED     9   1
  OMA1 WILD-TYPE 148  90
[1] "tbl2"
                cls
clus             [,1] [,2]
  OMA1 MUTATED      9    1
  OMA1 WILD-TYPE  148   90
     clus
vv    OMA1 MUTATED OMA1 WILD-TYPE
  NO             9            148
  YES            1             90
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  OMA1 MUTATED                                        10
  OMA1 WILD-TYPE                                     190
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  OMA1 MUTATED                               0
  OMA1 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  OMA1 MUTATED                                   0
  OMA1 WILD-TYPE                                44
D144V3, multiclass
                                         clus
vv                                        OMA1 MUTATED OMA1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           10            190
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  OMA1 MUTATED     6   1   0   0
  OMA1 WILD-TYPE 166   9   7  18
D144V4, multiclass
    clus
vv   OMA1 MUTATED OMA1 WILD-TYPE
  R0            6            166
  R1            1              9
  R2            0              7
  RX            0             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"

Clustering(145) Variable = DENND3 MUTATION ANALYSIS
D145V1, survival
                  sevent
clus2                0   1
  DENND3 MUTATED    14   1
  DENND3 WILD-TYPE 201  32
  DENND3 MUTATED DENND3 WILD-TYPE 
              15              233 
  DENND3 MUTATED DENND3 WILD-TYPE 
               1               32 
$`DENND3 MUTATED`
TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       42.35       129.80        48.03        27.12        71.51        40.11 
TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0TA TCGA-BS-A0UF TCGA-BS-A0UV 
       77.39        69.27        59.84        24.33        85.84        73.25 
TCGA-D1-A103 TCGA-D1-A15X TCGA-D1-A174 
       21.99        29.88        19.53 

$`DENND3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       24.62        29.06        28.77        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        80.55        88.24        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       37.78        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       55.30        86.01        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       24.99        46.95        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
      114.90        82.39        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       39.48        30.08         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.78        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  DENND3 MUTATED DENND3 WILD-TYPE 
           19.53             0.56 
  DENND3 MUTATED DENND3 WILD-TYPE 
          129.80           185.79 
  DENND3 MUTATED DENND3 WILD-TYPE 
           48.03            35.38 
[1] "19.5 - 129.8 (48.0)" "0.6 - 185.8 (35.4)" 
[1] "hr=" "2.7"
D145V2, binary
                  cls
clus                 0   1
  DENND3 MUTATED     8   7
  DENND3 WILD-TYPE 149  84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DENND3 MUTATED      8    7
  DENND3 WILD-TYPE  149   84
     clus
vv    DENND3 MUTATED DENND3 WILD-TYPE
  NO               8              149
  YES              7               84
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DENND3 MUTATED                                        14
  DENND3 WILD-TYPE                                     186
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  DENND3 MUTATED                               0
  DENND3 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  DENND3 MUTATED                                   1
  DENND3 WILD-TYPE                                43
D145V3, multiclass
                                         clus
vv                                        DENND3 MUTATED DENND3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             14              186
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    1               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DENND3 MUTATED    11   1   0   1
  DENND3 WILD-TYPE 161   9   7  17
D145V4, multiclass
    clus
vv   DENND3 MUTATED DENND3 WILD-TYPE
  R0             11              161
  R1              1                9
  R2              0                7
  RX              1               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"

Clustering(146) Variable = CHEK2 MUTATION ANALYSIS
D146V1, survival
                 sevent
clus2               0   1
  CHEK2 MUTATED    11   1
  CHEK2 WILD-TYPE 204  32
  CHEK2 MUTATED CHEK2 WILD-TYPE 
             12             236 
  CHEK2 MUTATED CHEK2 WILD-TYPE 
              1              32 
$`CHEK2 MUTATED`
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY 
       23.31        86.07        27.12        71.51        40.11        69.27 
TCGA-B5-A11E TCGA-B5-A11J TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A17Q TCGA-D1-A1NX 
       59.84        54.44        85.84        73.25         1.78        18.25 

$`CHEK2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
      129.80        21.99        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        55.30        86.01        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       27.85        13.45       185.79       113.36        88.34        75.72 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       44.78        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       31.00        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       97.41        92.88       114.90        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-DI-A0WH TCGA-DI-A1NN 
       24.30         2.33        22.92        13.22        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  CHEK2 MUTATED CHEK2 WILD-TYPE 
           1.78            0.56 
  CHEK2 MUTATED CHEK2 WILD-TYPE 
          86.07          185.79 
  CHEK2 MUTATED CHEK2 WILD-TYPE 
          57.14           35.56 
[1] "1.8 - 86.1 (57.1)"  "0.6 - 185.8 (35.6)"
[1] "hr=" "1.8"
D146V2, binary
                 cls
clus                0   1
  CHEK2 MUTATED    10   2
  CHEK2 WILD-TYPE 147  89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHEK2 MUTATED     10    2
  CHEK2 WILD-TYPE  147   89
     clus
vv    CHEK2 MUTATED CHEK2 WILD-TYPE
  NO             10             147
  YES             2              89
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CHEK2 MUTATED                                        11
  CHEK2 WILD-TYPE                                     189
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  CHEK2 MUTATED                               0
  CHEK2 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  CHEK2 MUTATED                                   1
  CHEK2 WILD-TYPE                                43
D146V3, multiclass
                                         clus
vv                                        CHEK2 MUTATED CHEK2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            11             189
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CHEK2 MUTATED     7   2   0   0
  CHEK2 WILD-TYPE 165   8   7  18
D146V4, multiclass
    clus
vv   CHEK2 MUTATED CHEK2 WILD-TYPE
  R0             7             165
  R1             2               8
  R2             0               7
  RX             0              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"

Clustering(147) Variable = ZMYM2 MUTATION ANALYSIS
D147V1, survival
                 sevent
clus2               0   1
  ZMYM2 MUTATED    16   1
  ZMYM2 WILD-TYPE 199  32
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
             17             231 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
              1              32 
$`ZMYM2 MUTATED`
TCGA-AP-A0LF TCGA-A5-A0VO TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AP-A0LT 
       93.99        28.77        86.07        48.03        27.12        49.22 
TCGA-AX-A063 TCGA-AX-A0J0 TCGA-B5-A0JS TCGA-B5-A0JY TCGA-B5-A11E TCGA-BG-A0MO 
       79.46        40.11        86.37        69.27        59.84        43.04 
TCGA-BS-A0UF TCGA-BS-A0UL TCGA-BS-A0UV TCGA-D1-A16Y TCGA-D1-A17Q 
       85.84        81.57        73.25        17.49         1.78 

$`ZMYM2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A1CP 
       88.18        60.53       110.63        57.80        67.66        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 
       29.06        42.35        15.95        20.25       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       23.31        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        46.72        83.97        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       80.78        25.08        46.78        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A064 
       80.55        88.24        71.51        35.34        45.99        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        61.08        35.74        37.78        77.39 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0JV 
       34.65        25.51        71.24        56.91        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MQ 
       63.68        74.63        41.52        48.56        23.47        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ 
       96.49        30.74        97.41        92.88       114.90        82.39 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A174 TCGA-D1-A176 
       10.65         0.69        18.67         3.65        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
           1.78            0.56 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
          93.99          185.79 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
          59.84           35.21 
[1] "1.8 - 94.0 (59.8)"  "0.6 - 185.8 (35.2)"
[1] "hr=" "3"  
D147V2, binary
                 cls
clus                0   1
  ZMYM2 MUTATED    13   4
  ZMYM2 WILD-TYPE 144  87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM2 MUTATED     13    4
  ZMYM2 WILD-TYPE  144   87
     clus
vv    ZMYM2 MUTATED ZMYM2 WILD-TYPE
  NO             13             144
  YES             4              87
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZMYM2 MUTATED                                        17
  ZMYM2 WILD-TYPE                                     183
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  ZMYM2 MUTATED                               0
  ZMYM2 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZMYM2 MUTATED                                   0
  ZMYM2 WILD-TYPE                                44
D147V3, multiclass
                                         clus
vv                                        ZMYM2 MUTATED ZMYM2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            17             183
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZMYM2 MUTATED    12   0   1   1
  ZMYM2 WILD-TYPE 160  10   6  17
D147V4, multiclass
    clus
vv   ZMYM2 MUTATED ZMYM2 WILD-TYPE
  R0            12             160
  R1             0              10
  R2             1               6
  RX             1              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"

Clustering(148) Variable = EPC2 MUTATION ANALYSIS
D148V1, survival
                sevent
clus2              0   1
  EPC2 MUTATED     5   0
  EPC2 WILD-TYPE 210  33
  EPC2 MUTATED EPC2 WILD-TYPE 
             5            243 
  EPC2 MUTATED EPC2 WILD-TYPE 
             0             33 
$`EPC2 MUTATED`
TCGA-AP-A059 TCGA-B5-A11G TCGA-BG-A0VZ TCGA-BS-A0UV TCGA-D1-A16X 
       48.03       113.36        52.64        73.25         3.65 

$`EPC2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        61.08        35.74        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       77.39        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       55.30        86.01        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       13.45        59.84       185.79        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       44.78        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0W1 TCGA-BG-A0W2 
       15.42        51.06        52.01        34.29        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       92.88       114.90        85.84        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
        0.69        18.67        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  EPC2 MUTATED EPC2 WILD-TYPE 
          3.65           0.56 
  EPC2 MUTATED EPC2 WILD-TYPE 
        113.36         185.79 
  EPC2 MUTATED EPC2 WILD-TYPE 
         52.64          35.74 
[1] "3.6 - 113.4 (52.6)" "0.6 - 185.8 (35.7)"
[1] "hr="     "2.6e+07"
D148V2, binary
                cls
clus               0   1
  EPC2 MUTATED     4   1
  EPC2 WILD-TYPE 153  90
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPC2 MUTATED      4    1
  EPC2 WILD-TYPE  153   90
     clus
vv    EPC2 MUTATED EPC2 WILD-TYPE
  NO             4            153
  YES            1             90
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  EPC2 MUTATED                                         5
  EPC2 WILD-TYPE                                     195
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  EPC2 MUTATED                               0
  EPC2 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  EPC2 MUTATED                                   0
  EPC2 WILD-TYPE                                44
D148V3, multiclass
                                         clus
vv                                        EPC2 MUTATED EPC2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            5            195
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EPC2 MUTATED     4   0   0   0
  EPC2 WILD-TYPE 168  10   7  18
D148V4, multiclass
    clus
vv   EPC2 MUTATED EPC2 WILD-TYPE
  R0            4            168
  R1            0             10
  R2            0              7
  RX            0             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"

Clustering(149) Variable = DEPDC1B MUTATION ANALYSIS
D149V1, survival
                   sevent
clus2                 0   1
  DEPDC1B MUTATED    10   1
  DEPDC1B WILD-TYPE 205  32
  DEPDC1B MUTATED DEPDC1B WILD-TYPE 
               11               237 
  DEPDC1B MUTATED DEPDC1B WILD-TYPE 
                1                32 
$`DEPDC1B MUTATED`
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A060 TCGA-BS-A0TC 
       23.31        86.07        48.03        27.12        35.34        85.55 
TCGA-BS-A0UF TCGA-D1-A103 TCGA-D1-A15X TCGA-D1-A16Y TCGA-D1-A17F 
       85.84        21.99        29.88        17.49         1.28 

$`DEPDC1B WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
      129.80        21.99        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A062 
       33.21        29.69        80.55        88.24        71.51        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       37.78        40.11        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        86.37        55.30        86.01        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       24.33        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ 
       96.49        30.74        97.41        92.88       114.90        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        86.93        72.72        73.25        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V 
        4.87        28.67        23.93        22.55         1.74        39.48 
TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       30.08         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A174 TCGA-D1-A176 
       10.65         0.69        18.67         3.65        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17H 
       18.02         1.58         7.00         0.99        30.44        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  DEPDC1B MUTATED DEPDC1B WILD-TYPE 
             1.28              0.56 
  DEPDC1B MUTATED DEPDC1B WILD-TYPE 
            86.07            185.79 
  DEPDC1B MUTATED DEPDC1B WILD-TYPE 
            29.88             36.10 
[1] "1.3 - 86.1 (29.9)"  "0.6 - 185.8 (36.1)"
[1] "hr=" "1.3"
D149V2, binary
                   cls
clus                  0   1
  DEPDC1B MUTATED     7   4
  DEPDC1B WILD-TYPE 150  87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DEPDC1B MUTATED      7    4
  DEPDC1B WILD-TYPE  150   87
     clus
vv    DEPDC1B MUTATED DEPDC1B WILD-TYPE
  NO                7               150
  YES               4                87
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEPDC1B MUTATED                                        10
  DEPDC1B WILD-TYPE                                     190
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  DEPDC1B MUTATED                               0
  DEPDC1B WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEPDC1B MUTATED                                   1
  DEPDC1B WILD-TYPE                                43
D149V3, multiclass
                                         clus
vv                                        DEPDC1B MUTATED DEPDC1B WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              10               190
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     1                43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  DEPDC1B MUTATED     8   2   0   1
  DEPDC1B WILD-TYPE 164   8   7  17
D149V4, multiclass
    clus
vv   DEPDC1B MUTATED DEPDC1B WILD-TYPE
  R0               8               164
  R1               2                 8
  R2               0                 7
  RX               1                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"

Clustering(150) Variable = C3AR1 MUTATION ANALYSIS
D150V1, survival
                 sevent
clus2               0   1
  C3AR1 MUTATED     7   0
  C3AR1 WILD-TYPE 208  33
  C3AR1 MUTATED C3AR1 WILD-TYPE 
              7             241 
  C3AR1 MUTATED C3AR1 WILD-TYPE 
              0              33 
$`C3AR1 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AX-A05Z TCGA-BG-A0M7 TCGA-BS-A0TC TCGA-BS-A0UA 
      129.80        86.07        71.51        63.68        85.55       114.90 
TCGA-BS-A0UF 
       85.84 

$`C3AR1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       35.21        71.24        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        24.33        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UJ 
       67.99        96.49        30.74        97.41        92.88        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        86.93        72.72        73.25        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  C3AR1 MUTATED C3AR1 WILD-TYPE 
          63.68            0.56 
  C3AR1 MUTATED C3AR1 WILD-TYPE 
         129.80          185.79 
  C3AR1 MUTATED C3AR1 WILD-TYPE 
          85.84           35.34 
[1] "63.7 - 129.8 (85.8)" "0.6 - 185.8 (35.3)" 
[1] "hr="   "3e+07"
D150V2, binary
                 cls
clus                0   1
  C3AR1 MUTATED     5   2
  C3AR1 WILD-TYPE 152  89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C3AR1 MUTATED      5    2
  C3AR1 WILD-TYPE  152   89
     clus
vv    C3AR1 MUTATED C3AR1 WILD-TYPE
  NO              5             152
  YES             2              89
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  C3AR1 MUTATED                                         7
  C3AR1 WILD-TYPE                                     193
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  C3AR1 MUTATED                               0
  C3AR1 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  C3AR1 MUTATED                                   0
  C3AR1 WILD-TYPE                                44
D150V3, multiclass
                                         clus
vv                                        C3AR1 MUTATED C3AR1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             7             193
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  C3AR1 MUTATED     6   1   0   0
  C3AR1 WILD-TYPE 166   9   7  18
D150V4, multiclass
    clus
vv   C3AR1 MUTATED C3AR1 WILD-TYPE
  R0             6             166
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(151) Variable = STK3 MUTATION ANALYSIS
D151V1, survival
                sevent
clus2              0   1
  STK3 MUTATED    10   0
  STK3 WILD-TYPE 205  33
  STK3 MUTATED STK3 WILD-TYPE 
            10            238 
  STK3 MUTATED STK3 WILD-TYPE 
             0             33 
$`STK3 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LM TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11R 
      129.80        48.03        27.12        69.27        59.84        77.23 
TCGA-B5-A11U TCGA-BS-A0UV TCGA-D1-A16X TCGA-D1-A17Q 
       16.73        73.25         3.65         1.78 

$`STK3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        86.07        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       32.09        73.28        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        92.88       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        86.93        72.72        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 
       33.63        10.65         0.69        18.67        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  STK3 MUTATED STK3 WILD-TYPE 
          1.78           0.56 
  STK3 MUTATED STK3 WILD-TYPE 
        129.80         185.79 
  STK3 MUTATED STK3 WILD-TYPE 
        53.935         35.820 
[1] "1.8 - 129.8 (53.9)" "0.6 - 185.8 (35.8)"
[1] "hr="     "2.7e+07"
D151V2, binary
                cls
clus               0   1
  STK3 MUTATED     5   5
  STK3 WILD-TYPE 152  86
[1] "tbl2"
                cls
clus             [,1] [,2]
  STK3 MUTATED      5    5
  STK3 WILD-TYPE  152   86
     clus
vv    STK3 MUTATED STK3 WILD-TYPE
  NO             5            152
  YES            5             86
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  STK3 MUTATED                                        10
  STK3 WILD-TYPE                                     190
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  STK3 MUTATED                               0
  STK3 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  STK3 MUTATED                                   0
  STK3 WILD-TYPE                                44
D151V3, multiclass
                                         clus
vv                                        STK3 MUTATED STK3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           10            190
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  STK3 MUTATED     6   0   0   0
  STK3 WILD-TYPE 166  10   7  18
D151V4, multiclass
    clus
vv   STK3 MUTATED STK3 WILD-TYPE
  R0            6            166
  R1            0             10
  R2            0              7
  RX            0             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"

Clustering(152) Variable = FOXJ3 MUTATION ANALYSIS
D152V1, survival
                 sevent
clus2               0   1
  FOXJ3 MUTATED    10   0
  FOXJ3 WILD-TYPE 205  33
  FOXJ3 MUTATED FOXJ3 WILD-TYPE 
             10             238 
  FOXJ3 MUTATED FOXJ3 WILD-TYPE 
              0              33 
$`FOXJ3 MUTATED`
TCGA-A5-A0GB TCGA-AP-A059 TCGA-AX-A05Z TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-BS-A0UF 
       32.78        48.03        71.51        77.39        69.27        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A167 
       82.39        73.25        21.99        15.72 

$`FOXJ3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       37.02        83.51        17.85       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        86.07        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 
       61.08        35.74        37.78        40.11        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       71.24        56.91        86.37        55.30        86.01        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        86.93        72.72        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W 
       28.67        23.93        22.55         1.74        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  FOXJ3 MUTATED FOXJ3 WILD-TYPE 
          15.72            0.56 
  FOXJ3 MUTATED FOXJ3 WILD-TYPE 
          85.84          185.79 
  FOXJ3 MUTATED FOXJ3 WILD-TYPE 
          70.39           35.56 
[1] "15.7 - 85.8 (70.4)" "0.6 - 185.8 (35.6)"
[1] "hr="     "2.7e+07"
D152V2, binary
                 cls
clus                0   1
  FOXJ3 MUTATED     7   3
  FOXJ3 WILD-TYPE 150  88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXJ3 MUTATED      7    3
  FOXJ3 WILD-TYPE  150   88
     clus
vv    FOXJ3 MUTATED FOXJ3 WILD-TYPE
  NO              7             150
  YES             3              88
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  FOXJ3 MUTATED                                        10
  FOXJ3 WILD-TYPE                                     190
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  FOXJ3 MUTATED                               0
  FOXJ3 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  FOXJ3 MUTATED                                   0
  FOXJ3 WILD-TYPE                                44
D152V3, multiclass
                                         clus
vv                                        FOXJ3 MUTATED FOXJ3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            10             190
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FOXJ3 MUTATED     8   1   0   0
  FOXJ3 WILD-TYPE 164   9   7  18
D152V4, multiclass
    clus
vv   FOXJ3 MUTATED FOXJ3 WILD-TYPE
  R0             8             164
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(153) Variable = EPS8 MUTATION ANALYSIS
D153V1, survival
                sevent
clus2              0   1
  EPS8 MUTATED    11   1
  EPS8 WILD-TYPE 204  32
  EPS8 MUTATED EPS8 WILD-TYPE 
            12            236 
  EPS8 MUTATED EPS8 WILD-TYPE 
             1             32 
$`EPS8 MUTATED`
TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JR TCGA-B5-A0JY 
       48.03        27.12        71.51        40.11        56.91        69.27 
TCGA-BG-A0M3 TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A16F TCGA-D1-A16I TCGA-D1-A17Q 
       35.21        82.39        73.25         2.63        11.51         1.78 

$`EPS8 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       61.08        35.74        37.78        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       71.24        86.37        55.30        86.01        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       20.19        19.33        20.94        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UL 
       30.74        97.41        92.88       114.90        85.84        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       18.67         3.65        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  EPS8 MUTATED EPS8 WILD-TYPE 
          1.78           0.56 
  EPS8 MUTATED EPS8 WILD-TYPE 
         82.39         185.79 
  EPS8 MUTATED EPS8 WILD-TYPE 
         44.07          35.82 
[1] "1.8 - 82.4 (44.1)"  "0.6 - 185.8 (35.8)"
[1] "hr=" "1.6"
D153V2, binary
                cls
clus               0   1
  EPS8 MUTATED     8   4
  EPS8 WILD-TYPE 149  87
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPS8 MUTATED      8    4
  EPS8 WILD-TYPE  149   87
     clus
vv    EPS8 MUTATED EPS8 WILD-TYPE
  NO             8            149
  YES            4             87
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  EPS8 MUTATED                                        11
  EPS8 WILD-TYPE                                     189
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  EPS8 MUTATED                               0
  EPS8 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  EPS8 MUTATED                                   1
  EPS8 WILD-TYPE                                43
D153V3, multiclass
                                         clus
vv                                        EPS8 MUTATED EPS8 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           11            189
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  1             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EPS8 MUTATED     9   1   0   0
  EPS8 WILD-TYPE 163   9   7  18
D153V4, multiclass
    clus
vv   EPS8 MUTATED EPS8 WILD-TYPE
  R0            9            163
  R1            1              9
  R2            0              7
  RX            0             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"

Clustering(154) Variable = ZNF385B MUTATION ANALYSIS
D154V1, survival
                   sevent
clus2                 0   1
  ZNF385B MUTATED     7   0
  ZNF385B WILD-TYPE 208  33
  ZNF385B MUTATED ZNF385B WILD-TYPE 
                7               241 
  ZNF385B MUTATED ZNF385B WILD-TYPE 
                0                33 
$`ZNF385B MUTATED`
TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-B5-A11E TCGA-BS-A0UF TCGA-D1-A103 
       86.07        27.12        40.11        59.84        85.84        21.99 
TCGA-D1-A16X 
        3.65 

$`ZNF385B WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       71.51        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        61.08        35.74        37.78        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       57.76        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        44.78        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        82.39        81.57        86.93        72.72        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  ZNF385B MUTATED ZNF385B WILD-TYPE 
             3.65              0.56 
  ZNF385B MUTATED ZNF385B WILD-TYPE 
            86.07            185.79 
  ZNF385B MUTATED ZNF385B WILD-TYPE 
            40.11             35.90 
[1] "3.6 - 86.1 (40.1)"  "0.6 - 185.8 (35.9)"
[1] "hr="     "2.5e+07"
D154V2, binary
                   cls
clus                  0   1
  ZNF385B MUTATED     6   1
  ZNF385B WILD-TYPE 151  90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF385B MUTATED      6    1
  ZNF385B WILD-TYPE  151   90
     clus
vv    ZNF385B MUTATED ZNF385B WILD-TYPE
  NO                6               151
  YES               1                90
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZNF385B MUTATED                                         7
  ZNF385B WILD-TYPE                                     193
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  ZNF385B MUTATED                               0
  ZNF385B WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZNF385B MUTATED                                   0
  ZNF385B WILD-TYPE                                44
D154V3, multiclass
                                         clus
vv                                        ZNF385B MUTATED ZNF385B WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               7               193
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     0                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZNF385B MUTATED     6   0   0   0
  ZNF385B WILD-TYPE 166  10   7  18
D154V4, multiclass
    clus
vv   ZNF385B MUTATED ZNF385B WILD-TYPE
  R0               6               166
  R1               0                10
  R2               0                 7
  RX               0                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"

Clustering(155) Variable = EFCAB4B MUTATION ANALYSIS
D155V1, survival
                   sevent
clus2                 0   1
  EFCAB4B MUTATED    11   0
  EFCAB4B WILD-TYPE 204  33
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
               11               237 
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
                0                33 
$`EFCAB4B MUTATED`
TCGA-AP-A0LM TCGA-AX-A05Z TCGA-B5-A0K2 TCGA-B5-A11E TCGA-B5-A11G TCGA-BS-A0U8 
       27.12        71.51        72.62        59.84       113.36        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A17Q TCGA-DI-A0WH 
       92.88        82.39        73.25         1.78        16.31 

$`EFCAB4B WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
      129.80        21.99        23.31        86.07        48.03        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89        23.87        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37        66.25        36.36        97.71        46.72 
TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       83.97        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       88.24        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        61.08        35.74        37.78        40.11        77.39 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K3 
       86.01        69.27        71.44        48.59        36.49        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       57.76        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UL 
       67.99        96.49        30.74       114.90        85.84        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69        18.67         3.65        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
             1.78              0.56 
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
           113.36            185.79 
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
            72.62             35.38 
[1] "1.8 - 113.4 (72.6)" "0.6 - 185.8 (35.4)"
[1] "hr="     "2.7e+07"
D155V2, binary
                   cls
clus                  0   1
  EFCAB4B MUTATED     8   3
  EFCAB4B WILD-TYPE 149  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EFCAB4B MUTATED      8    3
  EFCAB4B WILD-TYPE  149   88
     clus
vv    EFCAB4B MUTATED EFCAB4B WILD-TYPE
  NO                8               149
  YES               3                88
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  EFCAB4B MUTATED                                        11
  EFCAB4B WILD-TYPE                                     189
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  EFCAB4B MUTATED                               0
  EFCAB4B WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  EFCAB4B MUTATED                                   0
  EFCAB4B WILD-TYPE                                44
D155V3, multiclass
                                         clus
vv                                        EFCAB4B MUTATED EFCAB4B WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              11               189
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     0                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  EFCAB4B MUTATED     5   1   0   1
  EFCAB4B WILD-TYPE 167   9   7  17
D155V4, multiclass
    clus
vv   EFCAB4B MUTATED EFCAB4B WILD-TYPE
  R0               5               167
  R1               1                 9
  R2               0                 7
  RX               1                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"

Clustering(156) Variable = NPRL2 MUTATION ANALYSIS
D156V1, survival
                 sevent
clus2               0   1
  NPRL2 MUTATED     4   1
  NPRL2 WILD-TYPE 211  32
  NPRL2 MUTATED NPRL2 WILD-TYPE 
              5             243 
  NPRL2 MUTATED NPRL2 WILD-TYPE 
              1              32 
$`NPRL2 MUTATED`
TCGA-AP-A051 TCGA-AP-A054 TCGA-B5-A0JY TCGA-B5-A11J TCGA-D1-A17B 
      129.80        23.31        69.27        54.44         7.00 

$`NPRL2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        86.07        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       71.51        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        61.08        35.74        37.78        40.11        77.39 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       86.01        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11M TCGA-B5-A11N 
      185.79       113.36        88.34        75.72        44.78        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
      114.90        85.84        82.39        81.57        86.93        72.72 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       73.25        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
       18.02         1.58         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  NPRL2 MUTATED NPRL2 WILD-TYPE 
           7.00            0.56 
  NPRL2 MUTATED NPRL2 WILD-TYPE 
         129.80          185.79 
  NPRL2 MUTATED NPRL2 WILD-TYPE 
          54.44           35.90 
[1] "7.0 - 129.8 (54.4)" "0.6 - 185.8 (35.9)"
[1] "hr=" "1"  
D156V2, binary
                 cls
clus                0   1
  NPRL2 MUTATED     4   1
  NPRL2 WILD-TYPE 153  90
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPRL2 MUTATED      4    1
  NPRL2 WILD-TYPE  153   90
     clus
vv    NPRL2 MUTATED NPRL2 WILD-TYPE
  NO              4             153
  YES             1              90
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  NPRL2 MUTATED                                         5
  NPRL2 WILD-TYPE                                     195
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  NPRL2 MUTATED                               0
  NPRL2 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  NPRL2 MUTATED                                   0
  NPRL2 WILD-TYPE                                44
D156V3, multiclass
                                         clus
vv                                        NPRL2 MUTATED NPRL2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             5             195
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NPRL2 MUTATED     2   1   0   0
  NPRL2 WILD-TYPE 170   9   7  18
D156V4, multiclass
    clus
vv   NPRL2 MUTATED NPRL2 WILD-TYPE
  R0             2             170
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(157) Variable = ATF6 MUTATION ANALYSIS
D157V1, survival
                sevent
clus2              0   1
  ATF6 MUTATED    14   0
  ATF6 WILD-TYPE 201  33
  ATF6 MUTATED ATF6 WILD-TYPE 
            14            234 
  ATF6 MUTATED ATF6 WILD-TYPE 
             0             33 
$`ATF6 MUTATED`
TCGA-BG-A0MS TCGA-A5-A0GP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A05Z 
       61.87        46.55       129.80        86.07        48.03        71.51 
TCGA-B5-A0JR TCGA-B5-A11E TCGA-B5-A11H TCGA-BK-A0C9 TCGA-BS-A0UF TCGA-D1-A15X 
       56.91        59.84        88.34        35.90        85.84        29.88 
TCGA-D1-A167 TCGA-D1-A16X 
       15.72         3.65 

$`ATF6 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0VT 
       36.39        27.88        80.38        22.06        66.41        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       65.75        60.53        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 
       28.77        42.35        15.95        20.25        21.99        23.31 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       63.91        45.53        36.89        23.87        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       80.78        49.22        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        80.55        88.24        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JS 
       40.11        77.39        34.65        25.51        71.24        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       55.30        86.01        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
       13.45       185.79       113.36        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       23.70        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        82.39        81.57        86.93        72.72        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 
        1.74        21.99        39.48        30.08         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       29.33        32.58         0.66        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y 
       31.07        33.63        10.65         0.69        18.67        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  ATF6 MUTATED ATF6 WILD-TYPE 
          3.65           0.56 
  ATF6 MUTATED ATF6 WILD-TYPE 
        129.80         185.79 
  ATF6 MUTATED ATF6 WILD-TYPE 
        58.375         35.275 
[1] "3.6 - 129.8 (58.4)" "0.6 - 185.8 (35.3)"
[1] "hr="     "7.5e+07"
D157V2, binary
                cls
clus               0   1
  ATF6 MUTATED     9   5
  ATF6 WILD-TYPE 148  86
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATF6 MUTATED      9    5
  ATF6 WILD-TYPE  148   86
     clus
vv    ATF6 MUTATED ATF6 WILD-TYPE
  NO             9            148
  YES            5             86
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ATF6 MUTATED                                        13
  ATF6 WILD-TYPE                                     187
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  ATF6 MUTATED                               0
  ATF6 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  ATF6 MUTATED                                   1
  ATF6 WILD-TYPE                                43
D157V3, multiclass
                                         clus
vv                                        ATF6 MUTATED ATF6 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           13            187
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  1             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ATF6 MUTATED    10   1   0   0
  ATF6 WILD-TYPE 162   9   7  18
D157V4, multiclass
    clus
vv   ATF6 MUTATED ATF6 WILD-TYPE
  R0           10            162
  R1            1              9
  R2            0              7
  RX            0             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"

Clustering(158) Variable = LIMA1 MUTATION ANALYSIS
D158V1, survival
                 sevent
clus2               0   1
  LIMA1 MUTATED     8   0
  LIMA1 WILD-TYPE 207  33
  LIMA1 MUTATED LIMA1 WILD-TYPE 
              8             240 
  LIMA1 MUTATED LIMA1 WILD-TYPE 
              0              33 
$`LIMA1 MUTATED`
TCGA-BG-A0M8 TCGA-AP-A051 TCGA-AP-A059 TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0UF 
       66.41       129.80        48.03        69.27        59.84        85.84 
TCGA-D1-A103 TCGA-D1-A160 
       21.99         3.68 

$`LIMA1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT 
       36.39        27.88        80.38        22.06        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       29.06        28.77        42.35        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 
       82.39        81.57        86.93        72.72        73.25        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 
       39.48        30.08        29.88         1.91        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  LIMA1 MUTATED LIMA1 WILD-TYPE 
           3.68            0.56 
  LIMA1 MUTATED LIMA1 WILD-TYPE 
         129.80          185.79 
  LIMA1 MUTATED LIMA1 WILD-TYPE 
         63.125          35.560 
[1] "3.7 - 129.8 (63.1)" "0.6 - 185.8 (35.6)"
[1] "hr="     "2.7e+07"
D158V2, binary
                 cls
clus                0   1
  LIMA1 MUTATED     6   2
  LIMA1 WILD-TYPE 151  89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LIMA1 MUTATED      6    2
  LIMA1 WILD-TYPE  151   89
     clus
vv    LIMA1 MUTATED LIMA1 WILD-TYPE
  NO              6             151
  YES             2              89
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  LIMA1 MUTATED                                         8
  LIMA1 WILD-TYPE                                     192
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  LIMA1 MUTATED                               0
  LIMA1 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  LIMA1 MUTATED                                   0
  LIMA1 WILD-TYPE                                44
D158V3, multiclass
                                         clus
vv                                        LIMA1 MUTATED LIMA1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             8             192
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LIMA1 MUTATED     6   0   0   0
  LIMA1 WILD-TYPE 166  10   7  18
D158V4, multiclass
    clus
vv   LIMA1 MUTATED LIMA1 WILD-TYPE
  R0             6             166
  R1             0              10
  R2             0               7
  RX             0              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"

Clustering(159) Variable = PPIG MUTATION ANALYSIS
D159V1, survival
                sevent
clus2              0   1
  PPIG MUTATED    16   0
  PPIG WILD-TYPE 199  33
  PPIG MUTATED PPIG WILD-TYPE 
            16            232 
  PPIG MUTATED PPIG WILD-TYPE 
             0             33 
$`PPIG MUTATED`
TCGA-A5-A0GB TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z 
       32.78       129.80        86.07        48.03        27.12        71.51 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-BG-A0LX TCGA-D1-A0ZS TCGA-D1-A103 
       40.11        77.39        69.27        20.19         4.87        21.99 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A17M TCGA-D1-A17Q 
        3.65        17.49        10.22         1.78 

$`PPIG WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       37.02        83.51        17.85       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       29.06        28.77        42.35        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       23.31        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        46.72        83.97        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       80.78        49.22        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        80.55        88.24        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       86.01        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       50.89        11.87        18.61        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
      114.90        85.84        82.39        81.57        86.93        72.72 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       73.25        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
       29.95         8.55         0.56        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17N 
       30.44         1.28        28.01        28.08        26.37         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  PPIG MUTATED PPIG WILD-TYPE 
          1.78           0.56 
  PPIG MUTATED PPIG WILD-TYPE 
        129.80         185.79 
  PPIG MUTATED PPIG WILD-TYPE 
         29.95          36.00 
[1] "1.8 - 129.8 (30.0)" "0.6 - 185.8 (36.0)"
[1] "hr="     "2.7e+07"
D159V2, binary
                cls
clus               0   1
  PPIG MUTATED     9   7
  PPIG WILD-TYPE 148  84
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      9    7
  PPIG WILD-TYPE  148   84
     clus
vv    PPIG MUTATED PPIG WILD-TYPE
  NO             9            148
  YES            7             84
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PPIG MUTATED                                        16
  PPIG WILD-TYPE                                     184
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  PPIG MUTATED                               0
  PPIG WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  PPIG MUTATED                                   0
  PPIG WILD-TYPE                                44
D159V3, multiclass
                                         clus
vv                                        PPIG MUTATED PPIG WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           16            184
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PPIG MUTATED    13   1   0   1
  PPIG WILD-TYPE 159   9   7  17
D159V4, multiclass
    clus
vv   PPIG MUTATED PPIG WILD-TYPE
  R0           13            159
  R1            1              9
  R2            0              7
  RX            1             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"

Clustering(160) Variable = ZNF774 MUTATION ANALYSIS
D160V1, survival
                  sevent
clus2                0   1
  ZNF774 MUTATED    10   0
  ZNF774 WILD-TYPE 205  33
  ZNF774 MUTATED ZNF774 WILD-TYPE 
              10              238 
  ZNF774 MUTATED ZNF774 WILD-TYPE 
               0               33 
$`ZNF774 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A0K8 
      129.80        48.03        27.12        71.51        69.27        27.85 
TCGA-BS-A0UF TCGA-D1-A160 TCGA-D1-A16X TCGA-D1-A176 
       85.84         3.68         3.65        30.15 

$`ZNF774 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        86.07        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.74        37.78        40.11        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       71.24        56.91        86.37        55.30        86.01        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ 
       96.49        30.74        97.41        92.88       114.90        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        86.93        72.72        73.25        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 
       39.48        30.08        29.88         1.91        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 
       33.63        10.65         0.69        18.67        17.49        19.53 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  ZNF774 MUTATED ZNF774 WILD-TYPE 
            3.65             0.56 
  ZNF774 MUTATED ZNF774 WILD-TYPE 
          129.80           185.79 
  ZNF774 MUTATED ZNF774 WILD-TYPE 
           39.09            35.90 
[1] "3.6 - 129.8 (39.1)" "0.6 - 185.8 (35.9)"
[1] "hr="     "2.7e+07"
D160V2, binary
                  cls
clus                 0   1
  ZNF774 MUTATED     7   3
  ZNF774 WILD-TYPE 150  88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF774 MUTATED      7    3
  ZNF774 WILD-TYPE  150   88
     clus
vv    ZNF774 MUTATED ZNF774 WILD-TYPE
  NO               7              150
  YES              3               88
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZNF774 MUTATED                                         9
  ZNF774 WILD-TYPE                                     191
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ZNF774 MUTATED                               0
  ZNF774 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZNF774 MUTATED                                   1
  ZNF774 WILD-TYPE                                43
D160V3, multiclass
                                         clus
vv                                        ZNF774 MUTATED ZNF774 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              9              191
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    1               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF774 MUTATED     7   1   0   0
  ZNF774 WILD-TYPE 165   9   7  18
D160V4, multiclass
    clus
vv   ZNF774 MUTATED ZNF774 WILD-TYPE
  R0              7              165
  R1              1                9
  R2              0                7
  RX              0               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"

Clustering(161) Variable = MUTED MUTATION ANALYSIS
D161V1, survival
                 sevent
clus2               0   1
  MUTED MUTATED     7   0
  MUTED WILD-TYPE 208  33
  MUTED MUTATED MUTED WILD-TYPE 
              7             241 
  MUTED MUTATED MUTED WILD-TYPE 
              0              33 
$`MUTED MUTATED`
TCGA-AP-A056 TCGA-B5-A0JY TCGA-B5-A11R TCGA-BS-A0TC TCGA-BS-A0UF TCGA-D1-A103 
       86.07        69.27        77.23        85.55        85.84        21.99 
TCGA-D1-A17Q 
        1.78 

$`MUTED WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        61.08        35.74        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       77.39        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       55.30        86.01        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U 
       44.78        61.68        85.78        32.09        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       24.99        46.95        24.33        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        82.39        81.57        86.93        72.72        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       26.37        10.22         1.51        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  MUTED MUTATED MUTED WILD-TYPE 
           1.78            0.56 
  MUTED MUTATED MUTED WILD-TYPE 
          86.07          185.79 
  MUTED MUTATED MUTED WILD-TYPE 
          77.23           35.74 
[1] "1.8 - 86.1 (77.2)"  "0.6 - 185.8 (35.7)"
[1] "hr="     "2.6e+07"
D161V2, binary
                 cls
clus                0   1
  MUTED MUTATED     6   1
  MUTED WILD-TYPE 151  90
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUTED MUTATED      6    1
  MUTED WILD-TYPE  151   90
     clus
vv    MUTED MUTATED MUTED WILD-TYPE
  NO              6             151
  YES             1              90
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MUTED MUTATED                                         7
  MUTED WILD-TYPE                                     193
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  MUTED MUTATED                               0
  MUTED WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  MUTED MUTATED                                   0
  MUTED WILD-TYPE                                44
D161V3, multiclass
                                         clus
vv                                        MUTED MUTATED MUTED WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             7             193
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MUTED MUTATED     5   0   0   0
  MUTED WILD-TYPE 167  10   7  18
D161V4, multiclass
    clus
vv   MUTED MUTATED MUTED WILD-TYPE
  R0             5             167
  R1             0              10
  R2             0               7
  RX             0              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"

Clustering(162) Variable = TPX2 MUTATION ANALYSIS
D162V1, survival
                sevent
clus2              0   1
  TPX2 MUTATED     6   0
  TPX2 WILD-TYPE 209  33
  TPX2 MUTATED TPX2 WILD-TYPE 
             6            242 
  TPX2 MUTATED TPX2 WILD-TYPE 
             0             33 
$`TPX2 MUTATED`
TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A11E TCGA-D1-A16Y 
       48.03        27.12        71.51        69.27        59.84        17.49 

$`TPX2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       85.84        82.39        81.57        86.93        72.72        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       18.67         3.65        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  TPX2 MUTATED TPX2 WILD-TYPE 
         17.49           0.56 
  TPX2 MUTATED TPX2 WILD-TYPE 
         71.51         185.79 
  TPX2 MUTATED TPX2 WILD-TYPE 
        53.935         35.820 
[1] "17.5 - 71.5 (53.9)" "0.6 - 185.8 (35.8)"
[1] "hr="     "2.5e+07"
D162V2, binary
                cls
clus               0   1
  TPX2 MUTATED     4   2
  TPX2 WILD-TYPE 153  89
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPX2 MUTATED      4    2
  TPX2 WILD-TYPE  153   89
     clus
vv    TPX2 MUTATED TPX2 WILD-TYPE
  NO             4            153
  YES            2             89
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  TPX2 MUTATED                                         6
  TPX2 WILD-TYPE                                     194
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  TPX2 MUTATED                               0
  TPX2 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  TPX2 MUTATED                                   0
  TPX2 WILD-TYPE                                44
D162V3, multiclass
                                         clus
vv                                        TPX2 MUTATED TPX2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            6            194
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TPX2 MUTATED     2   1   0   1
  TPX2 WILD-TYPE 170   9   7  17
D162V4, multiclass
    clus
vv   TPX2 MUTATED TPX2 WILD-TYPE
  R0            2            170
  R1            1              9
  R2            0              7
  RX            1             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"

Clustering(163) Variable = PARG MUTATION ANALYSIS
D163V1, survival
                sevent
clus2              0   1
  PARG MUTATED     9   0
  PARG WILD-TYPE 206  33
  PARG MUTATED PARG WILD-TYPE 
             9            239 
  PARG MUTATED PARG WILD-TYPE 
             0             33 
$`PARG MUTATED`
TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JR TCGA-B5-A11E 
       48.03        27.12        40.11        77.39        56.91        59.84 
TCGA-BG-A0W1 TCGA-BS-A0UF TCGA-D1-A167 
       52.83        85.84        15.72 

$`PARG WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       71.51        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 
       60.66        61.08        35.74        37.78        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       71.24        86.37        55.30        86.01        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        13.45       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.64        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        92.88       114.90        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       86.93        72.72        73.25        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69        18.67         3.65        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.78        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  PARG MUTATED PARG WILD-TYPE 
         15.72           0.56 
  PARG MUTATED PARG WILD-TYPE 
         85.84         185.79 
  PARG MUTATED PARG WILD-TYPE 
         52.83          35.38 
[1] "15.7 - 85.8 (52.8)" "0.6 - 185.8 (35.4)"
[1] "hr="     "2.6e+07"
D163V2, binary
                cls
clus               0   1
  PARG MUTATED     6   3
  PARG WILD-TYPE 151  88
[1] "tbl2"
                cls
clus             [,1] [,2]
  PARG MUTATED      6    3
  PARG WILD-TYPE  151   88
     clus
vv    PARG MUTATED PARG WILD-TYPE
  NO             6            151
  YES            3             88
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PARG MUTATED                                         9
  PARG WILD-TYPE                                     191
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  PARG MUTATED                               0
  PARG WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  PARG MUTATED                                   0
  PARG WILD-TYPE                                44
D163V3, multiclass
                                         clus
vv                                        PARG MUTATED PARG WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            9            191
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PARG MUTATED     7   0   0   0
  PARG WILD-TYPE 165  10   7  18
D163V4, multiclass
    clus
vv   PARG MUTATED PARG WILD-TYPE
  R0            7            165
  R1            0             10
  R2            0              7
  RX            0             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"

Clustering(164) Variable = PSMD3 MUTATION ANALYSIS
D164V1, survival
                 sevent
clus2               0   1
  PSMD3 MUTATED    11   0
  PSMD3 WILD-TYPE 204  33
  PSMD3 MUTATED PSMD3 WILD-TYPE 
             11             237 
  PSMD3 MUTATED PSMD3 WILD-TYPE 
              0              33 
$`PSMD3 MUTATED`
TCGA-A5-A0GH TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A0J1 TCGA-B5-A0K6 
       74.10       129.80        48.03        27.12        77.39        64.21 
TCGA-B5-A11Y TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A15X TCGA-D1-A16F 
       18.41        82.39        73.25        29.88         2.63 

$`PSMD3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       29.06        28.77        42.35        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        40.11        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        86.37        55.30        86.01        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K7 
       48.59        36.49        72.62        27.29        57.76        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UL 
       30.74        97.41        92.88       114.90        85.84        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       18.67         3.65        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  PSMD3 MUTATED PSMD3 WILD-TYPE 
           2.63            0.56 
  PSMD3 MUTATED PSMD3 WILD-TYPE 
         129.80          185.79 
  PSMD3 MUTATED PSMD3 WILD-TYPE 
          64.21           35.74 
[1] "2.6 - 129.8 (64.2)" "0.6 - 185.8 (35.7)"
[1] "hr="     "2.7e+07"
D164V2, binary
                 cls
clus                0   1
  PSMD3 MUTATED     7   4
  PSMD3 WILD-TYPE 150  87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMD3 MUTATED      7    4
  PSMD3 WILD-TYPE  150   87
     clus
vv    PSMD3 MUTATED PSMD3 WILD-TYPE
  NO              7             150
  YES             4              87
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PSMD3 MUTATED                                        10
  PSMD3 WILD-TYPE                                     190
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  PSMD3 MUTATED                               0
  PSMD3 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  PSMD3 MUTATED                                   1
  PSMD3 WILD-TYPE                                43
D164V3, multiclass
                                         clus
vv                                        PSMD3 MUTATED PSMD3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            10             190
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PSMD3 MUTATED     9   0   0   0
  PSMD3 WILD-TYPE 163  10   7  18
D164V4, multiclass
    clus
vv   PSMD3 MUTATED PSMD3 WILD-TYPE
  R0             9             163
  R1             0              10
  R2             0               7
  RX             0              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"

Clustering(165) Variable = STRN3 MUTATION ANALYSIS
D165V1, survival
                 sevent
clus2               0   1
  STRN3 MUTATED    12   0
  STRN3 WILD-TYPE 203  33
  STRN3 MUTATED STRN3 WILD-TYPE 
             12             236 
  STRN3 MUTATED STRN3 WILD-TYPE 
              0              33 
$`STRN3 MUTATED`
TCGA-AX-A2HF TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 
       27.88        48.03        27.12        71.51        40.11        77.39 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0TC TCGA-BS-A0UF TCGA-D1-A160 TCGA-D1-A16Y 
       69.27        59.84        85.55        85.84         3.68        17.49 

$`STRN3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       36.39        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        86.07        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       35.74        37.78        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       13.45       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       44.78        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE 
       31.00        24.99        46.95        24.33        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       92.88       114.90        82.39        81.57        86.93        72.72 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       73.25        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        1.91        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       18.67         3.65        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  STRN3 MUTATED STRN3 WILD-TYPE 
           3.68            0.56 
  STRN3 MUTATED STRN3 WILD-TYPE 
          85.84          185.79 
  STRN3 MUTATED STRN3 WILD-TYPE 
         53.935          35.560 
[1] "3.7 - 85.8 (53.9)"  "0.6 - 185.8 (35.6)"
[1] "hr="     "2.7e+07"
D165V2, binary
                 cls
clus                0   1
  STRN3 MUTATED     9   3
  STRN3 WILD-TYPE 148  88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STRN3 MUTATED      9    3
  STRN3 WILD-TYPE  148   88
     clus
vv    STRN3 MUTATED STRN3 WILD-TYPE
  NO              9             148
  YES             3              88
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  STRN3 MUTATED                                        11
  STRN3 WILD-TYPE                                     189
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  STRN3 MUTATED                               0
  STRN3 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  STRN3 MUTATED                                   1
  STRN3 WILD-TYPE                                43
D165V3, multiclass
                                         clus
vv                                        STRN3 MUTATED STRN3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            11             189
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  STRN3 MUTATED     8   1   0   1
  STRN3 WILD-TYPE 164   9   7  17
D165V4, multiclass
    clus
vv   STRN3 MUTATED STRN3 WILD-TYPE
  R0             8             164
  R1             1               9
  R2             0               7
  RX             1              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"

Clustering(166) Variable = MLL4 MUTATION ANALYSIS
D166V1, survival
                sevent
clus2              0   1
  MLL4 MUTATED    30   0
  MLL4 WILD-TYPE 185  33
  MLL4 MUTATED MLL4 WILD-TYPE 
            30            218 
  MLL4 MUTATED MLL4 WILD-TYPE 
             0             33 
$`MLL4 MUTATED`
TCGA-A5-A0GI TCGA-A5-A0GP TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 
       88.18        46.55        42.35       129.80        86.07        48.03 
TCGA-AP-A0LE TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A06H TCGA-B5-A11E TCGA-B5-A11G 
      110.37        27.12        71.51        27.39        59.84       113.36 
TCGA-B5-A11J TCGA-B5-A11Y TCGA-BG-A0MQ TCGA-BK-A0CB TCGA-BS-A0UF TCGA-BS-A0UM 
       54.44        18.41        59.74        35.90        85.84        86.93 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-D1-A0ZS TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15X 
       73.25        89.59         4.87         1.74        21.99        29.88 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17Q 
       19.53        30.15        18.02         1.58         7.00         1.78 

$`MLL4 WILD-TYPE`
TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP 
       60.53       110.63        57.80        93.99        67.66        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       65.75        60.53        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A 
       28.77        15.95        20.25        21.99        23.31        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89        23.87        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06L TCGA-AX-A0IS 
       35.34        45.99        79.46        49.87        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.74        37.78        40.11        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       71.24        56.91        86.37        55.30        86.01        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11H 
       64.21        63.55        27.85        13.45       185.79        88.34 
TCGA-B5-A11I TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       75.72        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        19.59        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       48.56        23.47        43.04        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       23.70        35.90        34.98        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V7 TCGA-BS-A0V8 
      114.90        82.39        81.57        72.72        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZU 
       66.48        16.83        29.95         8.55         0.56        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 
       23.93        22.55        39.48        30.08         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        3.65        17.49         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  MLL4 MUTATED MLL4 WILD-TYPE 
          1.58           0.56 
  MLL4 MUTATED MLL4 WILD-TYPE 
        129.80         185.79 
  MLL4 MUTATED MLL4 WILD-TYPE 
         44.45          35.56 
[1] "1.6 - 129.8 (44.5)" "0.6 - 185.8 (35.6)"
[1] "hr="     "8.5e+07"
D166V2, binary
                cls
clus               0   1
  MLL4 MUTATED    20  10
  MLL4 WILD-TYPE 137  81
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     20   10
  MLL4 WILD-TYPE  137   81
     clus
vv    MLL4 MUTATED MLL4 WILD-TYPE
  NO            20            137
  YES           10             81
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MLL4 MUTATED                                        29
  MLL4 WILD-TYPE                                     171
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  MLL4 MUTATED                               0
  MLL4 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  MLL4 MUTATED                                   1
  MLL4 WILD-TYPE                                43
D166V3, multiclass
                                         clus
vv                                        MLL4 MUTATED MLL4 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           29            171
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  1             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MLL4 MUTATED    23   2   0   1
  MLL4 WILD-TYPE 149   8   7  17
D166V4, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  R0           23            149
  R1            2              8
  R2            0              7
  RX            1             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"

Clustering(167) Variable = MSN MUTATION ANALYSIS
D167V1, survival
               sevent
clus2             0   1
  MSN MUTATED    14   1
  MSN WILD-TYPE 201  32
  MSN MUTATED MSN WILD-TYPE 
           15           233 
  MSN MUTATED MSN WILD-TYPE 
            1            32 
$`MSN MUTATED`
TCGA-A5-A0GP TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM 
       46.55       129.80        21.99        86.07        48.03        27.12 
TCGA-AX-A05Z TCGA-B5-A0JY TCGA-BS-A0UJ TCGA-BS-A0UT TCGA-BS-A0UV TCGA-D1-A0ZP 
       71.51        69.27        82.39        72.72        73.25        29.95 
TCGA-D1-A103 TCGA-D1-A15X TCGA-FI-A2EW 
       21.99        29.88        59.01 

$`MSN WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A054 
       29.06        28.77        42.35        15.95        20.25        23.31 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       63.91        45.53        36.89        23.87        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       49.22        25.08        46.78        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       80.55        88.24        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        61.08        35.74        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       77.39        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       55.30        86.01        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       44.78        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       31.00        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UL TCGA-BS-A0UM 
       97.41        92.88       114.90        85.84        81.57        86.93 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ 
       89.59        63.58        83.64        66.48        16.83         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       39.48        30.08         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33         9.34        30.67 

  MSN MUTATED MSN WILD-TYPE 
        21.99          0.56 
  MSN MUTATED MSN WILD-TYPE 
       129.80        185.79 
  MSN MUTATED MSN WILD-TYPE 
        59.01         35.38 
[1] "22.0 - 129.8 (59.0)" "0.6 - 185.8 (35.4)" 
[1] "hr=" "2.8"
D167V2, binary
               cls
clus              0   1
  MSN MUTATED    10   5
  MSN WILD-TYPE 147  86
[1] "tbl2"
               cls
clus            [,1] [,2]
  MSN MUTATED     10    5
  MSN WILD-TYPE  147   86
     clus
vv    MSN MUTATED MSN WILD-TYPE
  NO           10           147
  YES           5            86
[1] 2 2
[1] FALSE
               vv
clus            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MSN MUTATED                                        11
  MSN WILD-TYPE                                     189
               vv
clus            MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  MSN MUTATED                               0                                 4
  MSN WILD-TYPE                             4                                40
D167V3, multiclass
                                         clus
vv                                        MSN MUTATED MSN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA          11           189
  MIXED SEROUS AND ENDOMETRIOID                     0             4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                 4            40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  MSN MUTATED    11   1   1   1
  MSN WILD-TYPE 161   9   6  17
D167V4, multiclass
    clus
vv   MSN MUTATED MSN WILD-TYPE
  R0          11           161
  R1           1             9
  R2           1             6
  RX           1            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"

Clustering(168) Variable = MAPK8 MUTATION ANALYSIS
D168V1, survival
                 sevent
clus2               0   1
  MAPK8 MUTATED    11   0
  MAPK8 WILD-TYPE 204  33
  MAPK8 MUTATED MAPK8 WILD-TYPE 
             11             237 
  MAPK8 MUTATED MAPK8 WILD-TYPE 
              0              33 
$`MAPK8 MUTATED`
TCGA-AP-A0LF TCGA-A5-A0GP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-B5-A0JR 
       93.99        46.55       129.80        86.07        48.03        56.91 
TCGA-B5-A0JY TCGA-BK-A0C9 TCGA-BS-A0UV TCGA-D1-A101 TCGA-D1-A17Q 
       69.27        35.90        73.25         1.74         1.78 

$`MAPK8 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A1CP 
       88.18        60.53       110.63        57.80        67.66        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       65.75        60.53        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 
       28.77        42.35        15.95        20.25        21.99        23.31 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       63.91        45.53        36.89        23.87        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       80.78        49.22        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       37.78        40.11        77.39        34.65        25.51        71.24 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        15.45        23.70        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       31.00        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        92.88       114.90        85.84        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93        22.55        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  MAPK8 MUTATED MAPK8 WILD-TYPE 
           1.74            0.56 
  MAPK8 MUTATED MAPK8 WILD-TYPE 
         129.80          185.79 
  MAPK8 MUTATED MAPK8 WILD-TYPE 
          56.91           35.34 
[1] "1.7 - 129.8 (56.9)" "0.6 - 185.8 (35.3)"
[1] "hr="     "2.7e+07"
D168V2, binary
                 cls
clus                0   1
  MAPK8 MUTATED     9   2
  MAPK8 WILD-TYPE 148  89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK8 MUTATED      9    2
  MAPK8 WILD-TYPE  148   89
     clus
vv    MAPK8 MUTATED MAPK8 WILD-TYPE
  NO              9             148
  YES             2              89
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MAPK8 MUTATED                                        11
  MAPK8 WILD-TYPE                                     189
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  MAPK8 MUTATED                               0
  MAPK8 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  MAPK8 MUTATED                                   0
  MAPK8 WILD-TYPE                                44
D168V3, multiclass
                                         clus
vv                                        MAPK8 MUTATED MAPK8 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            11             189
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MAPK8 MUTATED     7   0   1   1
  MAPK8 WILD-TYPE 165  10   6  17
D168V4, multiclass
    clus
vv   MAPK8 MUTATED MAPK8 WILD-TYPE
  R0             7             165
  R1             0              10
  R2             1               6
  RX             1              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"

Clustering(169) Variable = RBL2 MUTATION ANALYSIS
D169V1, survival
                sevent
clus2              0   1
  RBL2 MUTATED    11   1
  RBL2 WILD-TYPE 204  32
  RBL2 MUTATED RBL2 WILD-TYPE 
            12            236 
  RBL2 MUTATED RBL2 WILD-TYPE 
             1             32 
$`RBL2 MUTATED`
TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J1 TCGA-B5-A11E 
      129.80        23.31        27.12        71.51        77.39        59.84 
TCGA-BS-A0TJ TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A15W TCGA-D1-A160 TCGA-D1-A16X 
       67.99        85.84        73.25        30.08         3.68         3.65 

$`RBL2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        86.07        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        40.11        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        86.37        55.30        86.01        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        13.45       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0U5 
       85.55        78.21         4.80        77.95        61.87        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        92.88       114.90        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15X 
       23.93        22.55         1.74        21.99        39.48        29.88 
TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        1.91        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       18.67        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  RBL2 MUTATED RBL2 WILD-TYPE 
          3.65           0.56 
  RBL2 MUTATED RBL2 WILD-TYPE 
        129.80         185.79 
  RBL2 MUTATED RBL2 WILD-TYPE 
        63.915         35.820 
[1] "3.6 - 129.8 (63.9)" "0.6 - 185.8 (35.8)"
[1] "hr=" "2.1"
D169V2, binary
                cls
clus               0   1
  RBL2 MUTATED     8   4
  RBL2 WILD-TYPE 149  87
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED      8    4
  RBL2 WILD-TYPE  149   87
     clus
vv    RBL2 MUTATED RBL2 WILD-TYPE
  NO             8            149
  YES            4             87
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  RBL2 MUTATED                                        12
  RBL2 WILD-TYPE                                     188
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  RBL2 MUTATED                               0
  RBL2 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  RBL2 MUTATED                                   0
  RBL2 WILD-TYPE                                44
D169V3, multiclass
                                         clus
vv                                        RBL2 MUTATED RBL2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           12            188
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RBL2 MUTATED     8   2   0   1
  RBL2 WILD-TYPE 164   8   7  17
D169V4, multiclass
    clus
vv   RBL2 MUTATED RBL2 WILD-TYPE
  R0            8            164
  R1            2              8
  R2            0              7
  RX            1             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"

Clustering(170) Variable = PDGFRA MUTATION ANALYSIS
D170V1, survival
                  sevent
clus2                0   1
  PDGFRA MUTATED    11   1
  PDGFRA WILD-TYPE 204  32
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              12              236 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
               1               32 
$`PDGFRA MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A0K9 
      129.80        86.07        27.12        40.11        69.27        13.45 
TCGA-B5-A11E TCGA-B5-A11J TCGA-BS-A0TI TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A17Q 
       59.84        54.44        61.87        85.84        73.25         1.78 

$`PDGFRA WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       66.25        36.36        97.71        46.72        83.97        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       61.08        35.74        37.78        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       71.24        56.91        86.37        55.30        86.01        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       63.55        27.85       185.79       113.36        88.34        75.72 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       44.78        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       31.00        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
        4.80        77.95        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       92.88       114.90        82.39        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       18.67         3.65        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  PDGFRA MUTATED PDGFRA WILD-TYPE 
            1.78             0.56 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
          129.80           185.79 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
          60.855           35.360 
[1] "1.8 - 129.8 (60.9)" "0.6 - 185.8 (35.4)"
[1] "hr=" "2.3"
D170V2, binary
                  cls
clus                 0   1
  PDGFRA MUTATED     9   3
  PDGFRA WILD-TYPE 148  88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED      9    3
  PDGFRA WILD-TYPE  148   88
     clus
vv    PDGFRA MUTATED PDGFRA WILD-TYPE
  NO               9              148
  YES              3               88
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PDGFRA MUTATED                                        12
  PDGFRA WILD-TYPE                                     188
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  PDGFRA MUTATED                               0
  PDGFRA WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  PDGFRA MUTATED                                   0
  PDGFRA WILD-TYPE                                44
D170V3, multiclass
                                         clus
vv                                        PDGFRA MUTATED PDGFRA WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             12              188
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PDGFRA MUTATED     8   0   0   0
  PDGFRA WILD-TYPE 164  10   7  18
D170V4, multiclass
    clus
vv   PDGFRA MUTATED PDGFRA WILD-TYPE
  R0              8              164
  R1              0               10
  R2              0                7
  RX              0               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"

Clustering(171) Variable = TMEM62 MUTATION ANALYSIS
D171V1, survival
                  sevent
clus2                0   1
  TMEM62 MUTATED     9   0
  TMEM62 WILD-TYPE 206  33
  TMEM62 MUTATED TMEM62 WILD-TYPE 
               9              239 
  TMEM62 MUTATED TMEM62 WILD-TYPE 
               0               33 
$`TMEM62 MUTATED`
TCGA-A5-A0VP TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A063 TCGA-B5-A0JY TCGA-BG-A0VW 
       42.35        27.12        71.51        79.46        69.27        52.01 
TCGA-BK-A0CB TCGA-BS-A0UV TCGA-D1-A103 
       35.90        73.25        21.99 

$`TMEM62 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       24.62        29.06        28.77        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       35.34        45.99        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.74        37.78        40.11        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       71.24        56.91        86.37        55.30        86.01        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VX 
       59.74        21.17        20.28        15.42        51.06        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        92.88       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        86.93        72.72        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W 
       28.67        23.93        22.55         1.74        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69        18.67         3.65        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.78        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  TMEM62 MUTATED TMEM62 WILD-TYPE 
           21.99             0.56 
  TMEM62 MUTATED TMEM62 WILD-TYPE 
           79.46           185.79 
  TMEM62 MUTATED TMEM62 WILD-TYPE 
           52.01            35.38 
[1] "22.0 - 79.5 (52.0)" "0.6 - 185.8 (35.4)"
[1] "hr="     "2.6e+07"
D171V2, binary
                  cls
clus                 0   1
  TMEM62 MUTATED     7   2
  TMEM62 WILD-TYPE 150  89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM62 MUTATED      7    2
  TMEM62 WILD-TYPE  150   89
     clus
vv    TMEM62 MUTATED TMEM62 WILD-TYPE
  NO               7              150
  YES              2               89
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  TMEM62 MUTATED                                         9
  TMEM62 WILD-TYPE                                     191
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  TMEM62 MUTATED                               0
  TMEM62 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  TMEM62 MUTATED                                   0
  TMEM62 WILD-TYPE                                44
D171V3, multiclass
                                         clus
vv                                        TMEM62 MUTATED TMEM62 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              9              191
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TMEM62 MUTATED     7   1   0   0
  TMEM62 WILD-TYPE 165   9   7  18
D171V4, multiclass
    clus
vv   TMEM62 MUTATED TMEM62 WILD-TYPE
  R0              7              165
  R1              1                9
  R2              0                7
  RX              0               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"

Clustering(172) Variable = RG9MTD3 MUTATION ANALYSIS
D172V1, survival
                   sevent
clus2                 0   1
  RG9MTD3 MUTATED     7   1
  RG9MTD3 WILD-TYPE 208  32
  RG9MTD3 MUTATED RG9MTD3 WILD-TYPE 
                8               240 
  RG9MTD3 MUTATED RG9MTD3 WILD-TYPE 
                1                32 
$`RG9MTD3 MUTATED`
TCGA-AP-A051 TCGA-AX-A063 TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A0K8 TCGA-BS-A0UF 
      129.80        79.46        40.11        69.27        27.85        85.84 
TCGA-D1-A17Q TCGA-EY-A1GS 
        1.78        22.03 

$`RG9MTD3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06H 
       88.24        71.51        35.34        45.99        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        61.08        35.74        37.78        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 
       82.39        81.57        86.93        72.72        73.25        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       26.37        10.22         1.51        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       10.92        37.71        77.33        59.01         9.34        30.67 

  RG9MTD3 MUTATED RG9MTD3 WILD-TYPE 
             1.78              0.56 
  RG9MTD3 MUTATED RG9MTD3 WILD-TYPE 
           129.80            185.79 
  RG9MTD3 MUTATED RG9MTD3 WILD-TYPE 
            54.69             35.82 
[1] "1.8 - 129.8 (54.7)" "0.6 - 185.8 (35.8)"
[1] "hr=" "1.5"
D172V2, binary
                   cls
clus                  0   1
  RG9MTD3 MUTATED     7   1
  RG9MTD3 WILD-TYPE 150  90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RG9MTD3 MUTATED      7    1
  RG9MTD3 WILD-TYPE  150   90
     clus
vv    RG9MTD3 MUTATED RG9MTD3 WILD-TYPE
  NO                7               150
  YES               1                90
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  RG9MTD3 MUTATED                                         6
  RG9MTD3 WILD-TYPE                                     194
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  RG9MTD3 MUTATED                               0
  RG9MTD3 WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  RG9MTD3 MUTATED                                   2
  RG9MTD3 WILD-TYPE                                42
D172V3, multiclass
                                         clus
vv                                        RG9MTD3 MUTATED RG9MTD3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               6               194
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     2                42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  RG9MTD3 MUTATED     5   0   1   0
  RG9MTD3 WILD-TYPE 167  10   6  18
D172V4, multiclass
    clus
vv   RG9MTD3 MUTATED RG9MTD3 WILD-TYPE
  R0               5               167
  R1               0                10
  R2               1                 6
  RX               0                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"

Clustering(173) Variable = KANK4 MUTATION ANALYSIS
D173V1, survival
                 sevent
clus2               0   1
  KANK4 MUTATED    10   1
  KANK4 WILD-TYPE 205  32
  KANK4 MUTATED KANK4 WILD-TYPE 
             11             237 
  KANK4 MUTATED KANK4 WILD-TYPE 
              1              32 
$`KANK4 MUTATED`
TCGA-AP-A056 TCGA-AP-A0LM TCGA-AP-A0LT TCGA-B5-A11E TCGA-B5-A11N TCGA-BS-A0UV 
       86.07        27.12        49.22        59.84        61.68        73.25 
TCGA-D1-A15X TCGA-D1-A167 TCGA-D1-A16F TCGA-D1-A16X TCGA-D1-A17R 
       29.88        15.72         2.63         3.65        11.15 

$`KANK4 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LV TCGA-AP-A1DQ 
       82.52        33.40        61.64        80.78        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       57.76        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O 
      113.36        88.34        75.72        54.44        44.78        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       85.84        82.39        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       21.99        39.48        30.08         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
       10.65         0.69        18.67        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  KANK4 MUTATED KANK4 WILD-TYPE 
           2.63            0.56 
  KANK4 MUTATED KANK4 WILD-TYPE 
          86.07          185.79 
  KANK4 MUTATED KANK4 WILD-TYPE 
          29.88           35.90 
[1] "2.6 - 86.1 (29.9)"  "0.6 - 185.8 (35.9)"
[1] "hr=" "1.2"
D173V2, binary
                 cls
clus                0   1
  KANK4 MUTATED     8   3
  KANK4 WILD-TYPE 149  88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK4 MUTATED      8    3
  KANK4 WILD-TYPE  149   88
     clus
vv    KANK4 MUTATED KANK4 WILD-TYPE
  NO              8             149
  YES             3              88
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  KANK4 MUTATED                                        10
  KANK4 WILD-TYPE                                     190
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  KANK4 MUTATED                               0
  KANK4 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  KANK4 MUTATED                                   1
  KANK4 WILD-TYPE                                43
D173V3, multiclass
                                         clus
vv                                        KANK4 MUTATED KANK4 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            10             190
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KANK4 MUTATED     9   0   0   0
  KANK4 WILD-TYPE 163  10   7  18
D173V4, multiclass
    clus
vv   KANK4 MUTATED KANK4 WILD-TYPE
  R0             9             163
  R1             0              10
  R2             0               7
  RX             0              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"

Clustering(174) Variable = MYOM1 MUTATION ANALYSIS
D174V1, survival
                 sevent
clus2               0   1
  MYOM1 MUTATED    20   3
  MYOM1 WILD-TYPE 195  30
  MYOM1 MUTATED MYOM1 WILD-TYPE 
             23             225 
  MYOM1 MUTATED MYOM1 WILD-TYPE 
              3              30 
$`MYOM1 MUTATED`
TCGA-A5-A0GI TCGA-A5-A0GP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LG 
       88.18        46.55       129.80        86.07        48.03        66.25 
TCGA-AP-A0LM TCGA-AX-A05S TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A0K8 TCGA-B5-A11E 
       27.12        13.58        71.51        69.27        27.85        59.84 
TCGA-B5-A1MY TCGA-BK-A139 TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV 
       11.87        31.00        85.84        82.39        81.57        73.25 
TCGA-D1-A103 TCGA-D1-A15X TCGA-D1-A16X TCGA-D1-A17Q TCGA-DI-A0WH 
       21.99        29.88         3.65         1.78        16.31 

$`MYOM1 WILD-TYPE`
TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP 
       60.53       110.63        57.80        93.99        67.66        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       65.75        60.53        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 
       28.77        42.35        15.95        20.25        21.99        23.31 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       63.91        45.53        36.89        23.87        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      125.42       117.99       110.37        36.36        97.71        46.72 
TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       83.97        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       25.08        46.78        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       64.21        63.55        13.45       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-BG-A0LW TCGA-BG-A0LX 
       18.41        17.36        16.57        50.89        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       35.08        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       97.41        92.88       114.90        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       39.48        30.08         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 
       33.63        10.65         0.69        18.67        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  MYOM1 MUTATED MYOM1 WILD-TYPE 
           1.78            0.56 
  MYOM1 MUTATED MYOM1 WILD-TYPE 
         129.80          185.79 
  MYOM1 MUTATED MYOM1 WILD-TYPE 
          48.03           35.74 
[1] "1.8 - 129.8 (48.0)" "0.6 - 185.8 (35.7)"
[1] "hr=" "1.2"
D174V2, binary
                 cls
clus                0   1
  MYOM1 MUTATED    14   9
  MYOM1 WILD-TYPE 143  82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYOM1 MUTATED     14    9
  MYOM1 WILD-TYPE  143   82
     clus
vv    MYOM1 MUTATED MYOM1 WILD-TYPE
  NO             14             143
  YES             9              82
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MYOM1 MUTATED                                        20
  MYOM1 WILD-TYPE                                     180
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  MYOM1 MUTATED                               0
  MYOM1 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  MYOM1 MUTATED                                   3
  MYOM1 WILD-TYPE                                41
D174V3, multiclass
                                         clus
vv                                        MYOM1 MUTATED MYOM1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            20             180
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   3              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MYOM1 MUTATED    17   1   1   0
  MYOM1 WILD-TYPE 155   9   6  18
D174V4, multiclass
    clus
vv   MYOM1 MUTATED MYOM1 WILD-TYPE
  R0            17             155
  R1             1               9
  R2             1               6
  RX             0              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"

Clustering(175) Variable = MORC3 MUTATION ANALYSIS
D175V1, survival
                 sevent
clus2               0   1
  MORC3 MUTATED    10   0
  MORC3 WILD-TYPE 205  33
  MORC3 MUTATED MORC3 WILD-TYPE 
             10             238 
  MORC3 MUTATED MORC3 WILD-TYPE 
              0              33 
$`MORC3 MUTATED`
TCGA-AP-A0LF TCGA-AP-A056 TCGA-AP-A059 TCGA-B5-A0JY TCGA-B5-A11E TCGA-BG-A0MQ 
       93.99        86.07        48.03        69.27        59.84        59.74 
TCGA-BS-A0UF TCGA-D1-A103 TCGA-D1-A177 TCGA-E6-A1LZ 
       85.84        21.99        18.02        79.10 

$`MORC3 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A1CP 
       88.18        60.53       110.63        57.80        67.66        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ 
       96.49        30.74        97.41        92.88       114.90        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        86.93        72.72        73.25        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V 
        4.87        28.67        23.93        22.55         1.74        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       19.53        30.15         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.78        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       18.25        16.31        35.38        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  MORC3 MUTATED MORC3 WILD-TYPE 
          18.02            0.56 
  MORC3 MUTATED MORC3 WILD-TYPE 
          93.99          185.79 
  MORC3 MUTATED MORC3 WILD-TYPE 
         64.555          35.360 
[1] "18.0 - 94.0 (64.6)" "0.6 - 185.8 (35.4)"
[1] "hr="     "2.7e+07"
D175V2, binary
                 cls
clus                0   1
  MORC3 MUTATED     6   4
  MORC3 WILD-TYPE 151  87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC3 MUTATED      6    4
  MORC3 WILD-TYPE  151   87
     clus
vv    MORC3 MUTATED MORC3 WILD-TYPE
  NO              6             151
  YES             4              87
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MORC3 MUTATED                                         9
  MORC3 WILD-TYPE                                     191
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  MORC3 MUTATED                               0
  MORC3 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  MORC3 MUTATED                                   1
  MORC3 WILD-TYPE                                43
D175V3, multiclass
                                         clus
vv                                        MORC3 MUTATED MORC3 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             9             191
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MORC3 MUTATED     7   0   1   0
  MORC3 WILD-TYPE 165  10   6  18
D175V4, multiclass
    clus
vv   MORC3 MUTATED MORC3 WILD-TYPE
  R0             7             165
  R1             0              10
  R2             1               6
  RX             0              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"

Clustering(176) Variable = CCDC82 MUTATION ANALYSIS
D176V1, survival
                  sevent
clus2                0   1
  CCDC82 MUTATED    11   1
  CCDC82 WILD-TYPE 204  32
  CCDC82 MUTATED CCDC82 WILD-TYPE 
              12              236 
  CCDC82 MUTATED CCDC82 WILD-TYPE 
               1               32 
$`CCDC82 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-B5-A11E 
      129.80        86.07        48.03        27.12        71.51        59.84 
TCGA-B5-A11N TCGA-BK-A139 TCGA-BS-A0UF TCGA-D1-A103 TCGA-D1-A16Y TCGA-D1-A17Q 
       61.68        31.00        85.84        21.99        17.49         1.78 

$`CCDC82 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        80.55        88.24        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       37.78        40.11        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        86.37        55.30        86.01        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        13.45       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       75.72        54.44        44.78        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       35.08        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       97.41        92.88       114.90        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       72.72        73.25        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93        22.55         1.74        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
        0.69        18.67         3.65        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  CCDC82 MUTATED CCDC82 WILD-TYPE 
            1.78             0.56 
  CCDC82 MUTATED CCDC82 WILD-TYPE 
          129.80           185.79 
  CCDC82 MUTATED CCDC82 WILD-TYPE 
          53.935           35.820 
[1] "1.8 - 129.8 (53.9)" "0.6 - 185.8 (35.8)"
[1] "hr=" "2"  
D176V2, binary
                  cls
clus                 0   1
  CCDC82 MUTATED     9   3
  CCDC82 WILD-TYPE 148  88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC82 MUTATED      9    3
  CCDC82 WILD-TYPE  148   88
     clus
vv    CCDC82 MUTATED CCDC82 WILD-TYPE
  NO               9              148
  YES              3               88
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CCDC82 MUTATED                                        12
  CCDC82 WILD-TYPE                                     188
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  CCDC82 MUTATED                               0
  CCDC82 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  CCDC82 MUTATED                                   0
  CCDC82 WILD-TYPE                                44
D176V3, multiclass
                                         clus
vv                                        CCDC82 MUTATED CCDC82 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             12              188
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CCDC82 MUTATED     8   1   0   1
  CCDC82 WILD-TYPE 164   9   7  17
D176V4, multiclass
    clus
vv   CCDC82 MUTATED CCDC82 WILD-TYPE
  R0              8              164
  R1              1                9
  R2              0                7
  RX              1               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"

Clustering(177) Variable = B3GALT5 MUTATION ANALYSIS
D177V1, survival
                   sevent
clus2                 0   1
  B3GALT5 MUTATED     4   0
  B3GALT5 WILD-TYPE 211  33
  B3GALT5 MUTATED B3GALT5 WILD-TYPE 
                4               244 
  B3GALT5 MUTATED B3GALT5 WILD-TYPE 
                0                33 
$`B3GALT5 MUTATED`
TCGA-B5-A0JY TCGA-BS-A0UF TCGA-D1-A16X TCGA-D1-A17Q 
       69.27        85.84         3.65         1.78 

$`B3GALT5 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
      129.80        21.99        23.31        86.07        48.03        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89        23.87        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37        66.25        36.36        97.71        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       49.22        25.08        46.78        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       40.11        77.39        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        92.88       114.90        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       86.93        72.72        73.25        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.79         2.63        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 
       33.63        10.65         0.69        18.67        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92        13.22        18.25 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       16.31        35.38        79.10        10.92        37.71        22.03 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       77.33        59.01         9.34        30.67 

  B3GALT5 MUTATED B3GALT5 WILD-TYPE 
             1.78              0.56 
  B3GALT5 MUTATED B3GALT5 WILD-TYPE 
            85.84            185.79 
  B3GALT5 MUTATED B3GALT5 WILD-TYPE 
            36.46             35.90 
[1] "1.8 - 85.8 (36.5)"  "0.6 - 185.8 (35.9)"
[1] "hr="     "9100000"
D177V2, binary
                   cls
clus                  0   1
  B3GALT5 MUTATED     4   0
  B3GALT5 WILD-TYPE 153  91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B3GALT5 MUTATED      4    0
  B3GALT5 WILD-TYPE  153   91
     clus
vv    B3GALT5 MUTATED B3GALT5 WILD-TYPE
  NO                4               153
  YES               0                91
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  B3GALT5 MUTATED                                         4
  B3GALT5 WILD-TYPE                                     196
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  B3GALT5 MUTATED                               0
  B3GALT5 WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  B3GALT5 MUTATED                                   0
  B3GALT5 WILD-TYPE                                44
D177V3, multiclass
                                         clus
vv                                        B3GALT5 MUTATED B3GALT5 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               4               196
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     0                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  B3GALT5 MUTATED     3   0   0   0
  B3GALT5 WILD-TYPE 169  10   7  18
D177V4, multiclass
    clus
vv   B3GALT5 MUTATED B3GALT5 WILD-TYPE
  R0               3               169
  R1               0                10
  R2               0                 7
  RX               0                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"

Clustering(178) Variable = NOC3L MUTATION ANALYSIS
D178V1, survival
                 sevent
clus2               0   1
  NOC3L MUTATED    11   0
  NOC3L WILD-TYPE 204  33
  NOC3L MUTATED NOC3L WILD-TYPE 
             11             237 
  NOC3L MUTATED NOC3L WILD-TYPE 
              0              33 
$`NOC3L MUTATED`
TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J1 TCGA-B5-A11E TCGA-B5-A11N 
       86.07        27.12        71.51        77.39        59.84        61.68 
TCGA-BG-A0MC TCGA-BS-A0TC TCGA-BS-A0TJ TCGA-BS-A0UV TCGA-D1-A17Q 
       41.52        85.55        67.99        73.25         1.78 

$`NOC3L WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 
       61.08        35.74        37.78        40.11        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       71.24        56.91        86.37        55.30        86.01        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q 
       88.34        75.72        54.44        44.78        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       74.63        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD 
       35.08        31.00        24.99        46.95        24.33        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
        4.80        77.95        61.87        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       92.88       114.90        85.84        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  NOC3L MUTATED NOC3L WILD-TYPE 
           1.78            0.56 
  NOC3L MUTATED NOC3L WILD-TYPE 
          86.07          185.79 
  NOC3L MUTATED NOC3L WILD-TYPE 
          67.99           35.34 
[1] "1.8 - 86.1 (68.0)"  "0.6 - 185.8 (35.3)"
[1] "hr="     "2.7e+07"
D178V2, binary
                 cls
clus                0   1
  NOC3L MUTATED     9   2
  NOC3L WILD-TYPE 148  89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOC3L MUTATED      9    2
  NOC3L WILD-TYPE  148   89
     clus
vv    NOC3L MUTATED NOC3L WILD-TYPE
  NO              9             148
  YES             2              89
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  NOC3L MUTATED                                        11
  NOC3L WILD-TYPE                                     189
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  NOC3L MUTATED                               0
  NOC3L WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  NOC3L MUTATED                                   0
  NOC3L WILD-TYPE                                44
D178V3, multiclass
                                         clus
vv                                        NOC3L MUTATED NOC3L WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            11             189
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NOC3L MUTATED     8   1   0   0
  NOC3L WILD-TYPE 164   9   7  18
D178V4, multiclass
    clus
vv   NOC3L MUTATED NOC3L WILD-TYPE
  R0             8             164
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(179) Variable = NSUN4 MUTATION ANALYSIS
D179V1, survival
                 sevent
clus2               0   1
  NSUN4 MUTATED     6   0
  NSUN4 WILD-TYPE 209  33
  NSUN4 MUTATED NSUN4 WILD-TYPE 
              6             242 
  NSUN4 MUTATED NSUN4 WILD-TYPE 
              0              33 
$`NSUN4 MUTATED`
TCGA-AP-A056 TCGA-AX-A0J1 TCGA-B5-A11E TCGA-BK-A0CC TCGA-BS-A0UV TCGA-D1-A17Q 
       86.07        77.39        59.84        35.08        73.25         1.78 

$`NSUN4 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        61.08        35.74        37.78        40.11 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       86.01        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13C 
       23.70        35.90        34.98        35.90        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
      114.90        85.84        82.39        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       18.67         3.65        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  NSUN4 MUTATED NSUN4 WILD-TYPE 
           1.78            0.56 
  NSUN4 MUTATED NSUN4 WILD-TYPE 
          86.07          185.79 
  NSUN4 MUTATED NSUN4 WILD-TYPE 
         66.545          35.820 
[1] "1.8 - 86.1 (66.5)"  "0.6 - 185.8 (35.8)"
[1] "hr="     "2.5e+07"
D179V2, binary
                 cls
clus                0   1
  NSUN4 MUTATED     5   1
  NSUN4 WILD-TYPE 152  90
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN4 MUTATED      5    1
  NSUN4 WILD-TYPE  152   90
     clus
vv    NSUN4 MUTATED NSUN4 WILD-TYPE
  NO              5             152
  YES             1              90
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  NSUN4 MUTATED                                         5
  NSUN4 WILD-TYPE                                     195
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  NSUN4 MUTATED                               0
  NSUN4 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  NSUN4 MUTATED                                   1
  NSUN4 WILD-TYPE                                43
D179V3, multiclass
                                         clus
vv                                        NSUN4 MUTATED NSUN4 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             5             195
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NSUN4 MUTATED     4   0   0   1
  NSUN4 WILD-TYPE 168  10   7  17
D179V4, multiclass
    clus
vv   NSUN4 MUTATED NSUN4 WILD-TYPE
  R0             4             168
  R1             0              10
  R2             0               7
  RX             1              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"

Clustering(180) Variable = ASXL2 MUTATION ANALYSIS
D180V1, survival
                 sevent
clus2               0   1
  ASXL2 MUTATED    14   0
  ASXL2 WILD-TYPE 201  33
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             14             234 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
              0              33 
$`ASXL2 MUTATED`
TCGA-AX-A1CP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z 
       36.39       129.80        86.07        48.03        27.12        71.51 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11H TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A103 
       69.27        59.84        88.34        82.39        73.25        21.99 
TCGA-D1-A174 TCGA-D1-A17Q 
       19.53         1.78 

$`ASXL2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       29.06        28.77        42.35        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       23.31        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        46.72        83.97        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       80.78        49.22        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        80.55        88.24        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       40.11        77.39        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
       13.45       185.79       113.36        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       92.88       114.90        85.84        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
        3.65        17.49        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       10.22         1.51        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  ASXL2 MUTATED ASXL2 WILD-TYPE 
           1.78            0.56 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
         129.80          185.79 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
         64.555          35.360 
[1] "1.8 - 129.8 (64.6)" "0.6 - 185.8 (35.4)"
[1] "hr="     "7.5e+07"
D180V2, binary
                 cls
clus                0   1
  ASXL2 MUTATED    10   4
  ASXL2 WILD-TYPE 147  87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED     10    4
  ASXL2 WILD-TYPE  147   87
     clus
vv    ASXL2 MUTATED ASXL2 WILD-TYPE
  NO             10             147
  YES             4              87
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ASXL2 MUTATED                                        13
  ASXL2 WILD-TYPE                                     187
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  ASXL2 MUTATED                               0
  ASXL2 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  ASXL2 MUTATED                                   1
  ASXL2 WILD-TYPE                                43
D180V3, multiclass
                                         clus
vv                                        ASXL2 MUTATED ASXL2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            13             187
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ASXL2 MUTATED     9   2   0   0
  ASXL2 WILD-TYPE 163   8   7  18
D180V4, multiclass
    clus
vv   ASXL2 MUTATED ASXL2 WILD-TYPE
  R0             9             163
  R1             2               8
  R2             0               7
  RX             0              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"

Clustering(181) Variable = CHD4 MUTATION ANALYSIS
D181V1, survival
                sevent
clus2              0   1
  CHD4 MUTATED    29   6
  CHD4 WILD-TYPE 186  27
  CHD4 MUTATED CHD4 WILD-TYPE 
            35            213 
  CHD4 MUTATED CHD4 WILD-TYPE 
             6             27 
$`CHD4 MUTATED`
TCGA-AP-A05D TCGA-A5-A0R8 TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       57.80        19.59       129.80        86.07        48.03        63.91 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0LN TCGA-AX-A06L TCGA-AX-A0J0 TCGA-AX-A0J1 
       45.53        48.79        82.52        60.66        40.11        77.39 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-B5-A11Z TCGA-BG-A0MG TCGA-BG-A0MI 
       69.27        59.84        61.68        17.36        48.56        23.47 
TCGA-BG-A0MQ TCGA-BG-A0VV TCGA-BG-A2AE TCGA-BK-A0CB TCGA-BK-A13C TCGA-BS-A0T9 
       59.74        51.06        23.70        35.90        24.99        46.95 
TCGA-BS-A0TC TCGA-BS-A0UV TCGA-D1-A0ZP TCGA-D1-A0ZS TCGA-D1-A103 TCGA-D1-A16E 
       85.55        73.25        29.95         4.87        21.99        36.79 
TCGA-D1-A16G TCGA-D1-A176 TCGA-D1-A17Q TCGA-EO-A1Y5 TCGA-FI-A2D2 
       27.42        30.15         1.78        10.92        77.33 

$`CHD4 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP 
       88.18        60.53       110.63        93.99        67.66        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G5 
       12.56        19.79         4.44        10.19        46.95        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        37.91        17.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A054 
       28.77        42.35        15.95        20.25        21.99        23.31 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89        23.87        20.91       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A0IS 
       35.34        45.99        79.46        49.87        27.39        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       35.74        37.78        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       13.45       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       44.78        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A121 TCGA-B5-A1MU 
       19.56        19.50        19.59        18.41        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MO TCGA-BG-A0MT 
       71.24        63.68        74.63        41.52        43.04        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       20.28        15.42        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CC TCGA-BK-A139 TCGA-BS-A0TA 
       15.45        35.90        34.98        35.08        31.00        24.33 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        92.88       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        86.93        72.72        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZU TCGA-D1-A0ZV 
       66.48        16.83         8.55         0.56        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       22.55         1.74        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16F TCGA-D1-A16I TCGA-D1-A16J 
       37.32        36.36        37.51         2.63        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       17.49        19.53        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.51        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y8 TCGA-EY-A1GS 
       18.25        16.31        35.38        79.10        37.71        22.03 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  CHD4 MUTATED CHD4 WILD-TYPE 
          1.78           0.56 
  CHD4 MUTATED CHD4 WILD-TYPE 
        129.80         185.79 
  CHD4 MUTATED CHD4 WILD-TYPE 
         48.03          35.08 
[1] "1.8 - 129.8 (48.0)" "0.6 - 185.8 (35.1)"
[1] "hr=" "1.2"
D181V2, binary
                cls
clus               0   1
  CHD4 MUTATED    25  10
  CHD4 WILD-TYPE 132  81
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD4 MUTATED     25   10
  CHD4 WILD-TYPE  132   81
     clus
vv    CHD4 MUTATED CHD4 WILD-TYPE
  NO            25            132
  YES           10             81
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CHD4 MUTATED                                        27
  CHD4 WILD-TYPE                                     173
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  CHD4 MUTATED                               1
  CHD4 WILD-TYPE                             3
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  CHD4 MUTATED                                   7
  CHD4 WILD-TYPE                                37
D181V3, multiclass
                                         clus
vv                                        CHD4 MUTATED CHD4 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           27            173
  MIXED SEROUS AND ENDOMETRIOID                      1              3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  7             37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CHD4 MUTATED    26   1   1   2
  CHD4 WILD-TYPE 146   9   6  16
D181V4, multiclass
    clus
vv   CHD4 MUTATED CHD4 WILD-TYPE
  R0           26            146
  R1            1              9
  R2            1              6
  RX            2             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"

Clustering(182) Variable = FCN1 MUTATION ANALYSIS
D182V1, survival
                sevent
clus2              0   1
  FCN1 MUTATED     6   1
  FCN1 WILD-TYPE 209  32
  FCN1 MUTATED FCN1 WILD-TYPE 
             7            241 
  FCN1 MUTATED FCN1 WILD-TYPE 
             1             32 
$`FCN1 MUTATED`
TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-BG-A0MI TCGA-BS-A0TC TCGA-BS-A0UV 
       48.03        27.12        40.11        23.47        85.55        73.25 
TCGA-D1-A103 
       21.99 

$`FCN1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       71.51        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        61.08        35.74        37.78        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        24.33        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       85.84        82.39        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  FCN1 MUTATED FCN1 WILD-TYPE 
         21.99           0.56 
  FCN1 MUTATED FCN1 WILD-TYPE 
         85.55         185.79 
  FCN1 MUTATED FCN1 WILD-TYPE 
         40.11          35.90 
[1] "22.0 - 85.5 (40.1)" "0.6 - 185.8 (35.9)"
[1] "hr=" "1.1"
D182V2, binary
                cls
clus               0   1
  FCN1 MUTATED     5   2
  FCN1 WILD-TYPE 152  89
[1] "tbl2"
                cls
clus             [,1] [,2]
  FCN1 MUTATED      5    2
  FCN1 WILD-TYPE  152   89
     clus
vv    FCN1 MUTATED FCN1 WILD-TYPE
  NO             5            152
  YES            2             89
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  FCN1 MUTATED                                         7
  FCN1 WILD-TYPE                                     193
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  FCN1 MUTATED                               0
  FCN1 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  FCN1 MUTATED                                   0
  FCN1 WILD-TYPE                                44
D182V3, multiclass
                                         clus
vv                                        FCN1 MUTATED FCN1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            7            193
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FCN1 MUTATED     7   0   0   0
  FCN1 WILD-TYPE 165  10   7  18
D182V4, multiclass
    clus
vv   FCN1 MUTATED FCN1 WILD-TYPE
  R0            7            165
  R1            0             10
  R2            0              7
  RX            0             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"

Clustering(183) Variable = NIPA2 MUTATION ANALYSIS
D183V1, survival
                 sevent
clus2               0   1
  NIPA2 MUTATED     8   0
  NIPA2 WILD-TYPE 207  33
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              8             240 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              0              33 
$`NIPA2 MUTATED`
TCGA-A5-A0GP TCGA-AP-A059 TCGA-AX-A0J1 TCGA-B5-A11Y TCGA-BS-A0UF TCGA-BS-A0UJ 
       46.55        48.03        77.39        18.41        85.84        82.39 
TCGA-D1-A15X TCGA-D1-A17A 
       29.88         1.58 

$`NIPA2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        86.07        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       71.51        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 
       60.66        61.08        35.74        37.78        40.11        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.56        19.50        19.59        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 
      114.90        81.57        86.93        72.72        73.25        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       21.99        39.48        30.08         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17B TCGA-D1-A17C 
       17.49        19.53        30.15        18.02         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.25        16.31        35.38        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       37.71        22.03        77.33        59.01         9.34        30.67 

  NIPA2 MUTATED NIPA2 WILD-TYPE 
           1.58            0.56 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
          85.84          185.79 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
          47.29           35.82 
[1] "1.6 - 85.8 (47.3)"  "0.6 - 185.8 (35.8)"
[1] "hr="     "2.6e+07"
D183V2, binary
                 cls
clus                0   1
  NIPA2 MUTATED     6   2
  NIPA2 WILD-TYPE 151  89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPA2 MUTATED      6    2
  NIPA2 WILD-TYPE  151   89
     clus
vv    NIPA2 MUTATED NIPA2 WILD-TYPE
  NO              6             151
  YES             2              89
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  NIPA2 MUTATED                                         7
  NIPA2 WILD-TYPE                                     193
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  NIPA2 MUTATED                               0
  NIPA2 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  NIPA2 MUTATED                                   1
  NIPA2 WILD-TYPE                                43
D183V3, multiclass
                                         clus
vv                                        NIPA2 MUTATED NIPA2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             7             193
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   1              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NIPA2 MUTATED     7   0   0   0
  NIPA2 WILD-TYPE 165  10   7  18
D183V4, multiclass
    clus
vv   NIPA2 MUTATED NIPA2 WILD-TYPE
  R0             7             165
  R1             0              10
  R2             0               7
  RX             0              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"

Clustering(184) Variable = C14ORF118 MUTATION ANALYSIS
D184V1, survival
                     sevent
clus2                   0   1
  C14ORF118 MUTATED    13   0
  C14ORF118 WILD-TYPE 202  33
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                 13                 235 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                  0                  33 
$`C14ORF118 MUTATED`
TCGA-A5-A0GP TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AP-A0LT TCGA-AX-A05Z 
       46.55        86.07        48.03        27.12        49.22        71.51 
TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11J TCGA-BS-A0UF TCGA-D1-A16X TCGA-D1-A16Y 
       40.11        69.27        54.44        85.84         3.65        17.49 
TCGA-D1-A17Q 
        1.78 

$`C14ORF118 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       61.64        80.78        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        80.55        88.24        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS 
       77.39        34.65        25.51        71.24        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       55.30        86.01        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11M 
       59.84       185.79       113.36        88.34        75.72        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       92.88       114.90        82.39        81.57        86.93        72.72 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       73.25        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        0.69        18.67        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       26.37        10.22         1.51        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
               1.78                0.56 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
              86.07              185.79 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
              48.03               35.38 
[1] "1.8 - 86.1 (48.0)"  "0.6 - 185.8 (35.4)"
[1] "hr="     "2.7e+07"
D184V2, binary
                     cls
clus                    0   1
  C14ORF118 MUTATED    11   2
  C14ORF118 WILD-TYPE 146  89
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF118 MUTATED     11    2
  C14ORF118 WILD-TYPE  146   89
     clus
vv    C14ORF118 MUTATED C14ORF118 WILD-TYPE
  NO                 11                 146
  YES                 2                  89
[1] 2 2
[1] FALSE
                     vv
clus                  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  C14ORF118 MUTATED                                        13
  C14ORF118 WILD-TYPE                                     187
                     vv
clus                  MIXED SEROUS AND ENDOMETRIOID
  C14ORF118 MUTATED                               0
  C14ORF118 WILD-TYPE                             4
                     vv
clus                  SEROUS ENDOMETRIAL ADENOCARCINOMA
  C14ORF118 MUTATED                                   0
  C14ORF118 WILD-TYPE                                44
D184V3, multiclass
                                         clus
vv                                        C14ORF118 MUTATED C14ORF118 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                13                 187
  MIXED SEROUS AND ENDOMETRIOID                           0                   4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                       0                  44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  C14ORF118 MUTATED     9   1   0   1
  C14ORF118 WILD-TYPE 163   9   7  17
D184V4, multiclass
    clus
vv   C14ORF118 MUTATED C14ORF118 WILD-TYPE
  R0                 9                 163
  R1                 1                   9
  R2                 0                   7
  RX                 1                  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"

Clustering(185) Variable = THAP5 MUTATION ANALYSIS
D185V1, survival
                 sevent
clus2               0   1
  THAP5 MUTATED     6   0
  THAP5 WILD-TYPE 209  33
  THAP5 MUTATED THAP5 WILD-TYPE 
              6             242 
  THAP5 MUTATED THAP5 WILD-TYPE 
              0              33 
$`THAP5 MUTATED`
TCGA-AP-A056 TCGA-AX-A0J0 TCGA-B5-A11E TCGA-B5-A11N TCGA-BS-A0UV TCGA-D1-A17Q 
       86.07        40.11        59.84        61.68        73.25         1.78 

$`THAP5 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        61.08        35.74        37.78        77.39 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       86.01        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
      114.90        85.84        82.39        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       18.67         3.65        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  THAP5 MUTATED THAP5 WILD-TYPE 
           1.78            0.56 
  THAP5 MUTATED THAP5 WILD-TYPE 
          86.07          185.79 
  THAP5 MUTATED THAP5 WILD-TYPE 
          60.76           35.56 
[1] "1.8 - 86.1 (60.8)"  "0.6 - 185.8 (35.6)"
[1] "hr="     "2.5e+07"
D185V2, binary
                 cls
clus                0   1
  THAP5 MUTATED     6   0
  THAP5 WILD-TYPE 151  91
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THAP5 MUTATED      6    0
  THAP5 WILD-TYPE  151   91
     clus
vv    THAP5 MUTATED THAP5 WILD-TYPE
  NO              6             151
  YES             0              91
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  THAP5 MUTATED                                         6
  THAP5 WILD-TYPE                                     194
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  THAP5 MUTATED                               0
  THAP5 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  THAP5 MUTATED                                   0
  THAP5 WILD-TYPE                                44
D185V3, multiclass
                                         clus
vv                                        THAP5 MUTATED THAP5 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             6             194
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  THAP5 MUTATED     4   0   0   0
  THAP5 WILD-TYPE 168  10   7  18
D185V4, multiclass
    clus
vv   THAP5 MUTATED THAP5 WILD-TYPE
  R0             4             168
  R1             0              10
  R2             0               7
  RX             0              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"

Clustering(186) Variable = ZNF611 MUTATION ANALYSIS
D186V1, survival
                  sevent
clus2                0   1
  ZNF611 MUTATED    11   1
  ZNF611 WILD-TYPE 204  32
  ZNF611 MUTATED ZNF611 WILD-TYPE 
              12              236 
  ZNF611 MUTATED ZNF611 WILD-TYPE 
               1               32 
$`ZNF611 MUTATED`
TCGA-A5-A0GP TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       46.55        23.31        48.03        27.12        71.51        40.11 
TCGA-B5-A11I TCGA-B5-A11N TCGA-BS-A0UF TCGA-D1-A103 TCGA-D1-A163 TCGA-D1-A17Q 
       75.72        61.68        85.84        21.99        32.58         1.78 

$`ZNF611 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        86.07        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        80.55        88.24        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       37.78        77.39        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       86.37        55.30        86.01        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       54.44        44.78        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       31.00        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       97.41        92.88       114.90        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       72.72        73.25        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93        22.55         1.74        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        1.91         3.68        29.33         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       18.67         3.65        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  ZNF611 MUTATED ZNF611 WILD-TYPE 
            1.78             0.56 
  ZNF611 MUTATED ZNF611 WILD-TYPE 
           85.84           185.79 
  ZNF611 MUTATED ZNF611 WILD-TYPE 
           43.33            35.82 
[1] "1.8 - 85.8 (43.3)"  "0.6 - 185.8 (35.8)"
[1] "hr=" "1.6"
D186V2, binary
                  cls
clus                 0   1
  ZNF611 MUTATED     8   4
  ZNF611 WILD-TYPE 149  87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF611 MUTATED      8    4
  ZNF611 WILD-TYPE  149   87
     clus
vv    ZNF611 MUTATED ZNF611 WILD-TYPE
  NO               8              149
  YES              4               87
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZNF611 MUTATED                                        12
  ZNF611 WILD-TYPE                                     188
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ZNF611 MUTATED                               0
  ZNF611 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZNF611 MUTATED                                   0
  ZNF611 WILD-TYPE                                44
D186V3, multiclass
                                         clus
vv                                        ZNF611 MUTATED ZNF611 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             12              188
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF611 MUTATED     8   2   0   0
  ZNF611 WILD-TYPE 164   8   7  18
D186V4, multiclass
    clus
vv   ZNF611 MUTATED ZNF611 WILD-TYPE
  R0              8              164
  R1              2                8
  R2              0                7
  RX              0               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"

Clustering(187) Variable = ZCCHC18 MUTATION ANALYSIS
D187V1, survival
                   sevent
clus2                 0   1
  ZCCHC18 MUTATED     6   0
  ZCCHC18 WILD-TYPE 209  33
  ZCCHC18 MUTATED ZCCHC18 WILD-TYPE 
                6               242 
  ZCCHC18 MUTATED ZCCHC18 WILD-TYPE 
                0                33 
$`ZCCHC18 MUTATED`
TCGA-AP-A056 TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-BS-A0UF TCGA-D1-A103 TCGA-D1-A160 
       86.07        40.11        69.27        85.84        21.99         3.68 

$`ZCCHC18 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        61.08        35.74        37.78        77.39 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       86.01        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       92.88       114.90        82.39        81.57        86.93        72.72 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       73.25        89.59        63.58        83.64        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       22.55         1.74        39.48        30.08        29.88         1.91 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  ZCCHC18 MUTATED ZCCHC18 WILD-TYPE 
             3.68              0.56 
  ZCCHC18 MUTATED ZCCHC18 WILD-TYPE 
            86.07            185.79 
  ZCCHC18 MUTATED ZCCHC18 WILD-TYPE 
            54.69             35.82 
[1] "3.7 - 86.1 (54.7)"  "0.6 - 185.8 (35.8)"
[1] "hr="     "2.5e+07"
D187V2, binary
                   cls
clus                  0   1
  ZCCHC18 MUTATED     6   0
  ZCCHC18 WILD-TYPE 151  91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZCCHC18 MUTATED      6    0
  ZCCHC18 WILD-TYPE  151   91
     clus
vv    ZCCHC18 MUTATED ZCCHC18 WILD-TYPE
  NO                6               151
  YES               0                91
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZCCHC18 MUTATED                                         6
  ZCCHC18 WILD-TYPE                                     194
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  ZCCHC18 MUTATED                               0
  ZCCHC18 WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZCCHC18 MUTATED                                   0
  ZCCHC18 WILD-TYPE                                44
D187V3, multiclass
                                         clus
vv                                        ZCCHC18 MUTATED ZCCHC18 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               6               194
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     0                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZCCHC18 MUTATED     5   0   0   0
  ZCCHC18 WILD-TYPE 167  10   7  18
D187V4, multiclass
    clus
vv   ZCCHC18 MUTATED ZCCHC18 WILD-TYPE
  R0               5               167
  R1               0                10
  R2               0                 7
  RX               0                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"

Clustering(188) Variable = PRKCE MUTATION ANALYSIS
D188V1, survival
                 sevent
clus2               0   1
  PRKCE MUTATED     9   0
  PRKCE WILD-TYPE 206  33
  PRKCE MUTATED PRKCE WILD-TYPE 
              9             239 
  PRKCE MUTATED PRKCE WILD-TYPE 
              0              33 
$`PRKCE MUTATED`
TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-B5-A11E 
       42.35       129.80        48.03        27.12        40.11        59.84 
TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A16E 
       73.25        21.99        36.79 

$`PRKCE WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       24.62        29.06        28.77        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        86.37        55.30        86.01        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        13.45       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        92.88       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 
       82.39        81.57        86.93        72.72        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V 
        4.87        28.67        23.93        22.55         1.74        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69        18.67         3.65        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.78        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  PRKCE MUTATED PRKCE WILD-TYPE 
          21.99            0.56 
  PRKCE MUTATED PRKCE WILD-TYPE 
         129.80          185.79 
  PRKCE MUTATED PRKCE WILD-TYPE 
          42.35           35.38 
[1] "22.0 - 129.8 (42.4)" "0.6 - 185.8 (35.4)" 
[1] "hr="     "2.7e+07"
D188V2, binary
                 cls
clus                0   1
  PRKCE MUTATED     5   4
  PRKCE WILD-TYPE 152  87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCE MUTATED      5    4
  PRKCE WILD-TYPE  152   87
     clus
vv    PRKCE MUTATED PRKCE WILD-TYPE
  NO              5             152
  YES             4              87
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PRKCE MUTATED                                         9
  PRKCE WILD-TYPE                                     191
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  PRKCE MUTATED                               0
  PRKCE WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  PRKCE MUTATED                                   0
  PRKCE WILD-TYPE                                44
D188V3, multiclass
                                         clus
vv                                        PRKCE MUTATED PRKCE WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             9             191
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PRKCE MUTATED     8   0   0   0
  PRKCE WILD-TYPE 164  10   7  18
D188V4, multiclass
    clus
vv   PRKCE MUTATED PRKCE WILD-TYPE
  R0             8             164
  R1             0              10
  R2             0               7
  RX             0              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"

Clustering(189) Variable = BMP2K MUTATION ANALYSIS
D189V1, survival
                 sevent
clus2               0   1
  BMP2K MUTATED    13   0
  BMP2K WILD-TYPE 202  33
  BMP2K MUTATED BMP2K WILD-TYPE 
             13             235 
  BMP2K MUTATED BMP2K WILD-TYPE 
              0              33 
$`BMP2K MUTATED`
TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A059 TCGA-AX-A05Z TCGA-AX-A0J1 TCGA-B5-A0JR 
       42.35       129.80        48.03        71.51        77.39        56.91 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-D1-A103 TCGA-D1-A16X TCGA-D1-A17A TCGA-D1-A17Q 
       69.27        59.84        21.99         3.65         1.58         1.78 
TCGA-D1-A17T 
        2.33 

$`BMP2K WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       24.62        29.06        28.77        15.95        20.25        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        33.21        29.69        80.55        88.24        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        40.11        34.65        25.51        71.24 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.37        55.30        86.01        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       13.45       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       44.78        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       31.00        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        92.88       114.90        85.84        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       86.93        72.72        73.25        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W 
       28.67        23.93        22.55         1.74        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
        2.63        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
       10.65         0.69        18.67        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
       18.02         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  BMP2K MUTATED BMP2K WILD-TYPE 
           1.58            0.56 
  BMP2K MUTATED BMP2K WILD-TYPE 
         129.80          185.79 
  BMP2K MUTATED BMP2K WILD-TYPE 
          48.03           35.74 
[1] "1.6 - 129.8 (48.0)" "0.6 - 185.8 (35.7)"
[1] "hr="     "2.7e+07"
D189V2, binary
                 cls
clus                0   1
  BMP2K MUTATED    10   3
  BMP2K WILD-TYPE 147  88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP2K MUTATED     10    3
  BMP2K WILD-TYPE  147   88
     clus
vv    BMP2K MUTATED BMP2K WILD-TYPE
  NO             10             147
  YES             3              88
[1] 2 2
[1] FALSE
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  BMP2K MUTATED                                        13
  BMP2K WILD-TYPE                                     187
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  BMP2K MUTATED                               0
  BMP2K WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  BMP2K MUTATED                                   0
  BMP2K WILD-TYPE                                44
D189V3, multiclass
                                         clus
vv                                        BMP2K MUTATED BMP2K WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            13             187
  MIXED SEROUS AND ENDOMETRIOID                       0               4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                   0              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BMP2K MUTATED     9   1   0   0
  BMP2K WILD-TYPE 163   9   7  18
D189V4, multiclass
    clus
vv   BMP2K MUTATED BMP2K WILD-TYPE
  R0             9             163
  R1             1               9
  R2             0               7
  RX             0              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"

Clustering(190) Variable = PRPF38B MUTATION ANALYSIS
D190V1, survival
                   sevent
clus2                 0   1
  PRPF38B MUTATED    11   0
  PRPF38B WILD-TYPE 204  33
  PRPF38B MUTATED PRPF38B WILD-TYPE 
               11               237 
  PRPF38B MUTATED PRPF38B WILD-TYPE 
                0                33 
$`PRPF38B MUTATED`
TCGA-A5-A0VP TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY 
       42.35        27.12        71.51        40.11        77.39        69.27 
TCGA-B5-A11E TCGA-BS-A0UJ TCGA-D1-A103 TCGA-D1-A167 TCGA-D1-A17Q 
       59.84        82.39        21.99        15.72         1.78 

$`PRPF38B WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       24.62        29.06        28.77        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       61.08        35.74        37.78        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        55.30        86.01        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       27.85        13.45       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       17.36        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       15.45        15.45        23.70        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UL 
       30.74        97.41        92.88       114.90        85.84        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       86.93        72.72        73.25        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W 
       28.67        23.93        22.55         1.74        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  PRPF38B MUTATED PRPF38B WILD-TYPE 
             1.78              0.56 
  PRPF38B MUTATED PRPF38B WILD-TYPE 
            82.39            185.79 
  PRPF38B MUTATED PRPF38B WILD-TYPE 
            42.35             35.74 
[1] "1.8 - 82.4 (42.4)"  "0.6 - 185.8 (35.7)"
[1] "hr="     "2.6e+07"
D190V2, binary
                   cls
clus                  0   1
  PRPF38B MUTATED     8   3
  PRPF38B WILD-TYPE 149  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRPF38B MUTATED      8    3
  PRPF38B WILD-TYPE  149   88
     clus
vv    PRPF38B MUTATED PRPF38B WILD-TYPE
  NO                8               149
  YES               3                88
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PRPF38B MUTATED                                        11
  PRPF38B WILD-TYPE                                     189
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  PRPF38B MUTATED                               0
  PRPF38B WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  PRPF38B MUTATED                                   0
  PRPF38B WILD-TYPE                                44
D190V3, multiclass
                                         clus
vv                                        PRPF38B MUTATED PRPF38B WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              11               189
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     0                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PRPF38B MUTATED     8   1   0   0
  PRPF38B WILD-TYPE 164   9   7  18
D190V4, multiclass
    clus
vv   PRPF38B MUTATED PRPF38B WILD-TYPE
  R0               8               164
  R1               1                 9
  R2               0                 7
  RX               0                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"

Clustering(191) Variable = LGMN MUTATION ANALYSIS
D191V1, survival
                sevent
clus2              0   1
  LGMN MUTATED     5   2
  LGMN WILD-TYPE 210  31
  LGMN MUTATED LGMN WILD-TYPE 
             7            241 
  LGMN MUTATED LGMN WILD-TYPE 
             2             31 
$`LGMN MUTATED`
TCGA-A5-A0GA TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A05S TCGA-B5-A0JY TCGA-B5-A11E 
       17.85        86.07        48.03        13.58        69.27        59.84 
TCGA-BS-A0TG 
       77.95 

$`LGMN WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       37.02        83.51        32.78       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       33.40        61.64        80.78        49.22        25.08        46.78 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        79.46        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.74        37.78        40.11        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       71.24        56.91        86.37        55.30        86.01        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        13.45       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       85.55        78.21         4.80        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        92.88       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        86.93        72.72        73.25        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       17.49        19.53        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        37.71        22.03        77.33        59.01         9.34 
TCGA-FI-A2F8 
       30.67 

  LGMN MUTATED LGMN WILD-TYPE 
         13.58           0.56 
  LGMN MUTATED LGMN WILD-TYPE 
         86.07         185.79 
  LGMN MUTATED LGMN WILD-TYPE 
         59.84          35.74 
[1] "13.6 - 86.1 (59.8)" "0.6 - 185.8 (35.7)"
[1] "hr=" "1.9"
D191V2, binary
                cls
clus               0   1
  LGMN MUTATED     4   3
  LGMN WILD-TYPE 153  88
[1] "tbl2"
                cls
clus             [,1] [,2]
  LGMN MUTATED      4    3
  LGMN WILD-TYPE  153   88
     clus
vv    LGMN MUTATED LGMN WILD-TYPE
  NO             4            153
  YES            3             88
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  LGMN MUTATED                                         7
  LGMN WILD-TYPE                                     193
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  LGMN MUTATED                               0
  LGMN WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  LGMN MUTATED                                   0
  LGMN WILD-TYPE                                44
D191V3, multiclass
                                         clus
vv                                        LGMN MUTATED LGMN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            7            193
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LGMN MUTATED     4   0   1   0
  LGMN WILD-TYPE 168  10   6  18
D191V4, multiclass
    clus
vv   LGMN MUTATED LGMN WILD-TYPE
  R0            4            168
  R1            0             10
  R2            1              6
  RX            0             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"

Clustering(192) Variable = SSH2 MUTATION ANALYSIS
D192V1, survival
                sevent
clus2              0   1
  SSH2 MUTATED    12   0
  SSH2 WILD-TYPE 203  33
  SSH2 MUTATED SSH2 WILD-TYPE 
            12            236 
  SSH2 MUTATED SSH2 WILD-TYPE 
             0             33 
$`SSH2 MUTATED`
TCGA-A5-A0GP TCGA-A5-A0VQ TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LT TCGA-AX-A05Z 
       46.55        15.95        86.07        48.03        49.22        71.51 
TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-D1-A15X TCGA-D1-A16X TCGA-D1-A17Q 
       85.55        85.84        82.39        29.88         3.65         1.78 

$`SSH2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 
       29.06        28.77        42.35        20.25       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       23.31        63.91        45.53        36.89        23.87        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       61.64        80.78        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        80.55        88.24        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       49.87        27.39        60.66        61.08        35.74        37.78 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       40.11        77.39        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       86.37        55.30        86.01        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        44.78        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       77.23        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.01        15.45        15.45        23.70        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
       35.90        35.08        31.00        24.99        46.95        24.33 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0UM 
       30.74        97.41        92.88       114.90        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       72.72        73.25        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
        0.69        18.67        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.08        26.37        10.22         1.51        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  SSH2 MUTATED SSH2 WILD-TYPE 
          1.78           0.56 
  SSH2 MUTATED SSH2 WILD-TYPE 
         86.07         185.79 
  SSH2 MUTATED SSH2 WILD-TYPE 
        48.625         35.560 
[1] "1.8 - 86.1 (48.6)"  "0.6 - 185.8 (35.6)"
[1] "hr="     "2.7e+07"
D192V2, binary
                cls
clus               0   1
  SSH2 MUTATED     9   3
  SSH2 WILD-TYPE 148  88
[1] "tbl2"
                cls
clus             [,1] [,2]
  SSH2 MUTATED      9    3
  SSH2 WILD-TYPE  148   88
     clus
vv    SSH2 MUTATED SSH2 WILD-TYPE
  NO             9            148
  YES            3             88
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SSH2 MUTATED                                        11
  SSH2 WILD-TYPE                                     189
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  SSH2 MUTATED                               0
  SSH2 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  SSH2 MUTATED                                   1
  SSH2 WILD-TYPE                                43
D192V3, multiclass
                                         clus
vv                                        SSH2 MUTATED SSH2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           11            189
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  1             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SSH2 MUTATED    11   1   0   0
  SSH2 WILD-TYPE 161   9   7  18
D192V4, multiclass
    clus
vv   SSH2 MUTATED SSH2 WILD-TYPE
  R0           11            161
  R1            1              9
  R2            0              7
  RX            0             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"

Clustering(193) Variable = EMR1 MUTATION ANALYSIS
D193V1, survival
                sevent
clus2              0   1
  EMR1 MUTATED    11   0
  EMR1 WILD-TYPE 204  33
  EMR1 MUTATED EMR1 WILD-TYPE 
            11            237 
  EMR1 MUTATED EMR1 WILD-TYPE 
             0             33 
$`EMR1 MUTATED`
TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A063 TCGA-AX-A0J0 TCGA-B5-A0JY 
       48.03        27.12        71.51        79.46        40.11        69.27 
TCGA-B5-A0K2 TCGA-B5-A11N TCGA-BS-A0UF TCGA-D1-A103 TCGA-D1-A17Q 
       72.62        61.68        85.84        21.99         1.78 

$`EMR1 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       35.34        45.99        49.87        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       35.74        37.78        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        86.37        55.30        86.01        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       36.49        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       54.44        44.78        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       16.73        19.56        19.50        19.59        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       16.57        50.89        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       31.00        24.99        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       97.41        92.88       114.90        82.39        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       72.72        73.25        89.59        63.58        83.64        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93        22.55         1.74        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F 
       36.10        37.32        36.36        37.51        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 
        0.69        18.67         3.65        17.49        19.53        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
       28.01        28.08        26.37        10.22         1.51        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  EMR1 MUTATED EMR1 WILD-TYPE 
          1.78           0.56 
  EMR1 MUTATED EMR1 WILD-TYPE 
         85.84         185.79 
  EMR1 MUTATED EMR1 WILD-TYPE 
         61.68          35.38 
[1] "1.8 - 85.8 (61.7)"  "0.6 - 185.8 (35.4)"
[1] "hr="     "2.6e+07"
D193V2, binary
                cls
clus               0   1
  EMR1 MUTATED     9   2
  EMR1 WILD-TYPE 148  89
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMR1 MUTATED      9    2
  EMR1 WILD-TYPE  148   89
     clus
vv    EMR1 MUTATED EMR1 WILD-TYPE
  NO             9            148
  YES            2             89
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  EMR1 MUTATED                                        11
  EMR1 WILD-TYPE                                     189
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  EMR1 MUTATED                               0
  EMR1 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  EMR1 MUTATED                                   0
  EMR1 WILD-TYPE                                44
D193V3, multiclass
                                         clus
vv                                        EMR1 MUTATED EMR1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           11            189
  MIXED SEROUS AND ENDOMETRIOID                      0              4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                  0             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EMR1 MUTATED     7   1   0   0
  EMR1 WILD-TYPE 165   9   7  18
D193V4, multiclass
    clus
vv   EMR1 MUTATED EMR1 WILD-TYPE
  R0            7            165
  R1            1              9
  R2            0              7
  RX            0             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"

Clustering(194) Variable = OR5AK2 MUTATION ANALYSIS
D194V1, survival
                  sevent
clus2                0   1
  OR5AK2 MUTATED     5   0
  OR5AK2 WILD-TYPE 210  33
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
               5              243 
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
               0               33 
$`OR5AK2 MUTATED`
TCGA-AP-A051 TCGA-AX-A05Z TCGA-B5-A11E TCGA-BS-A0UF TCGA-BS-A0UV 
      129.80        71.51        59.84        85.84        73.25 

$`OR5AK2 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        46.78        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H 
       88.24        35.34        45.99        79.46        49.87        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        61.08        35.74        37.78        40.11        77.39 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       34.65        25.51        71.24        56.91        86.37        55.30 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       86.01        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
      185.79       113.36        88.34        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       19.56        19.50        19.59        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       50.89        11.87        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        71.24        63.68        74.63        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       92.88       114.90        82.39        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       18.67         3.65        17.49        19.53        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       24.30         2.33        22.92        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 
       35.38        79.10        10.92        37.71        22.03        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.34        30.67 

  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
           59.84             0.56 
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
          129.80           185.79 
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
           73.25            35.38 
[1] "59.8 - 129.8 (73.2)" "0.6 - 185.8 (35.4)" 
[1] "hr="     "2.7e+07"
D194V2, binary
                  cls
clus                 0   1
  OR5AK2 MUTATED     4   1
  OR5AK2 WILD-TYPE 153  90
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5AK2 MUTATED      4    1
  OR5AK2 WILD-TYPE  153   90
     clus
vv    OR5AK2 MUTATED OR5AK2 WILD-TYPE
  NO               4              153
  YES              1               90
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  OR5AK2 MUTATED                                         5
  OR5AK2 WILD-TYPE                                     195
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  OR5AK2 MUTATED                               0
  OR5AK2 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  OR5AK2 MUTATED                                   0
  OR5AK2 WILD-TYPE                                44
D194V3, multiclass
                                         clus
vv                                        OR5AK2 MUTATED OR5AK2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              5              195
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR5AK2 MUTATED     3   1   0   0
  OR5AK2 WILD-TYPE 169   9   7  18
D194V4, multiclass
    clus
vv   OR5AK2 MUTATED OR5AK2 WILD-TYPE
  R0              3              169
  R1              1                9
  R2              0                7
  RX              0               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"

Clustering(195) Variable = C1ORF101 MUTATION ANALYSIS
D195V1, survival
                    sevent
clus2                  0   1
  C1ORF101 MUTATED    12   0
  C1ORF101 WILD-TYPE 203  33
  C1ORF101 MUTATED C1ORF101 WILD-TYPE 
                12                236 
  C1ORF101 MUTATED C1ORF101 WILD-TYPE 
                 0                 33 
$`C1ORF101 MUTATED`
TCGA-A5-A0GP TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       46.55        86.07        48.03        27.12        71.51        40.11 
TCGA-B5-A0K6 TCGA-BG-A0LX TCGA-BK-A0C9 TCGA-BS-A0TC TCGA-BS-A0UV TCGA-D1-A16Y 
       64.21        20.19        35.90        85.55        73.25        17.49 

$`C1ORF101 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        60.53        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       29.06        28.77        42.35        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        46.72        83.97        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S 
       61.64        80.78        49.22        25.08        46.78        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        80.55        88.24        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR 
       37.78        77.39        34.65        25.51        71.24        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       86.37        55.30        86.01        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K7 TCGA-B5-A0K8 
       36.49        72.62        27.29        57.76        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       73.28        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0M0 
       17.36        16.57        50.89        11.87        18.61        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC 
       20.94        35.21        71.24        63.68        74.63        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       15.45        23.70        34.98        35.90        35.08        31.00 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       24.99        46.95        24.33        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
      114.90        85.84        82.39        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        83.64        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G 
       37.32        36.36        37.51        36.79         2.63        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       18.67         3.65        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  C1ORF101 MUTATED C1ORF101 WILD-TYPE 
             17.49               0.56 
  C1ORF101 MUTATED C1ORF101 WILD-TYPE 
             86.07             185.79 
  C1ORF101 MUTATED C1ORF101 WILD-TYPE 
             47.29              35.36 
[1] "17.5 - 86.1 (47.3)" "0.6 - 185.8 (35.4)"
[1] "hr="     "2.7e+07"
D195V2, binary
                    cls
clus                   0   1
  C1ORF101 MUTATED     9   3
  C1ORF101 WILD-TYPE 148  88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF101 MUTATED      9    3
  C1ORF101 WILD-TYPE  148   88
     clus
vv    C1ORF101 MUTATED C1ORF101 WILD-TYPE
  NO                 9                148
  YES                3                 88
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  C1ORF101 MUTATED                                        12
  C1ORF101 WILD-TYPE                                     188
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  C1ORF101 MUTATED                               0
  C1ORF101 WILD-TYPE                             4
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  C1ORF101 MUTATED                                   0
  C1ORF101 WILD-TYPE                                44
D195V3, multiclass
                                         clus
vv                                        C1ORF101 MUTATED C1ORF101 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               12                188
  MIXED SEROUS AND ENDOMETRIOID                          0                  4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      0                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C1ORF101 MUTATED     9   1   0   1
  C1ORF101 WILD-TYPE 163   9   7  17
D195V4, multiclass
    clus
vv   C1ORF101 MUTATED C1ORF101 WILD-TYPE
  R0                9                163
  R1                1                  9
  R2                0                  7
  RX                1                 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"

Clustering(196) Variable = ZNF534 MUTATION ANALYSIS
D196V1, survival
                  sevent
clus2                0   1
  ZNF534 MUTATED     9   0
  ZNF534 WILD-TYPE 206  33
  ZNF534 MUTATED ZNF534 WILD-TYPE 
               9              239 
  ZNF534 MUTATED ZNF534 WILD-TYPE 
               0               33 
$`ZNF534 MUTATED`
TCGA-A5-A0VP TCGA-AP-A056 TCGA-AX-A05Z TCGA-B5-A11E TCGA-BS-A0UF TCGA-BS-A0UV 
       42.35        86.07        71.51        59.84        85.84        73.25 
TCGA-D1-A103 TCGA-D1-A174 TCGA-D1-A17Q 
       21.99        19.53         1.78 

$`ZNF534 WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 
       24.62        29.06        28.77        15.95        20.25       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       46.78        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       61.08        35.74        37.78        40.11        77.39        34.65 
TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       25.51        71.24        56.91        86.37        55.30        86.01 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       57.76        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        44.78        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       19.50        19.59        18.41        17.36        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       11.87        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       13.78        14.73        14.01        15.45        15.45        23.70 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
      114.90        82.39        81.57        86.93        72.72        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.51        36.79         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       17.49        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
        1.51        11.15        24.30         2.33        22.92        13.22 
TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        79.10        10.92        37.71 
TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       22.03        77.33        59.01         9.34        30.67 

  ZNF534 MUTATED ZNF534 WILD-TYPE 
            1.78             0.56 
  ZNF534 MUTATED ZNF534 WILD-TYPE 
           86.07           185.79 
  ZNF534 MUTATED ZNF534 WILD-TYPE 
           59.84            35.74 
[1] "1.8 - 86.1 (59.8)"  "0.6 - 185.8 (35.7)"
[1] "hr="     "2.6e+07"
D196V2, binary
                  cls
clus                 0   1
  ZNF534 MUTATED     7   2
  ZNF534 WILD-TYPE 150  89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF534 MUTATED      7    2
  ZNF534 WILD-TYPE  150   89
     clus
vv    ZNF534 MUTATED ZNF534 WILD-TYPE
  NO               7              150
  YES              2               89
[1] 2 2
[1] FALSE
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZNF534 MUTATED                                         9
  ZNF534 WILD-TYPE                                     191
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ZNF534 MUTATED                               0
  ZNF534 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZNF534 MUTATED                                   0
  ZNF534 WILD-TYPE                                44
D196V3, multiclass
                                         clus
vv                                        ZNF534 MUTATED ZNF534 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              9              191
  MIXED SEROUS AND ENDOMETRIOID                        0                4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    0               44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF534 MUTATED     7   1   0   0
  ZNF534 WILD-TYPE 165   9   7  18
D196V4, multiclass
    clus
vv   ZNF534 MUTATED ZNF534 WILD-TYPE
  R0              7              165
  R1              1                9
  R2              0                7
  RX              0               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"

Clustering(197) Variable = FAM122A MUTATION ANALYSIS
D197V1, survival
                   sevent
clus2                 0   1
  FAM122A MUTATED     5   1
  FAM122A WILD-TYPE 210  32
  FAM122A MUTATED FAM122A WILD-TYPE 
                6               242 
  FAM122A MUTATED FAM122A WILD-TYPE 
                1                32 
$`FAM122A MUTATED`
TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A05S TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-BS-A0UF 
       86.07        48.03        13.58        40.11        69.27        85.84 

$`FAM122A WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       88.18        60.53       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       36.39        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 
       51.55        12.56        19.79         4.44        10.19        46.95 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       24.62        29.06        28.77        42.35        15.95        20.25 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
      129.80        21.99        23.31        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DQ TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       46.78        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        79.46        49.87        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       61.08        35.74        37.78        77.39        34.65        25.51 
TCGA-AX-A2H5 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       71.24        56.91        86.37        55.30        86.01        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY 
       19.59        18.41        17.36        16.57        50.89        11.87 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       63.68        74.63        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       14.73        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98        35.90        35.08        31.00        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 
       82.39        81.57        86.93        72.72        73.25        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
       36.36        37.51        36.79         2.63        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
        2.33        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-FI-A2D2 TCGA-FI-A2EW 
       79.10        10.92        37.71        22.03        77.33        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.34        30.67 

  FAM122A MUTATED FAM122A WILD-TYPE 
            13.58              0.56 
  FAM122A MUTATED FAM122A WILD-TYPE 
            86.07            185.79 
  FAM122A MUTATED FAM122A WILD-TYPE 
            58.65             35.56 
[1] "13.6 - 86.1 (58.6)" "0.6 - 185.8 (35.6)"
[1] "hr=" "1"  
D197V2, binary
                   cls
clus                  0   1
  FAM122A MUTATED     4   2
  FAM122A WILD-TYPE 153  89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM122A MUTATED      4    2
  FAM122A WILD-TYPE  153   89
     clus
vv    FAM122A MUTATED FAM122A WILD-TYPE
  NO                4               153
  YES               2                89
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  FAM122A MUTATED                                         6
  FAM122A WILD-TYPE                                     194
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  FAM122A MUTATED                               0
  FAM122A WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  FAM122A MUTATED                                   0
  FAM122A WILD-TYPE                                44
D197V3, multiclass
                                         clus
vv                                        FAM122A MUTATED FAM122A WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               6               194
  MIXED SEROUS AND ENDOMETRIOID                         0                 4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     0                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM122A MUTATED     4   0   1   0
  FAM122A WILD-TYPE 168  10   6  18
D197V4, multiclass
    clus
vv   FAM122A MUTATED FAM122A WILD-TYPE
  R0               4               168
  R1               0                10
  R2               1                 6
  RX               0                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"
