[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[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/10006384/UCEC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCEC-TP/10689339/transformed.cor.cli.txt"

nPatients in clinical file=497, 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 
              83              165 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              83              165 
[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 
             39             209 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             39             209 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            53            195 
  KRAS MUTATED KRAS WILD-TYPE 
            53            195 
[1] "ARHGAP35 MUTATION ANALYSIS"
[1] 3
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                36                212 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                36                212 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             132              116 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             132              116 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              83              165 
  ARID1A MUTATED ARID1A WILD-TYPE 
              83              165 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              74              174 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              74              174 
[1] "FGFR2 MUTATION ANALYSIS"
[1] 3
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             31             217 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             31             217 
[1] "ZFHX3 MUTATION ANALYSIS"
[1] 3
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             44             204 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             44             204 
[1] "TCP11L2 MUTATION ANALYSIS"
[1] 3
  TCP11L2 MUTATED TCP11L2 WILD-TYPE 
               14               234 
  TCP11L2 MUTATED TCP11L2 WILD-TYPE 
               14               234 
[1] "SPOP MUTATION ANALYSIS"
[1] 3
  SPOP MUTATED SPOP WILD-TYPE 
            21            227 
  SPOP MUTATED SPOP WILD-TYPE 
            21            227 
[1] "RBMX MUTATION ANALYSIS"
[1] 3
  RBMX MUTATED RBMX WILD-TYPE 
            13            235 
  RBMX MUTATED RBMX WILD-TYPE 
            13            235 
[1] "SOX17 MUTATION ANALYSIS"
[1] 3
  SOX17 MUTATED SOX17 WILD-TYPE 
              7             241 
  SOX17 MUTATED SOX17 WILD-TYPE 
              7             241 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              15              233 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              15              233 
[1] "CCND1 MUTATION ANALYSIS"
[1] 3
  CCND1 MUTATED CCND1 WILD-TYPE 
             14             234 
  CCND1 MUTATED CCND1 WILD-TYPE 
             14             234 
[1] "GNPTAB MUTATION ANALYSIS"
[1] 3
  GNPTAB MUTATED GNPTAB WILD-TYPE 
              20              228 
  GNPTAB MUTATED GNPTAB WILD-TYPE 
              20              228 
[1] "ARID5B MUTATION ANALYSIS"
[1] 3
  ARID5B MUTATED ARID5B WILD-TYPE 
              29              219 
  ARID5B MUTATED ARID5B WILD-TYPE 
              29              219 
[1] "DNER MUTATION ANALYSIS"
[1] 3
  DNER MUTATED DNER WILD-TYPE 
            18            230 
  DNER MUTATED DNER WILD-TYPE 
            18            230 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
             21             227 
  EP300 MUTATED EP300 WILD-TYPE 
             21             227 
[1] "MAX MUTATION ANALYSIS"
[1] 3
  MAX MUTATED MAX WILD-TYPE 
           11           237 
  MAX MUTATED MAX WILD-TYPE 
           11           237 
[1] "SGK1 MUTATION ANALYSIS"
[1] 3
  SGK1 MUTATED SGK1 WILD-TYPE 
            15            233 
  SGK1 MUTATED SGK1 WILD-TYPE 
            15            233 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             9            239 
  NRAS MUTATED NRAS WILD-TYPE 
             9            239 
[1] "KLHL8 MUTATION ANALYSIS"
[1] 3
  KLHL8 MUTATED KLHL8 WILD-TYPE 
             12             236 
  KLHL8 MUTATED KLHL8 WILD-TYPE 
             12             236 
[1] "MORC4 MUTATION ANALYSIS"
[1] 3
  MORC4 MUTATED MORC4 WILD-TYPE 
             20             228 
  MORC4 MUTATED MORC4 WILD-TYPE 
             20             228 
[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] "ING1 MUTATION ANALYSIS"
[1] 3
  ING1 MUTATED ING1 WILD-TYPE 
            13            235 
  ING1 MUTATED ING1 WILD-TYPE 
            13            235 
[1] "INTS7 MUTATION ANALYSIS"
[1] 3
  INTS7 MUTATED INTS7 WILD-TYPE 
              8             240 
  INTS7 MUTATED INTS7 WILD-TYPE 
              8             240 
[1] "CCDC6 MUTATION ANALYSIS"
[1] 3
  CCDC6 MUTATED CCDC6 WILD-TYPE 
              6             242 
  CCDC6 MUTATED CCDC6 WILD-TYPE 
              6             242 
[1] "EIF2S2 MUTATION ANALYSIS"
[1] 3
  EIF2S2 MUTATED EIF2S2 WILD-TYPE 
               9              239 
  EIF2S2 MUTATED EIF2S2 WILD-TYPE 
               9              239 
[1] "RBBP6 MUTATION ANALYSIS"
[1] 3
  RBBP6 MUTATED RBBP6 WILD-TYPE 
             22             226 
  RBBP6 MUTATED RBBP6 WILD-TYPE 
             22             226 
[1] "SOS1 MUTATION ANALYSIS"
[1] 3
  SOS1 MUTATED SOS1 WILD-TYPE 
            12            236 
  SOS1 MUTATED SOS1 WILD-TYPE 
            12            236 
[1] "NAT1 MUTATION ANALYSIS"
[1] 3
  NAT1 MUTATED NAT1 WILD-TYPE 
             7            241 
  NAT1 MUTATED NAT1 WILD-TYPE 
             7            241 
[1] "ADNP MUTATION ANALYSIS"
[1] 3
  ADNP MUTATED ADNP WILD-TYPE 
            14            234 
  ADNP MUTATED ADNP WILD-TYPE 
            14            234 
[1] "VPS11 MUTATION ANALYSIS"
[1] 3
  VPS11 MUTATED VPS11 WILD-TYPE 
             12             236 
  VPS11 MUTATED VPS11 WILD-TYPE 
             12             236 
[1] "L1TD1 MUTATION ANALYSIS"
[1] 3
  L1TD1 MUTATED L1TD1 WILD-TYPE 
             16             232 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
             16             232 
[1] "MARK3 MUTATION ANALYSIS"
[1] 3
  MARK3 MUTATED MARK3 WILD-TYPE 
             11             237 
  MARK3 MUTATED MARK3 WILD-TYPE 
             11             237 
[1] "CTNND1 MUTATION ANALYSIS"
[1] 3
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              19              229 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              19              229 
[1] "GFAP MUTATION ANALYSIS"
[1] 3
  GFAP MUTATED GFAP WILD-TYPE 
             9            239 
  GFAP MUTATED GFAP WILD-TYPE 
             9            239 
[1] "PPP2R1A MUTATION ANALYSIS"
[1] 3
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               27               221 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               27               221 
[1] "C9ORF102 MUTATION ANALYSIS"
[1] 3
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
                16                232 
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
                16                232 
[1] "EIF4A2 MUTATION ANALYSIS"
[1] 3
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
               7              241 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
               7              241 
[1] "ZNF471 MUTATION ANALYSIS"
[1] 3
  ZNF471 MUTATED ZNF471 WILD-TYPE 
              15              233 
  ZNF471 MUTATED ZNF471 WILD-TYPE 
              15              233 
[1] "CDK17 MUTATION ANALYSIS"
[1] 3
  CDK17 MUTATED CDK17 WILD-TYPE 
             14             234 
  CDK17 MUTATED CDK17 WILD-TYPE 
             14             234 
[1] "SIN3A MUTATION ANALYSIS"
[1] 3
  SIN3A MUTATED SIN3A WILD-TYPE 
             21             227 
  SIN3A MUTATED SIN3A WILD-TYPE 
             21             227 
[1] "ZNF485 MUTATION ANALYSIS"
[1] 3
  ZNF485 MUTATED ZNF485 WILD-TYPE 
               9              239 
  ZNF485 MUTATED ZNF485 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] "CUX1 MUTATION ANALYSIS"
[1] 3
  CUX1 MUTATED CUX1 WILD-TYPE 
            23            225 
  CUX1 MUTATED CUX1 WILD-TYPE 
            23            225 
[1] "BCOR MUTATION ANALYSIS"
[1] 3
  BCOR MUTATED BCOR WILD-TYPE 
            30            218 
  BCOR MUTATED BCOR WILD-TYPE 
            30            218 
[1] "WDR45 MUTATION ANALYSIS"
[1] 3
  WDR45 MUTATED WDR45 WILD-TYPE 
             11             237 
  WDR45 MUTATED WDR45 WILD-TYPE 
             11             237 
[1] "CAB39L MUTATION ANALYSIS"
[1] 3
  CAB39L MUTATED CAB39L WILD-TYPE 
               8              240 
  CAB39L MUTATED CAB39L WILD-TYPE 
               8              240 
[1] "TAB3 MUTATION ANALYSIS"
[1] 3
  TAB3 MUTATED TAB3 WILD-TYPE 
            18            230 
  TAB3 MUTATED TAB3 WILD-TYPE 
            18            230 
[1] "OAZ3 MUTATION ANALYSIS"
[1] 3
  OAZ3 MUTATED OAZ3 WILD-TYPE 
             8            240 
  OAZ3 MUTATED OAZ3 WILD-TYPE 
             8            240 
[1] "AHCYL1 MUTATION ANALYSIS"
[1] 3
  AHCYL1 MUTATED AHCYL1 WILD-TYPE 
               6              242 
  AHCYL1 MUTATED AHCYL1 WILD-TYPE 
               6              242 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           29           219 
  ATM MUTATED ATM WILD-TYPE 
           29           219 
[1] "MSH4 MUTATION ANALYSIS"
[1] 3
  MSH4 MUTATED MSH4 WILD-TYPE 
            15            233 
  MSH4 MUTATED MSH4 WILD-TYPE 
            15            233 
[1] "FAM65B MUTATION ANALYSIS"
[1] 3
  FAM65B MUTATED FAM65B WILD-TYPE 
              16              232 
  FAM65B MUTATED FAM65B WILD-TYPE 
              16              232 
[1] "FN1 MUTATION ANALYSIS"
[1] 3
  FN1 MUTATED FN1 WILD-TYPE 
           24           224 
  FN1 MUTATED FN1 WILD-TYPE 
           24           224 
[1] "JAKMIP2 MUTATION ANALYSIS"
[1] 3
  JAKMIP2 MUTATED JAKMIP2 WILD-TYPE 
               12               236 
  JAKMIP2 MUTATED JAKMIP2 WILD-TYPE 
               12               236 
[1] "WBP4 MUTATION ANALYSIS"
[1] 3
  WBP4 MUTATED WBP4 WILD-TYPE 
             8            240 
  WBP4 MUTATED WBP4 WILD-TYPE 
             8            240 
[1] "RASA1 MUTATION ANALYSIS"
[1] 3
  RASA1 MUTATED RASA1 WILD-TYPE 
             22             226 
  RASA1 MUTATED RASA1 WILD-TYPE 
             22             226 
[1] "ALPK2 MUTATION ANALYSIS"
[1] 3
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             19             229 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             19             229 
[1] "POLE MUTATION ANALYSIS"
[1] 3
  POLE MUTATED POLE WILD-TYPE 
            27            221 
  POLE MUTATED POLE WILD-TYPE 
            27            221 
[1] "KIF20B MUTATION ANALYSIS"
[1] 3
  KIF20B MUTATED KIF20B WILD-TYPE 
              21              227 
  KIF20B MUTATED KIF20B WILD-TYPE 
              21              227 
[1] "C14ORF166B MUTATION ANALYSIS"
[1] 3
  C14ORF166B MUTATED C14ORF166B WILD-TYPE 
                  10                  238 
  C14ORF166B MUTATED C14ORF166B WILD-TYPE 
                  10                  238 
[1] "SLC26A8 MUTATION ANALYSIS"
[1] 3
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
               12               236 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
               12               236 
[1] "ZNF334 MUTATION ANALYSIS"
[1] 3
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              17              231 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              17              231 
[1] "RRAS2 MUTATION ANALYSIS"
[1] 3
  RRAS2 MUTATED RRAS2 WILD-TYPE 
              4             244 
  RRAS2 MUTATED RRAS2 WILD-TYPE 
              4             244 
[1] "PPM1N MUTATION ANALYSIS"
[1] 3
  PPM1N MUTATED PPM1N WILD-TYPE 
              7             241 
  PPM1N MUTATED PPM1N WILD-TYPE 
              7             241 
[1] "FCN1 MUTATION ANALYSIS"
[1] 3
  FCN1 MUTATED FCN1 WILD-TYPE 
             8            240 
  FCN1 MUTATED FCN1 WILD-TYPE 
             8            240 
[1] "TIAL1 MUTATION ANALYSIS"
[1] 3
  TIAL1 MUTATED TIAL1 WILD-TYPE 
             10             238 
  TIAL1 MUTATED TIAL1 WILD-TYPE 
             10             238 
[1] "PSMC4 MUTATION ANALYSIS"
[1] 3
  PSMC4 MUTATED PSMC4 WILD-TYPE 
             11             237 
  PSMC4 MUTATED PSMC4 WILD-TYPE 
             11             237 
[1] "MFAP5 MUTATION ANALYSIS"
[1] 3
  MFAP5 MUTATED MFAP5 WILD-TYPE 
              9             239 
  MFAP5 MUTATED MFAP5 WILD-TYPE 
              9             239 
[1] "RAB3GAP1 MUTATION ANALYSIS"
[1] 3
  RAB3GAP1 MUTATED RAB3GAP1 WILD-TYPE 
                16                232 
  RAB3GAP1 MUTATED RAB3GAP1 WILD-TYPE 
                16                232 
[1] "MSH6 MUTATION ANALYSIS"
[1] 3
  MSH6 MUTATED MSH6 WILD-TYPE 
            17            231 
  MSH6 MUTATED MSH6 WILD-TYPE 
            17            231 
[1] "BMP2K MUTATION ANALYSIS"
[1] 3
  BMP2K MUTATED BMP2K WILD-TYPE 
             13             235 
  BMP2K MUTATED BMP2K WILD-TYPE 
             13             235 
[1] "ZNF606 MUTATION ANALYSIS"
[1] 3
  ZNF606 MUTATED ZNF606 WILD-TYPE 
              16              232 
  ZNF606 MUTATED ZNF606 WILD-TYPE 
              16              232 
[1] "ZNF263 MUTATION ANALYSIS"
[1] 3
  ZNF263 MUTATED ZNF263 WILD-TYPE 
               7              241 
  ZNF263 MUTATED ZNF263 WILD-TYPE 
               7              241 
[1] "CHEK2 MUTATION ANALYSIS"
[1] 3
  CHEK2 MUTATED CHEK2 WILD-TYPE 
             13             235 
  CHEK2 MUTATED CHEK2 WILD-TYPE 
             13             235 
[1] "MGA MUTATION ANALYSIS"
[1] 3
  MGA MUTATED MGA WILD-TYPE 
           26           222 
  MGA MUTATED MGA WILD-TYPE 
           26           222 
[1] "RHBDD3 MUTATION ANALYSIS"
[1] 3
  RHBDD3 MUTATED RHBDD3 WILD-TYPE 
               4              244 
  RHBDD3 MUTATED RHBDD3 WILD-TYPE 
               4              244 
[1] "TAP1 MUTATION ANALYSIS"
[1] 3
  TAP1 MUTATED TAP1 WILD-TYPE 
             8            240 
  TAP1 MUTATED TAP1 WILD-TYPE 
             8            240 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           20           228 
  RB1 MUTATED RB1 WILD-TYPE 
           20           228 
[1] "SLC1A3 MUTATION ANALYSIS"
[1] 3
  SLC1A3 MUTATED SLC1A3 WILD-TYPE 
              12              236 
  SLC1A3 MUTATED SLC1A3 WILD-TYPE 
              12              236 
[1] "ATAD5 MUTATION ANALYSIS"
[1] 3
  ATAD5 MUTATED ATAD5 WILD-TYPE 
             17             231 
  ATAD5 MUTATED ATAD5 WILD-TYPE 
             17             231 
[1] "ALG8 MUTATION ANALYSIS"
[1] 3
  ALG8 MUTATED ALG8 WILD-TYPE 
            10            238 
  ALG8 MUTATED ALG8 WILD-TYPE 
            10            238 
[1] "TIGD4 MUTATION ANALYSIS"
[1] 3
  TIGD4 MUTATED TIGD4 WILD-TYPE 
             13             235 
  TIGD4 MUTATED TIGD4 WILD-TYPE 
             13             235 
[1] "PARG MUTATION ANALYSIS"
[1] 3
  PARG MUTATED PARG WILD-TYPE 
             9            239 
  PARG MUTATED PARG WILD-TYPE 
             9            239 
[1] "FAT1 MUTATION ANALYSIS"
[1] 3
  FAT1 MUTATED FAT1 WILD-TYPE 
            40            208 
  FAT1 MUTATED FAT1 WILD-TYPE 
            40            208 
[1] "DYM MUTATION ANALYSIS"
[1] 3
  DYM MUTATED DYM WILD-TYPE 
           10           238 
  DYM MUTATED DYM WILD-TYPE 
           10           238 
[1] "PSMD3 MUTATION ANALYSIS"
[1] 3
  PSMD3 MUTATED PSMD3 WILD-TYPE 
             11             237 
  PSMD3 MUTATED PSMD3 WILD-TYPE 
             11             237 
[1] "PPM1D MUTATION ANALYSIS"
[1] 3
  PPM1D MUTATED PPM1D WILD-TYPE 
             11             237 
  PPM1D MUTATED PPM1D WILD-TYPE 
             11             237 
[1] "ZMYM2 MUTATION ANALYSIS"
[1] 3
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
             17             231 
  ZMYM2 MUTATED ZMYM2 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] "USP28 MUTATION ANALYSIS"
[1] 3
  USP28 MUTATED USP28 WILD-TYPE 
             10             238 
  USP28 MUTATED USP28 WILD-TYPE 
             10             238 
[1] "EMR1 MUTATION ANALYSIS"
[1] 3
  EMR1 MUTATED EMR1 WILD-TYPE 
            13            235 
  EMR1 MUTATED EMR1 WILD-TYPE 
            13            235 
[1] "ZNF385B MUTATION ANALYSIS"
[1] 3
  ZNF385B MUTATED ZNF385B WILD-TYPE 
                7               241 
  ZNF385B MUTATED ZNF385B WILD-TYPE 
                7               241 
[1] "RAE1 MUTATION ANALYSIS"
[1] 3
  RAE1 MUTATED RAE1 WILD-TYPE 
            11            237 
  RAE1 MUTATED RAE1 WILD-TYPE 
            11            237 
[1] "TRIM59 MUTATION ANALYSIS"
[1] 3
  TRIM59 MUTATED TRIM59 WILD-TYPE 
               9              239 
  TRIM59 MUTATED TRIM59 WILD-TYPE 
               9              239 
[1] "ZNF721 MUTATION ANALYSIS"
[1] 3
  ZNF721 MUTATED ZNF721 WILD-TYPE 
              13              235 
  ZNF721 MUTATED ZNF721 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] "ZNF774 MUTATION ANALYSIS"
[1] 3
  ZNF774 MUTATED ZNF774 WILD-TYPE 
              10              238 
  ZNF774 MUTATED ZNF774 WILD-TYPE 
              10              238 
[1] "FAM9A MUTATION ANALYSIS"
[1] 3
  FAM9A MUTATED FAM9A WILD-TYPE 
             14             234 
  FAM9A MUTATED FAM9A WILD-TYPE 
             14             234 
[1] "CFP MUTATION ANALYSIS"
[1] 3
  CFP MUTATED CFP WILD-TYPE 
            8           240 
  CFP MUTATED CFP WILD-TYPE 
            8           240 
[1] "PER3 MUTATION ANALYSIS"
[1] 3
  PER3 MUTATED PER3 WILD-TYPE 
            12            236 
  PER3 MUTATED PER3 WILD-TYPE 
            12            236 
[1] "ZRANB3 MUTATION ANALYSIS"
[1] 3
  ZRANB3 MUTATED ZRANB3 WILD-TYPE 
               8              240 
  ZRANB3 MUTATED ZRANB3 WILD-TYPE 
               8              240 
[1] "OMA1 MUTATION ANALYSIS"
[1] 3
  OMA1 MUTATED OMA1 WILD-TYPE 
            10            238 
  OMA1 MUTATED OMA1 WILD-TYPE 
            10            238 
[1] "CLDN15 MUTATION ANALYSIS"
[1] 3
  CLDN15 MUTATED CLDN15 WILD-TYPE 
               5              243 
  CLDN15 MUTATED CLDN15 WILD-TYPE 
               5              243 
[1] "TTC39C MUTATION ANALYSIS"
[1] 3
  TTC39C MUTATED TTC39C WILD-TYPE 
               7              241 
  TTC39C MUTATED TTC39C WILD-TYPE 
               7              241 
[1] "TXNRD1 MUTATION ANALYSIS"
[1] 3
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
               8              240 
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
               8              240 
[1] "MECOM MUTATION ANALYSIS"
[1] 3
  MECOM MUTATED MECOM WILD-TYPE 
             12             236 
  MECOM MUTATED MECOM WILD-TYPE 
             12             236 
[1] "CCDC147 MUTATION ANALYSIS"
[1] 3
  CCDC147 MUTATED CCDC147 WILD-TYPE 
               15               233 
  CCDC147 MUTATED CCDC147 WILD-TYPE 
               15               233 
[1] "SACS MUTATION ANALYSIS"
[1] 3
  SACS MUTATED SACS WILD-TYPE 
            26            222 
  SACS MUTATED SACS WILD-TYPE 
            26            222 
[1] "MUTED MUTATION ANALYSIS"
[1] 3
  MUTED MUTATED MUTED WILD-TYPE 
              7             241 
  MUTED MUTATED MUTED 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] "ZNF674 MUTATION ANALYSIS"
[1] 3
  ZNF674 MUTATED ZNF674 WILD-TYPE 
              14              234 
  ZNF674 MUTATED ZNF674 WILD-TYPE 
              14              234 
[1] "CCDC144A MUTATION ANALYSIS"
[1] 3
  CCDC144A MUTATED CCDC144A WILD-TYPE 
                18                230 
  CCDC144A MUTATED CCDC144A WILD-TYPE 
                18                230 
[1] "OR8B8 MUTATION ANALYSIS"
[1] 3
  OR8B8 MUTATED OR8B8 WILD-TYPE 
              7             241 
  OR8B8 MUTATED OR8B8 WILD-TYPE 
              7             241 
[1] "LNX2 MUTATION ANALYSIS"
[1] 3
  LNX2 MUTATED LNX2 WILD-TYPE 
            14            234 
  LNX2 MUTATED LNX2 WILD-TYPE 
            14            234 
[1] "TMEM62 MUTATION ANALYSIS"
[1] 3
  TMEM62 MUTATED TMEM62 WILD-TYPE 
               9              239 
  TMEM62 MUTATED TMEM62 WILD-TYPE 
               9              239 
[1] "ATF7IP MUTATION ANALYSIS"
[1] 3
  ATF7IP MUTATED ATF7IP WILD-TYPE 
              17              231 
  ATF7IP MUTATED ATF7IP WILD-TYPE 
              17              231 
[1] "IL20 MUTATION ANALYSIS"
[1] 3
  IL20 MUTATED IL20 WILD-TYPE 
             7            241 
  IL20 MUTATED IL20 WILD-TYPE 
             7            241 
[1] "C3AR1 MUTATION ANALYSIS"
[1] 3
  C3AR1 MUTATED C3AR1 WILD-TYPE 
              8             240 
  C3AR1 MUTATED C3AR1 WILD-TYPE 
              8             240 
[1] "PKD2 MUTATION ANALYSIS"
[1] 3
  PKD2 MUTATED PKD2 WILD-TYPE 
             8            240 
  PKD2 MUTATED PKD2 WILD-TYPE 
             8            240 
[1] "BMP5 MUTATION ANALYSIS"
[1] 3
  BMP5 MUTATED BMP5 WILD-TYPE 
            13            235 
  BMP5 MUTATED BMP5 WILD-TYPE 
            13            235 
[1] "OR52I2 MUTATION ANALYSIS"
[1] 3
  OR52I2 MUTATED OR52I2 WILD-TYPE 
               8              240 
  OR52I2 MUTATED OR52I2 WILD-TYPE 
               8              240 
[1] "C1ORF100 MUTATION ANALYSIS"
[1] 3
  C1ORF100 MUTATED C1ORF100 WILD-TYPE 
                 9                239 
  C1ORF100 MUTATED C1ORF100 WILD-TYPE 
                 9                239 
[1] "CCDC160 MUTATION ANALYSIS"
[1] 3
  CCDC160 MUTATED CCDC160 WILD-TYPE 
               11               237 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
               11               237 
[1] "NAA15 MUTATION ANALYSIS"
[1] 3
  NAA15 MUTATED NAA15 WILD-TYPE 
             14             234 
  NAA15 MUTATED NAA15 WILD-TYPE 
             14             234 
[1] "RNF31 MUTATION ANALYSIS"
[1] 3
  RNF31 MUTATED RNF31 WILD-TYPE 
             17             231 
  RNF31 MUTATED RNF31 WILD-TYPE 
             17             231 
[1] "NFE2L3 MUTATION ANALYSIS"
[1] 3
  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
              12              236 
  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
              12              236 
[1] "ZKSCAN1 MUTATION ANALYSIS"
[1] 3
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                7               241 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                7               241 
[1] "CDKL1 MUTATION ANALYSIS"
[1] 3
  CDKL1 MUTATED CDKL1 WILD-TYPE 
              7             241 
  CDKL1 MUTATED CDKL1 WILD-TYPE 
              7             241 
[1] "ERBB3 MUTATION ANALYSIS"
[1] 3
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             17             231 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             17             231 
[1] "SELP MUTATION ANALYSIS"
[1] 3
  SELP MUTATED SELP WILD-TYPE 
             9            239 
  SELP MUTATED SELP WILD-TYPE 
             9            239 
[1] "PPIG MUTATION ANALYSIS"
[1] 3
  PPIG MUTATED PPIG WILD-TYPE 
            16            232 
  PPIG MUTATED PPIG WILD-TYPE 
            16            232 
[1] "GPRASP1 MUTATION ANALYSIS"
[1] 3
  GPRASP1 MUTATED GPRASP1 WILD-TYPE 
               21               227 
  GPRASP1 MUTATED GPRASP1 WILD-TYPE 
               21               227 
[1] "REV3L MUTATION ANALYSIS"
[1] 3
  REV3L MUTATED REV3L WILD-TYPE 
             20             228 
  REV3L MUTATED REV3L WILD-TYPE 
             20             228 
[1] "CTNNA1 MUTATION ANALYSIS"
[1] 3
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
              13              235 
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
              13              235 
[1] "MRPL47 MUTATION ANALYSIS"
[1] 3
  MRPL47 MUTATED MRPL47 WILD-TYPE 
               6              242 
  MRPL47 MUTATED MRPL47 WILD-TYPE 
               6              242 
[1] "DEPDC1B MUTATION ANALYSIS"
[1] 3
  DEPDC1B MUTATED DEPDC1B WILD-TYPE 
               11               237 
  DEPDC1B MUTATED DEPDC1B WILD-TYPE 
               11               237 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
             17             231 
  CASP8 MUTATED CASP8 WILD-TYPE 
             17             231 
[1] "CACNB4 MUTATION ANALYSIS"
[1] 3
  CACNB4 MUTATED CACNB4 WILD-TYPE 
              10              238 
  CACNB4 MUTATED CACNB4 WILD-TYPE 
              10              238 
[1] "BHLHB9 MUTATION ANALYSIS"
[1] 3
  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
               8              240 
  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
               8              240 
[1] "C22ORF25 MUTATION ANALYSIS"
[1] 3
  C22ORF25 MUTATED C22ORF25 WILD-TYPE 
                 6                242 
  C22ORF25 MUTATED C22ORF25 WILD-TYPE 
                 6                242 
[1] "GALNT7 MUTATION ANALYSIS"
[1] 3
  GALNT7 MUTATED GALNT7 WILD-TYPE 
              11              237 
  GALNT7 MUTATED GALNT7 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] "EPS8 MUTATION ANALYSIS"
[1] 3
  EPS8 MUTATED EPS8 WILD-TYPE 
            12            236 
  EPS8 MUTATED EPS8 WILD-TYPE 
            12            236 
[1] "TGOLN2 MUTATION ANALYSIS"
[1] 3
  TGOLN2 MUTATED TGOLN2 WILD-TYPE 
               3              245 
  TGOLN2 MUTATED TGOLN2 WILD-TYPE 
               3              245 
[1] "TPX2 MUTATION ANALYSIS"
[1] 3
  TPX2 MUTATED TPX2 WILD-TYPE 
             6            242 
  TPX2 MUTATED TPX2 WILD-TYPE 
             6            242 
[1] "C14ORF118 MUTATION ANALYSIS"
[1] 3
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                 15                 233 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                 15                 233 
[1] "SLC34A3 MUTATION ANALYSIS"
[1] 3
  SLC34A3 MUTATED SLC34A3 WILD-TYPE 
                6               242 
  SLC34A3 MUTATED SLC34A3 WILD-TYPE 
                6               242 
[1] "ZNF662 MUTATION ANALYSIS"
[1] 3
  ZNF662 MUTATED ZNF662 WILD-TYPE 
              13              235 
  ZNF662 MUTATED ZNF662 WILD-TYPE 
              13              235 
[1] "ZDBF2 MUTATION ANALYSIS"
[1] 3
  ZDBF2 MUTATED ZDBF2 WILD-TYPE 
             18             230 
  ZDBF2 MUTATED ZDBF2 WILD-TYPE 
             18             230 
[1] "SFRP4 MUTATION ANALYSIS"
[1] 3
  SFRP4 MUTATED SFRP4 WILD-TYPE 
              8             240 
  SFRP4 MUTATED SFRP4 WILD-TYPE 
              8             240 
[1] "CCDC146 MUTATION ANALYSIS"
[1] 3
  CCDC146 MUTATED CCDC146 WILD-TYPE 
               14               234 
  CCDC146 MUTATED CCDC146 WILD-TYPE 
               14               234 
[1] "C7ORF60 MUTATION ANALYSIS"
[1] 3
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
               10               238 
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
               10               238 
[1] "ZNF649 MUTATION ANALYSIS"
[1] 3
  ZNF649 MUTATED ZNF649 WILD-TYPE 
              14              234 
  ZNF649 MUTATED ZNF649 WILD-TYPE 
              14              234 
[1] "RASSF9 MUTATION ANALYSIS"
[1] 3
  RASSF9 MUTATED RASSF9 WILD-TYPE 
               9              239 
  RASSF9 MUTATED RASSF9 WILD-TYPE 
               9              239 
[1] "NIPA2 MUTATION ANALYSIS"
[1] 3
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              8             240 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              8             240 
[1] "FILIP1 MUTATION ANALYSIS"
[1] 3
  FILIP1 MUTATED FILIP1 WILD-TYPE 
              16              232 
  FILIP1 MUTATED FILIP1 WILD-TYPE 
              16              232 
[1] "PHKA2 MUTATION ANALYSIS"
[1] 3
  PHKA2 MUTATED PHKA2 WILD-TYPE 
             16             232 
  PHKA2 MUTATED PHKA2 WILD-TYPE 
             16             232 
[1] "COBLL1 MUTATION ANALYSIS"
[1] 3
  COBLL1 MUTATED COBLL1 WILD-TYPE 
              15              233 
  COBLL1 MUTATED COBLL1 WILD-TYPE 
              15              233 
[1] "AGPAT9 MUTATION ANALYSIS"
[1] 3
  AGPAT9 MUTATED AGPAT9 WILD-TYPE 
               8              240 
  AGPAT9 MUTATED AGPAT9 WILD-TYPE 
               8              240 
[1] "NOP56 MUTATION ANALYSIS"
[1] 3
  NOP56 MUTATED NOP56 WILD-TYPE 
             11             237 
  NOP56 MUTATED NOP56 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] "ABCC6 MUTATION ANALYSIS"
[1] 3
  ABCC6 MUTATED ABCC6 WILD-TYPE 
             12             236 
  ABCC6 MUTATED ABCC6 WILD-TYPE 
             12             236 
[1] "CCDC104 MUTATION ANALYSIS"
[1] 3
  CCDC104 MUTATED CCDC104 WILD-TYPE 
               10               238 
  CCDC104 MUTATED CCDC104 WILD-TYPE 
               10               238 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            33            215 
  MLL2 MUTATED MLL2 WILD-TYPE 
            33            215 
[1] "SSH2 MUTATION ANALYSIS"
[1] 3
  SSH2 MUTATED SSH2 WILD-TYPE 
            12            236 
  SSH2 MUTATED SSH2 WILD-TYPE 
            12            236 
[1] "ZNF709 MUTATION ANALYSIS"
[1] 3
  ZNF709 MUTATED ZNF709 WILD-TYPE 
              12              236 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
              12              236 
[1] "BRDT MUTATION ANALYSIS"
[1] 3
  BRDT MUTATED BRDT WILD-TYPE 
            14            234 
  BRDT MUTATED BRDT WILD-TYPE 
            14            234 
[1] "SH3BGRL MUTATION ANALYSIS"
[1] 3
  SH3BGRL MUTATED SH3BGRL WILD-TYPE 
                6               242 
  SH3BGRL MUTATED SH3BGRL 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] "CCDC150 MUTATION ANALYSIS"
[1] 3
  CCDC150 MUTATED CCDC150 WILD-TYPE 
               12               236 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
               12               236 
[1] "NT5C3 MUTATION ANALYSIS"
[1] 3
  NT5C3 MUTATED NT5C3 WILD-TYPE 
              7             241 
  NT5C3 MUTATED NT5C3 WILD-TYPE 
              7             241 
[1] "APAF1 MUTATION ANALYSIS"
[1] 3
  APAF1 MUTATED APAF1 WILD-TYPE 
             13             235 
  APAF1 MUTATED APAF1 WILD-TYPE 
             13             235 
[1] "KANK4 MUTATION ANALYSIS"
[1] 3
  KANK4 MUTATED KANK4 WILD-TYPE 
             11             237 
  KANK4 MUTATED KANK4 WILD-TYPE 
             11             237 
[1] "NRIP1 MUTATION ANALYSIS"
[1] 3
  NRIP1 MUTATED NRIP1 WILD-TYPE 
             13             235 
  NRIP1 MUTATED NRIP1 WILD-TYPE 
             13             235 
[1] "GTF2H1 MUTATION ANALYSIS"
[1] 3
  GTF2H1 MUTATED GTF2H1 WILD-TYPE 
               8              240 
  GTF2H1 MUTATED GTF2H1 WILD-TYPE 
               8              240 
[1] "ASXL2 MUTATION ANALYSIS"
[1] 3
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             14             234 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             14             234 
[1] "ZNF611 MUTATION ANALYSIS"
[1] 3
  ZNF611 MUTATED ZNF611 WILD-TYPE 
              12              236 
  ZNF611 MUTATED ZNF611 WILD-TYPE 
              12              236 
[1] "SUN3 MUTATION ANALYSIS"
[1] 3
  SUN3 MUTATED SUN3 WILD-TYPE 
             6            242 
  SUN3 MUTATED SUN3 WILD-TYPE 
             6            242 
[1] "ZNF195 MUTATION ANALYSIS"
[1] 3
  ZNF195 MUTATED ZNF195 WILD-TYPE 
              11              237 
  ZNF195 MUTATED ZNF195 WILD-TYPE 
              11              237 
[1] "EXOSC9 MUTATION ANALYSIS"
[1] 3
  EXOSC9 MUTATED EXOSC9 WILD-TYPE 
              10              238 
  EXOSC9 MUTATED EXOSC9 WILD-TYPE 
              10              238 
[1] "MFN2 MUTATION ANALYSIS"
[1] 3
  MFN2 MUTATED MFN2 WILD-TYPE 
             9            239 
  MFN2 MUTATED MFN2 WILD-TYPE 
             9            239 
[1] "LIMA1 MUTATION ANALYSIS"
[1] 3
  LIMA1 MUTATED LIMA1 WILD-TYPE 
              8             240 
  LIMA1 MUTATED LIMA1 WILD-TYPE 
              8             240 
[1] "PTPN12 MUTATION ANALYSIS"
[1] 3
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              10              238 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              10              238 
[1] "MTF2 MUTATION ANALYSIS"
[1] 3
  MTF2 MUTATED MTF2 WILD-TYPE 
             9            239 
  MTF2 MUTATED MTF2 WILD-TYPE 
             9            239 
[1] "MLL4 MUTATION ANALYSIS"
[1] 3
  MLL4 MUTATED MLL4 WILD-TYPE 
            30            218 
  MLL4 MUTATED MLL4 WILD-TYPE 
            30            218 
[1] "C1ORF101 MUTATION ANALYSIS"
[1] 3
  C1ORF101 MUTATED C1ORF101 WILD-TYPE 
                12                236 
  C1ORF101 MUTATED C1ORF101 WILD-TYPE 
                12                236 
[1] "MBOAT2 MUTATION ANALYSIS"
[1] 3
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               7              241 
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               7              241 
[1] "CHD4 MUTATION ANALYSIS"
[1] 3
  CHD4 MUTATED CHD4 WILD-TYPE 
            35            213 
  CHD4 MUTATED CHD4 WILD-TYPE 
            35            213 
[1] "SESN3 MUTATION ANALYSIS"
[1] 3
  SESN3 MUTATED SESN3 WILD-TYPE 
             13             235 
  SESN3 MUTATED SESN3 WILD-TYPE 
             13             235 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 248 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
        1428         1126         2540           NA          997           98 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
        3205         2254         1750         2000         1841         1841 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
        1416         1167          860          633          706         2088 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
         607          535          596          749          884          364 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
        1288          485           36         2545           NA          181 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
          NA         2618          250         1199         1758         1385 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
        1122          239          636           NA         3815         3589 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
        3357          103         1921           NA         2972          965 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
        2554          825         2510           NA         1875         2457 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
        1497          763         1276           NA          603          903 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
        2079         2191         1413         1075         1399         2025 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
        1064         1640          833         1845         1065          868 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
        1149         1220         2004          516          412         1107 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        2167          589         2445         1731         1422         1312 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
        1237          990          871          862          928          788 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
         700          544          418          520          543          335 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
         265         5651         3448         2687         2303         1656 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
        1362         1337         1232          976         1019          832 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
         509          595          593          596          560          528 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
         504           NA           NA          566          614          588 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
         637         1071         1064          241         1167         1110 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
         860         1263         1477           NA         1309         1196 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
         937          644          617          469          742          811 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
         497         1043          868         1607         1721          451 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
         382          419          448          426          470          470 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
         721         1092         1064          189          311          309 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
         760           NA          714         2602         2379           NA 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
        2371         1882         2068         2935           NA         2963 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
        2044         2687         2611         2506         2481         2644 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
        2212         2228         1910         1934         1507         2022 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
         512          602          911          260           17          148 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
         872          728          686           53          135          669 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
        1201          915          909           NA          112          892 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
         991           20          478         1098         1135         1106 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
        1141         1119           80           NA           NA          910 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
         945         1023          324           21          568          111 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
         532          594          917          548           48          213 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
          30          926           39          852          854          802 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
         311           46           54           NA          739           71 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
         697          402          555          496         1076         1471 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
         332          328          459          110         1095         1795 
TCGA-FI-A2EX TCGA-FI-A2F8 
         276          761 
Variable 1:'AGE':	nDistinctValues=53,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=221,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "HISTOLOGICAL.TYPE"                     
[3] "RADIATIONS.RADIATION.REGIMENINDICATION"
[4] "COMPLETENESS.OF.RESECTION"             
[5] "RACE"                                  
[6] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 248 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=53, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = PTEN MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  PTEN MUTATED   152   9
  PTEN WILD-TYPE  72  15
  PTEN MUTATED PTEN WILD-TYPE 
           161             87 
  PTEN MUTATED PTEN WILD-TYPE 
             9             15 
$`PTEN MUTATED`
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GM 
       83.51        17.85        32.78       105.37        74.10        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N 
       15.95        83.67        23.31        86.07         8.22         7.86 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LN TCGA-AP-A0LO 
      117.99       110.37        63.16        31.73        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        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 
       29.69        68.35        72.03        46.45        35.34        66.58 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0J0 TCGA-AX-A0J1 
       34.98        27.39        60.66        35.01        40.11        65.88 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        46.75        43.13        40.67        32.55        28.64 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       30.51        25.91        17.88        13.74        17.10        11.01 
TCGA-B5-A11E TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
        8.71        88.34        54.44        44.78        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       32.09        33.50        27.35        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       18.41        17.36        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 
       34.98        38.37        28.27        41.52        48.56        23.47 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VW 
       39.32        30.81        21.17        20.28        15.42        16.34 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       28.54        52.83        56.58        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       14.01        15.45        35.90        34.98         6.21        10.16 
TCGA-BK-A13C TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TI TCGA-BS-A0TJ 
       24.99        23.47        85.55        78.21        61.87        67.99 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UM 
       30.74        97.41        88.34        85.84        82.39        86.93 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       73.25        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 
       19.79         0.56         4.87        28.67        23.93         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
        4.44        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0GD TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GN 
       46.95        37.02         3.22        57.53        65.75        60.53 
TCGA-A5-A0R6 TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D 
       19.96         1.18        21.99         5.95        39.42        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF 
       45.53        36.89        20.91        48.79       125.42         3.39 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A1DQ TCGA-AX-A062 
       36.36        97.71        83.97        27.12        41.95        45.99 
TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       53.92        28.54        37.78        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0K0 TCGA-B5-A0K3 TCGA-B5-A0K8 
       71.24        19.36        80.38        28.34        23.01        17.85 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11U TCGA-B5-A121 TCGA-B5-A1MU 
      185.79       113.36        75.72        16.73        16.57        50.89 
TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MO TCGA-BG-A0VT 
       11.87        18.61         7.92        36.49        43.04        24.39 
TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0YU TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0CC 
       26.66        34.29        14.83        15.45        23.70        10.22 
TCGA-BS-A0T9 TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0U5 TCGA-BS-A0U9 TCGA-BS-A0UL 
       46.95         4.80        77.95        96.49        67.20        81.57 
TCGA-BS-A0UT TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A15X 
       72.72        29.95         8.55        22.55        39.48        29.88 
TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       32.58        15.72        36.10        27.42        11.51        29.92 
TCGA-D1-A16S TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
       18.67        28.08        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  PTEN MUTATED PTEN WILD-TYPE 
          0.56           1.18 
  PTEN MUTATED PTEN WILD-TYPE 
        117.99         185.79 
  PTEN MUTATED PTEN WILD-TYPE 
         29.06          29.88 
[1] "0.6 - 118.0 (29.1)" "1.2 - 185.8 (29.9)"
[1] "hr=" "3"  
D1V2, continuous
                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"
D1V4, binary
                cls
clus               0   1
  PTEN MUTATED    48 113
  PTEN WILD-TYPE  38  49
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     48  113
  PTEN WILD-TYPE   38   49
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO            48             38
  YES          113             49
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED   113   8   1  11
  PTEN WILD-TYPE  58   3   6   7
D1V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0          113             58
  R1            8              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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTEN MUTATED                                  3    10
  PTEN WILD-TYPE                                0     3
                vv
clus             BLACK OR AFRICAN AMERICAN
  PTEN MUTATED                           7
  PTEN WILD-TYPE                        18
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTEN MUTATED                                           4   133
  PTEN WILD-TYPE                                         3    60
D1V6, multiclass
                                           clus
vv                                          PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     3              0
  ASIAN                                               10              3
  BLACK OR AFRICAN AMERICAN                            7             18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            4              3
  WHITE                                              133             60
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                cls
clus               0   1
  PTEN MUTATED     3 112
  PTEN WILD-TYPE   1  55
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      3  112
  PTEN WILD-TYPE    1   55
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                3              1
  NOT HISPANIC OR LATINO          112             55
[1] 2 2
[1] FALSE

Clustering(2) Variable = PIK3R1 MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2                0   1
  PIK3R1 MUTATED    75   8
  PIK3R1 WILD-TYPE 149  16
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              83              165 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               8               16 
$`PIK3R1 MUTATED`
TCGA-A5-A0G9 TCGA-A5-A0GE TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0R7 
       83.51       105.37        28.27        20.81        23.21        17.59 
TCGA-A5-A0R9 TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A056 TCGA-AP-A059 
       24.62        11.97        15.95         1.18        86.07         8.22 
TCGA-AP-A05N TCGA-AP-A0LH TCGA-AP-A0LO TCGA-AX-A05S TCGA-AX-A05U TCGA-AX-A05W 
        7.86        36.36        33.40        13.58        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A063 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       72.03        46.45        66.58        27.39        60.66        35.01 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JZ TCGA-B5-A0K1 
       40.11        65.88        80.38        56.91        28.64        30.51 
TCGA-B5-A0K3 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11J 
       23.01        11.01         8.71       185.79        88.34        54.44 
TCGA-B5-A11N TCGA-B5-A11R TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Z TCGA-BG-A0LX 
       43.96        33.50        19.56        19.50        17.36        20.19 
TCGA-BG-A0M3 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MS 
       35.21        36.49        28.27        48.56        23.47        30.81 
TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0W1 TCGA-BG-A18B TCGA-BK-A139 TCGA-BS-A0T9 
       20.28        26.66        52.83        15.45        10.16        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0U5 TCGA-BS-A0U9 TCGA-BS-A0UA 
       23.47        85.55        78.21        96.49        67.20        88.34 
TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZS TCGA-D1-A101 
       82.39        73.25        16.83         8.55         4.87         1.74 
TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       21.99        30.08         3.68        29.33        32.58         0.66 
TCGA-D1-A169 TCGA-D1-A16Q TCGA-D1-A16X TCGA-D1-A176 TCGA-D1-A17B TCGA-D1-A17C 
       37.32        10.65         3.65        30.15         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17M TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17U 
       30.44        10.22         1.78        11.15        22.92 

$`PIK3R1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GH 
       46.95        37.02        17.85        32.78         3.22        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-AP-A051 
       68.65        19.96        19.59        29.06        42.35        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       21.99         5.95        23.31        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
        3.39        63.16        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ 
       82.52        61.64        80.78        49.22        25.08        41.95 
TCGA-AX-A05T TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A0IU 
       19.82        35.34        45.99        34.98        53.92        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       37.78        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0K0 TCGA-B5-A0K2 
       46.75        43.13        40.67        32.55        28.34        25.91 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A11G TCGA-B5-A11I 
       17.88        13.74        17.10        17.85       113.36        75.72 
TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11X 
       44.78        40.50        32.09        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0MC TCGA-BG-A0MO 
       20.94        34.98         7.92        38.37        41.52        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VW TCGA-BG-A0VX 
       39.32        21.17        15.42        24.39        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       28.54        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       14.01        15.45        23.70        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A13C TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       10.22        24.99         4.80        77.95        61.87        67.99 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UF TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       30.74        97.41        85.84        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZO TCGA-D1-A0ZP 
       62.79        63.58        49.55        66.48        19.79        29.95 
TCGA-D1-A0ZR TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A102 TCGA-D1-A15V 
        0.56        28.67        23.93        22.55         4.44        39.48 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D 
       29.88         1.91        15.72        36.10        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-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A177 
       33.63         0.69        18.67        17.49        19.53        18.02 
TCGA-D1-A17A TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17N 
        1.58         1.28        28.01        28.08        26.37         1.51 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
       24.30         2.33        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
            0.66             0.56 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
          185.79           125.42 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           28.64            29.88 
[1] "0.7 - 185.8 (28.6)" "0.6 - 125.4 (29.9)"
[1] "hr=" "1"  
D2V2, continuous
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PIK3R1 MUTATED                                        80
  PIK3R1 WILD-TYPE                                     120
                  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             80              120
  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"
D2V4, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED    25  58
  PIK3R1 WILD-TYPE  61 104
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED     25   58
  PIK3R1 WILD-TYPE   61  104
     clus
vv    PIK3R1 MUTATED PIK3R1 WILD-TYPE
  NO              25               61
  YES             58              104
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIK3R1 MUTATED    56   4   2   5
  PIK3R1 WILD-TYPE 115   7   5  13
D2V5, multiclass
    clus
vv   PIK3R1 MUTATED PIK3R1 WILD-TYPE
  R0             56              115
  R1              4                7
  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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3R1 MUTATED                                  2     5
  PIK3R1 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN
  PIK3R1 MUTATED                           4
  PIK3R1 WILD-TYPE                        21
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIK3R1 MUTATED                                           4    66
  PIK3R1 WILD-TYPE                                         3   127
D2V6, multiclass
                                           clus
vv                                          PIK3R1 MUTATED PIK3R1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       2                1
  ASIAN                                                  5                8
  BLACK OR AFRICAN AMERICAN                              4               21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              4                3
  WHITE                                                 66              127
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     3  59
  PIK3R1 WILD-TYPE   1 108
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      3   59
  PIK3R1 WILD-TYPE    1  108
                        clus
vv                       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  HISPANIC OR LATINO                  3                1
  NOT HISPANIC OR LATINO             59              108
[1] 2 2
[1] FALSE

Clustering(3) Variable = TP53 MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  TP53 MUTATED    57  12
  TP53 WILD-TYPE 167  12
  TP53 MUTATED TP53 WILD-TYPE 
            69            179 
  TP53 MUTATED TP53 WILD-TYPE 
            12             12 
$`TP53 MUTATED`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0GW TCGA-A5-A0R6 TCGA-A5-A0R7 
       46.95        37.02        65.75        23.21        19.96        17.59 
TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A 
        1.18        21.99         5.95        23.31         8.22        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF 
       57.80        45.53        36.89        48.79       125.42         3.39 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AX-A060 TCGA-AX-A06B TCGA-AX-A0IU 
       36.36        97.71        41.95        35.34        53.92        28.54 
TCGA-AX-A0IW TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       37.78        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0K3 TCGA-B5-A11E TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11N TCGA-B5-A1MU 
       23.01         8.71        75.72        54.44        43.96        50.89 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A18C TCGA-BK-A0CC 
        7.92        38.37        36.49        12.56        15.45        10.22 
TCGA-BK-A139 TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0UF TCGA-BS-A0UV TCGA-BS-A0V8 
       10.16        61.87        67.20        85.84        73.25        49.55 
TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16N 
       22.55        39.48        37.32        27.42        11.51        31.07 
TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A1NN 
       18.67        17.49        28.08        13.22        18.25        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

$`TP53 WILD-TYPE`
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78         3.22       105.37        74.10 
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       57.53        60.53        60.53        46.55        38.37        28.27 
TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       20.81        68.65        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A05N TCGA-AP-A05P 
       42.35        15.95        83.67        86.07         7.86        20.91 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      117.99       110.37        63.16        31.73        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-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        66.58        34.98        27.39        60.66        35.01 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       40.11        65.88        16.96        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       40.67        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       17.88        13.74        17.10        17.85        11.01       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
      113.36        88.34        44.78        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        16.73        19.56        19.50        19.59        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       17.36        16.57        11.87        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
       20.94        35.21        34.98        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
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-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13C 
       15.45        23.70        35.90        34.98         6.21        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UJ 
       67.99        96.49        30.74        97.41        88.34        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0WQ 
       81.57        86.93        72.72        62.79        63.58        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W 
       28.67        23.93         1.74         4.44        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 
          1.18           0.56 
  TP53 MUTATED TP53 WILD-TYPE 
        125.42         185.79 
  TP53 MUTATED TP53 WILD-TYPE 
         35.34          28.67 
[1] "1.2 - 125.4 (35.3)" "0.6 - 185.8 (28.7)"
[1] "hr=" "2.5"
D3V2, continuous
                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"
D3V4, binary
                cls
clus               0   1
  TP53 MUTATED    28  41
  TP53 WILD-TYPE  58 121
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     28   41
  TP53 WILD-TYPE   58  121
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            28             58
  YES           41            121
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TP53 MUTATED    46   6   4   5
  TP53 WILD-TYPE 125   5   3  13
D3V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           46            125
  R1            6              5
  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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  1     2
  TP53 WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN
  TP53 MUTATED                          14
  TP53 WILD-TYPE                        11
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TP53 MUTATED                                           3    46
  TP53 WILD-TYPE                                         4   147
D3V6, multiclass
                                           clus
vv                                          TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     1              2
  ASIAN                                                2             11
  BLACK OR AFRICAN AMERICAN                           14             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            3              4
  WHITE                                               46            147
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                cls
clus               0   1
  TP53 MUTATED     1  45
  TP53 WILD-TYPE   3 122
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1   45
  TP53 WILD-TYPE    3  122
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           45            122
[1] 2 2
[1] FALSE

Clustering(4) Variable = CTCF MUTATION ANALYSIS
D4V1, survival
                sevent
clus2              0   1
  CTCF MUTATED    42   2
  CTCF WILD-TYPE 182  22
  CTCF MUTATED CTCF WILD-TYPE 
            44            204 
  CTCF MUTATED CTCF WILD-TYPE 
             2             22 
$`CTCF MUTATED`
TCGA-A5-A0GA TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0R9 
       17.85        74.10        57.53        60.53        46.55        24.62 
TCGA-A5-A0VO TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LP 
       11.97        83.67         8.22        83.97        27.12        61.64 
TCGA-AX-A05T TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A06H TCGA-AX-A0J0 TCGA-B5-A0JV 
       19.82        72.03        46.45        27.39        40.11        40.67 
TCGA-B5-A0K7 TCGA-B5-A11R TCGA-B5-A11X TCGA-B5-A11Y TCGA-BG-A0LX TCGA-BG-A0M4 
       17.10        33.50        19.59        18.41        20.19        34.98 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A186 TCGA-BK-A0C9 
       28.27        41.52        43.04        39.32        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        62.79         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-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       46.95        37.02        83.51        32.78         3.22       105.37 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       65.75        60.53        38.37        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        19.96        17.59        19.59        29.06        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
       15.95         1.18        21.99         5.95        23.31        86.07 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LQ 
       36.36        97.71        31.73        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        41.95        13.58        29.69        68.35 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06L 
       35.34        45.99        66.58        34.98        53.92        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        65.88        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       23.01        17.88        13.74        17.85        11.01         8.71 
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 
       43.96        40.50        32.09        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       19.50        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       19.33        20.94        35.21         7.92        38.37        36.49 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       48.56        23.47        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       24.99        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       61.87        67.99        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V7 TCGA-BS-A0V8 
       85.84        81.57        72.72        73.25        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZS 
       66.48        16.83        19.79        29.95         8.55         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A165 
       30.08        29.88         1.91         3.68        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16E TCGA-D1-A16F 
       15.72        36.10        37.32        36.36        36.79         2.63 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16R 
       27.42        11.51        29.92        31.07        33.63         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-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-A17T TCGA-D1-A1NU 
       10.22         1.51         1.78        11.15         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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  CTCF MUTATED CTCF WILD-TYPE 
          0.56           0.66 
  CTCF MUTATED CTCF WILD-TYPE 
         96.49         185.79 
  CTCF MUTATED CTCF WILD-TYPE 
         34.24          28.59 
[1] "0.6 - 96.5 (34.2)"  "0.7 - 185.8 (28.6)"
[1] "hr=" "2.7"
D4V2, continuous
                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"
D4V4, binary
                cls
clus               0   1
  CTCF MUTATED    15  29
  CTCF WILD-TYPE  71 133
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     15   29
  CTCF WILD-TYPE   71  133
     clus
vv    CTCF MUTATED CTCF WILD-TYPE
  NO            15             71
  YES           29            133
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CTCF MUTATED    33   3   1   2
  CTCF WILD-TYPE 138   8   6  16
D4V5, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  R0           33            138
  R1            3              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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTCF MUTATED                                  1     3
  CTCF WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN
  CTCF MUTATED                           5
  CTCF WILD-TYPE                        20
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTCF MUTATED                                           1    33
  CTCF WILD-TYPE                                         6   160
D4V6, multiclass
                                           clus
vv                                          CTCF MUTATED CTCF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     1              2
  ASIAN                                                3             10
  BLACK OR AFRICAN AMERICAN                            5             20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                               33            160
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                cls
clus               0   1
  CTCF MUTATED     1  33
  CTCF WILD-TYPE   3 134
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED      1   33
  CTCF WILD-TYPE    3  134
                        clus
vv                       CTCF MUTATED CTCF WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           33            134
[1] 2 2
[1] FALSE

Clustering(5) Variable = FBXW7 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED    35   4
  FBXW7 WILD-TYPE 189  20
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             39             209 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              4              20 
$`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        83.67        86.07        39.42 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05P TCGA-AP-A0LM TCGA-AX-A05S TCGA-AX-A05Y 
       45.53        36.89        20.91        27.12        13.58        72.03 
TCGA-AX-A05Z TCGA-AX-A0IU TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-B5-A0JY 
       46.45        28.54        40.11        16.96        13.55        32.55 
TCGA-B5-A11E TCGA-B5-A11N TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A13C TCGA-BS-A0TC 
        8.71        43.96        35.90        34.98        24.99        85.55 
TCGA-BS-A0U8 TCGA-D1-A0ZP TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15X TCGA-D1-A160 
       97.41        29.95         1.74        21.99        29.88         3.68 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A17Q TCGA-DI-A1NN 
       27.42        11.51         3.65        17.49         1.78        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-FI-A2EX 
       48.36        10.92         9.07 

$`FBXW7 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M 
       17.59        24.62        29.06        11.97        15.95         1.18 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05N 
       21.99         5.95        23.31         8.22        57.80         7.86 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       29.69        68.35        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0J1 
       53.92        27.39        60.66        35.01        37.78        65.88 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        40.67        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
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 
       40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0CB 
       14.73        14.01        15.45        15.45        23.70         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE 
       10.22        10.16        46.95        23.47        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U9 
       77.95        61.87        67.99        96.49        30.74        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       19.79         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A161 
       22.55         4.44        39.48        30.08         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-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79         2.63        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 
       10.65         0.69        18.67        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-EO-A1Y8 
        2.33        22.92        13.22        18.25        16.31        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01        25.02 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           1.74            0.56 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          97.41          185.79 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          29.88           29.06 
[1] "1.7 - 97.4 (29.9)"  "0.6 - 185.8 (29.1)"
[1] "hr=" "1.2"
D5V2, continuous
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  FBXW7 MUTATED                                        24
  FBXW7 WILD-TYPE                                     176
                 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            24             176
  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"
D5V4, binary
                 cls
clus                0   1
  FBXW7 MUTATED    14  25
  FBXW7 WILD-TYPE  72 137
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     14   25
  FBXW7 WILD-TYPE   72  137
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO             14              72
  YES            25             137
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FBXW7 MUTATED    27   2   1   5
  FBXW7 WILD-TYPE 144   9   6  13
D5V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  R0            27             144
  R1             2               9
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXW7 MUTATED                                  0     3
  FBXW7 WILD-TYPE                                3    10
                 vv
clus              BLACK OR AFRICAN AMERICAN
  FBXW7 MUTATED                           4
  FBXW7 WILD-TYPE                        21
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FBXW7 MUTATED                                           0    30
  FBXW7 WILD-TYPE                                         7   163
D5V6, multiclass
                                           clus
vv                                          FBXW7 MUTATED FBXW7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 3              10
  BLACK OR AFRICAN AMERICAN                             4              21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                30             163
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                 cls
clus                0   1
  FBXW7 MUTATED     1  28
  FBXW7 WILD-TYPE   3 139
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      1   28
  FBXW7 WILD-TYPE    3  139
                        clus
vv                       FBXW7 MUTATED FBXW7 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            28             139
[1] 2 2
[1] FALSE

Clustering(6) Variable = KRAS MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  KRAS MUTATED    51   2
  KRAS WILD-TYPE 173  22
  KRAS MUTATED KRAS WILD-TYPE 
            53            195 
  KRAS MUTATED KRAS WILD-TYPE 
             2             22 
$`KRAS MUTATED`
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GP TCGA-A5-A0VO TCGA-AP-A051 TCGA-AP-A056 
       17.85        32.78        46.55        11.97        83.67        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        63.16        27.12        49.22 
TCGA-AX-A05W TCGA-AX-A060 TCGA-AX-A0J0 TCGA-B5-A0JS TCGA-B5-A0JV TCGA-B5-A0K3 
       68.35        35.34        40.11        46.75        40.67        23.01 
TCGA-B5-A0K6 TCGA-B5-A11E TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       13.74         8.71        54.44        44.78        43.96        40.50 
TCGA-B5-A11W TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0VW TCGA-BG-A0VZ 
       19.50        36.49        28.27        41.52        16.34        28.54 
TCGA-BG-A187 TCGA-BG-A18B TCGA-BG-A2AE TCGA-BS-A0TC TCGA-BS-A0TG TCGA-BS-A0TJ 
       14.73        15.45        23.70        85.55        77.95        67.99 
TCGA-BS-A0U8 TCGA-BS-A0UL TCGA-BS-A0V7 TCGA-D1-A0ZS TCGA-D1-A101 TCGA-D1-A15W 
       97.41        81.57        63.58         4.87         1.74        30.08 
TCGA-D1-A15X TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A168 TCGA-D1-A16D TCGA-D1-A16F 
       29.88         3.68        32.58        36.10        37.51         2.63 
TCGA-D1-A16O TCGA-D1-A16Y TCGA-D1-A17A TCGA-D1-A17H TCGA-D1-A17U 
       33.63        17.49         1.58        28.01        22.92 

$`KRAS WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       46.95        37.02        83.51         3.22       105.37        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU 
       57.53        65.75        60.53        60.53        38.37        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 
       24.62        29.06        42.35        15.95         1.18        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
        5.95        23.31         8.22        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LH 
       36.89         7.86        48.79       125.42         3.39        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        31.73        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        41.95        13.58        19.82        29.69 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       72.03        46.45        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        35.01        28.54        37.78        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       56.91        43.13        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       25.91        17.88        17.10        17.85        11.01       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
      113.36        88.34        75.72        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0MG TCGA-BG-A0MI 
       35.21        34.98         7.92        38.37        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       24.39        26.66        34.29        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A18A TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BK-A0CA 
       12.56        13.78        14.01        15.45        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA 
        6.21        10.22        10.16        24.99        46.95        23.47 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U9 
       78.21         4.80        61.87        96.49        30.74        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        86.93        72.72        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       62.79        49.55        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A102 
        8.55         0.56        28.67        23.93        22.55         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A167 
       21.99        39.48         1.91        29.33         0.66        15.72 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       37.32        36.36        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A174 
       31.07        10.65         0.69        18.67         3.65        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       30.15        18.02         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-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
       24.30         2.33        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  KRAS MUTATED KRAS WILD-TYPE 
          1.58           0.56 
  KRAS MUTATED KRAS WILD-TYPE 
        117.99         185.79 
  KRAS MUTATED KRAS WILD-TYPE 
         33.63          28.34 
[1] "1.6 - 118.0 (33.6)" "0.6 - 185.8 (28.3)"
[1] "hr=" "3.3"
D6V2, continuous
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  KRAS MUTATED                                        52
  KRAS WILD-TYPE                                     148
                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
D6V3, multiclass
                                         clus
vv                                        KRAS MUTATED KRAS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           52            148
  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"
D6V4, binary
                cls
clus               0   1
  KRAS MUTATED    22  31
  KRAS WILD-TYPE  64 131
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     22   31
  KRAS WILD-TYPE   64  131
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO            22             64
  YES           31            131
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KRAS MUTATED    35   1   0   5
  KRAS WILD-TYPE 136  10   7  13
D6V5, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           35            136
  R1            1             10
  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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRAS MUTATED                                  1     4
  KRAS WILD-TYPE                                2     9
                vv
clus             BLACK OR AFRICAN AMERICAN
  KRAS MUTATED                           3
  KRAS WILD-TYPE                        22
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KRAS MUTATED                                           2    43
  KRAS WILD-TYPE                                         5   150
D6V6, multiclass
                                           clus
vv                                          KRAS MUTATED KRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     1              2
  ASIAN                                                4              9
  BLACK OR AFRICAN AMERICAN                            3             22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            2              5
  WHITE                                               43            150
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                cls
clus               0   1
  KRAS MUTATED     0  35
  KRAS WILD-TYPE   4 132
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0   35
  KRAS WILD-TYPE    4  132
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           35            132
[1] 2 2
[1] FALSE

Clustering(7) Variable = ARHGAP35 MUTATION ANALYSIS
D7V1, survival
                    sevent
clus2                  0   1
  ARHGAP35 MUTATED    33   3
  ARHGAP35 WILD-TYPE 191  21
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                36                212 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 3                 21 
$`ARHGAP35 MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0VP TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A054 
       37.02       105.37        42.35         1.18        83.67        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A0LM TCGA-AX-A05U 
       86.07         8.22        39.42        36.89        27.12        29.69 
TCGA-AX-A05Z TCGA-AX-A064 TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JN TCGA-B5-A11E 
       46.45        34.98        40.11        65.88        80.38         8.71 
TCGA-B5-A11H TCGA-B5-A11Y TCGA-BG-A0MQ TCGA-BK-A0C9 TCGA-BS-A0UF TCGA-BS-A0UL 
       88.34        18.41        39.32        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        48.36        15.09 

$`ARHGAP35 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GH 
       46.95        83.51        17.85        32.78         3.22        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AP-A052 
       19.59        24.62        29.06        11.97        15.95        21.99 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
        5.95        57.80        45.53         7.86        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        31.73        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        41.95        13.58        19.82 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A06B 
       68.35        72.03        35.34        45.99        66.58        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       27.39        60.66        35.01        28.54        37.78        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JR TCGA-B5-A0JS 
       13.55        36.39        71.24        19.36        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       43.13        40.67        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
       11.01       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 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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-A0UM 
       30.74        97.41        67.20        88.34        82.39        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-D1-A0ZN TCGA-D1-A0ZO 
       72.72        62.79        63.58        49.55        16.83        19.79 
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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74         4.44        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
        1.91         3.68        29.33        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79         2.63        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-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-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       35.38        10.92        10.78         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
              0.66               0.56 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
            105.37             185.79 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
            36.395             28.540 
[1] "0.7 - 105.4 (36.4)" "0.6 - 185.8 (28.5)"
[1] "hr=" "1.3"
D7V2, continuous
                    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
D7V3, 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"
D7V4, binary
                    cls
clus                   0   1
  ARHGAP35 MUTATED    12  24
  ARHGAP35 WILD-TYPE  74 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP35 MUTATED     12   24
  ARHGAP35 WILD-TYPE   74  138
     clus
vv    ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  NO                12                 74
  YES               24                138
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  ARHGAP35 MUTATED    25   2   1   2
  ARHGAP35 WILD-TYPE 146   9   6  16
D7V5, multiclass
    clus
vv   ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  R0               25                146
  R1                2                  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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP35 MUTATED                                  1     3
  ARHGAP35 WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  ARHGAP35 MUTATED                           5
  ARHGAP35 WILD-TYPE                        20
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARHGAP35 MUTATED                                           2    24
  ARHGAP35 WILD-TYPE                                         5   169
D7V6, multiclass
                                           clus
vv                                          ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  2
  ASIAN                                                    3                 10
  BLACK OR AFRICAN AMERICAN                                5                 20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  5
  WHITE                                                   24                169
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                    cls
clus                   0   1
  ARHGAP35 MUTATED     1  23
  ARHGAP35 WILD-TYPE   3 144
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP35 MUTATED      1   23
  ARHGAP35 WILD-TYPE    3  144
                        clus
vv                       ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               23                144
[1] 2 2
[1] FALSE

Clustering(8) Variable = PIK3CA MUTATION ANALYSIS
D8V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED   123   9
  PIK3CA WILD-TYPE 101  15
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             132              116 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               9               15 
$`PIK3CA MUTATED`
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       17.85        32.78        57.53        60.53        60.53        46.55 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M 
       68.65        19.96        29.06        42.35        15.95         1.18 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05D 
       83.67        21.99         5.95        23.31        86.07        57.80 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      125.42       117.99       110.37        63.16        36.36        31.73 
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 
       41.95        19.82        68.35        46.45        35.34        45.99 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A0J0 TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JS 
       34.98        53.92        40.11        36.39        19.36        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0K0 TCGA-B5-A0K2 TCGA-B5-A0K3 
       43.13        40.67        32.55        28.34        25.91        23.01 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.74        17.10       185.79       113.36        88.34        75.72 
TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11X TCGA-B5-A11Y 
       44.78        40.50        33.50        27.35        19.59        18.41 
TCGA-B5-A1MU TCGA-BG-A0M0 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       50.89        19.33        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0VX 
       28.27        41.52        39.32        21.17        15.42        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       28.54        52.83        56.58        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         6.21 
TCGA-BS-A0TC TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       85.55        77.95        67.99        85.84        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0WQ 
       86.93        72.72        73.25        62.79        63.58        66.48 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A102 TCGA-D1-A103 
       19.79        29.95        28.67        23.93         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15X TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A168 TCGA-D1-A16B 
       39.48        29.88        29.33        32.58        36.10        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79         2.63        27.42        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A174 TCGA-D1-A17A TCGA-D1-A17F 
       33.63         0.69        18.67        19.53         1.58         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17Q TCGA-D1-A17S 
       28.01        28.08        26.37        10.22         1.78        24.30 
TCGA-D1-A17T TCGA-D1-A1NU TCGA-D1-A1NX TCGA-E6-A1LZ TCGA-EO-A1Y8 TCGA-FI-A2D2 
        2.33        13.22        18.25        48.36        10.78        36.00 

$`PIK3CA WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       46.95        37.02        83.51         3.22       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0R7 
       65.75        38.37        28.27        20.81        23.21        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0VO TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       19.59        24.62        11.97         8.22        39.42        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LF TCGA-AP-A0LI 
       36.89         7.86        20.91        48.79         3.39        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        72.03        66.58 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        35.01        28.54        37.78        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JZ 
       16.96        13.55        71.24        80.38        56.91        28.64 
TCGA-B5-A0K1 TCGA-B5-A0K4 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11J 
       30.51        17.88        17.85        11.01         8.71        54.44 
TCGA-B5-A11N TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Z 
       43.96        32.09        16.73        19.56        19.50        17.36 
TCGA-B5-A121 TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M2 TCGA-BG-A0M3 
       16.57        11.87        18.61        20.19        20.94        35.21 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MS TCGA-BG-A0MU TCGA-BG-A0VT 
       48.56        23.47        43.04        30.81        20.28        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BK-A0CC TCGA-BK-A139 
       26.66        16.34        14.83        12.56        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TI 
       24.99        46.95        23.47        78.21         4.80        61.87 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0V8 
       96.49        30.74        97.41        67.20        88.34        49.55 
TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZZ TCGA-D1-A101 
       16.83         8.55         0.56         4.87        22.55         1.74 
TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A169 
       30.08         1.91         3.68         0.66        15.72        37.32 
TCGA-D1-A16I TCGA-D1-A16Q TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A176 TCGA-D1-A177 
       11.51        10.65         3.65        17.49        30.15        18.02 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17N TCGA-D1-A17R TCGA-D1-A17U 
        7.00         0.99        30.44         1.51        11.15        22.92 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-EO-A1Y5 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2EW 
       16.31        35.38        10.92        15.09         3.62        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.69             0.56 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          185.79           105.37 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           33.96            23.34 
[1] "0.7 - 185.8 (34.0)" "0.6 - 105.4 (23.3)"
[1] "hr=" "2.4"
D8V2, continuous
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PIK3CA MUTATED                                       110
  PIK3CA WILD-TYPE                                      90
                  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
D8V3, multiclass
                                         clus
vv                                        PIK3CA MUTATED PIK3CA WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            110               90
  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"
D8V4, binary
                  cls
clus                0  1
  PIK3CA MUTATED   44 88
  PIK3CA WILD-TYPE 42 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     44   88
  PIK3CA WILD-TYPE   42   74
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              44               42
  YES             88               74
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2 RX
  PIK3CA MUTATED   92  5  1 11
  PIK3CA WILD-TYPE 79  6  6  7
D8V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0             92               79
  R1              5                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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3CA MUTATED                                  1     8
  PIK3CA WILD-TYPE                                2     5
                  vv
clus               BLACK OR AFRICAN AMERICAN
  PIK3CA MUTATED                          11
  PIK3CA WILD-TYPE                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIK3CA MUTATED                                           3   105
  PIK3CA WILD-TYPE                                         4    88
D8V6, multiclass
                                           clus
vv                                          PIK3CA MUTATED PIK3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       1                2
  ASIAN                                                  8                5
  BLACK OR AFRICAN AMERICAN                             11               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              3                4
  WHITE                                                105               88
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                  cls
clus                0  1
  PIK3CA MUTATED    2 85
  PIK3CA WILD-TYPE  2 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      2   85
  PIK3CA WILD-TYPE    2   82
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  2                2
  NOT HISPANIC OR LATINO             85               82
[1] 2 2
[1] FALSE

Clustering(9) Variable = ARID1A MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    81   2
  ARID1A WILD-TYPE 143  22
  ARID1A MUTATED ARID1A WILD-TYPE 
              83              165 
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               22 
$`ARID1A MUTATED`
TCGA-A5-A0GB TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ 
       32.78        74.10        57.53        60.53        46.55        38.37 
TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N 
       19.96        19.59        83.67        86.07         8.22         7.86 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AX-A05T TCGA-AX-A05W 
      110.37        63.16        83.97        27.12        19.82        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A0IS 
       72.03        46.45        35.34        45.99        66.58        35.01 
TCGA-AX-A0J0 TCGA-AX-A2HF TCGA-B5-A0JS TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0K0 
       40.11        19.36        46.75        40.67        32.55        28.34 
TCGA-B5-A0K4 TCGA-B5-A11E TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11R TCGA-B5-A11W 
       17.88         8.71        44.78        40.50        33.50        19.50 
TCGA-B5-A11X TCGA-B5-A121 TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M9 TCGA-BG-A0MG 
       19.59        16.57        20.19        35.21        28.27        48.56 
TCGA-BG-A0MT TCGA-BG-A0VV TCGA-BG-A0YV TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A2AE 
       21.17        26.66        12.56        14.01        15.45        23.70 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BS-A0TC TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 
       34.98         6.21        85.55        77.95        67.99        96.49 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UM TCGA-BS-A0UV TCGA-BS-A0V6 
       97.41        88.34        82.39        86.93        73.25        62.79 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A15W TCGA-D1-A15X 
       16.83        19.79         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-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         3.22       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        20.81        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        11.97        42.35        15.95 
TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D 
        1.18        21.99         5.95        23.31        39.42        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       45.53        36.89        20.91        48.79       125.42       117.99 
TCGA-AP-A0LF TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LN TCGA-AP-A0LO 
        3.39        36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05U TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IU 
       29.69        34.98        53.92        27.39        60.66        28.54 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       37.78        65.88        16.96        13.55        36.39        71.24 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 
       80.38        56.91        43.13        28.64        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       23.01        13.74        17.10        17.85        11.01       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        43.96        32.09 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A1MU 
       27.35        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-A0M6 
       11.87        18.61        19.33        20.94        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       38.37        36.49        41.52        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VW TCGA-BG-A0VX 
       30.81        20.28        15.42        24.39        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       28.54        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       15.45        35.90        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0U7 TCGA-BS-A0U9 
       23.47        78.21         4.80        61.87        30.74        67.20 
TCGA-BS-A0UF TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       85.84        81.57        72.72        63.58        49.55        66.48 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
       29.95         8.55         0.56        23.93        22.55         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 
        4.44        21.99        39.48         1.91        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A169 TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
        0.66        37.32         2.63        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A177 
       31.07         0.69        18.67        17.49        19.53        18.02 
TCGA-D1-A17B TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17K TCGA-D1-A17M TCGA-D1-A17N 
        7.00        30.44         1.28        28.08        10.22         1.51 
TCGA-D1-A17S TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
       24.30        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.99             0.56 
  ARID1A MUTATED ARID1A WILD-TYPE 
          110.37           185.79 
  ARID1A MUTATED ARID1A WILD-TYPE 
           32.78            28.27 
[1] "1.0 - 110.4 (32.8)" "0.6 - 185.8 (28.3)"
[1] "hr=" "6"  
D9V2, continuous
                  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
D9V3, 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"
D9V4, binary
                  cls
clus                 0   1
  ARID1A MUTATED    31  52
  ARID1A WILD-TYPE  55 110
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     31   52
  ARID1A WILD-TYPE   55  110
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO              31               55
  YES             52              110
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ARID1A MUTATED    60   4   0   5
  ARID1A WILD-TYPE 111   7   7  13
D9V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             60              111
  R1              4                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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID1A MUTATED                                  1     5
  ARID1A WILD-TYPE                                2     8
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ARID1A MUTATED                           4
  ARID1A WILD-TYPE                        21
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARID1A MUTATED                                           1    69
  ARID1A WILD-TYPE                                         6   124
D9V6, multiclass
                                           clus
vv                                          ARID1A MUTATED ARID1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       1                2
  ASIAN                                                  5                8
  BLACK OR AFRICAN AMERICAN                              4               21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                 69              124
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED     1  59
  ARID1A WILD-TYPE   3 108
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      1   59
  ARID1A WILD-TYPE    3  108
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             59              108
[1] 2 2
[1] FALSE

Clustering(10) Variable = CTNNB1 MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2                0   1
  CTNNB1 MUTATED    68   6
  CTNNB1 WILD-TYPE 156  18
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              74              174 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               6               18 
$`CTNNB1 MUTATED`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       57.53        60.53        60.53        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R9 TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AP-A054 TCGA-AP-A056 
       68.65        24.62        11.97        15.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL 
        8.22         7.86       110.37        63.16        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LV TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       27.12        82.52        25.08        19.82        29.69        68.35 
TCGA-AX-A062 TCGA-AX-A0IS TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JT TCGA-B5-A0JY 
       45.99        35.01        40.11        65.88        43.13        32.55 
TCGA-B5-A0K0 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11U 
       28.34        13.74        17.10         8.71       185.79        16.73 
TCGA-B5-A11V TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A121 TCGA-BG-A0LW TCGA-BG-A0M3 
       19.56        19.59        17.36        16.57        18.61        35.21 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VX 
       48.56        23.47        43.04        20.28        24.39        34.29 
TCGA-BG-A0W2 TCGA-BG-A187 TCGA-BK-A0CB TCGA-BS-A0T9 TCGA-BS-A0TG TCGA-BS-A0UJ 
       56.58        14.73         6.21        46.95        77.95        82.39 
TCGA-BS-A0UT TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ 
       72.72        63.58        49.55        66.48        16.83         8.55 
TCGA-D1-A0ZU TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15Z TCGA-D1-A165 TCGA-D1-A16B 
       28.67         4.44        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-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0R6 
      105.37        74.10        65.75        46.55        38.37        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-AJ-A23M TCGA-AP-A051 
       17.59        19.59        29.06        42.35         1.18        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       21.99         5.95        39.42        57.80        45.53        36.89 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LF TCGA-AP-A0LH 
       20.91        48.79       125.42       117.99         3.39        36.36 
TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A1DQ 
       97.71        33.40        61.64        80.78        49.22        41.95 
TCGA-AX-A05S TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A064 
       13.58        72.03        46.45        35.34        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       53.92        27.39        60.66        28.54        37.78        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       46.75        40.67        28.64        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.88        17.85        11.01       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LX 
       27.35        19.50        18.41        50.89        11.87        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       19.33        20.94        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0RY 
       28.27        41.52        39.32        30.81        21.17        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0YU TCGA-BG-A0YV 
       26.66        16.34        28.54        52.83        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       13.78        14.01        15.45        15.45        23.70        35.90 
TCGA-BK-A0CA TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0TA TCGA-BS-A0TC 
       34.98        10.22        10.16        24.99        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21         4.80        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        67.20        88.34        85.84        81.57        86.93 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZS 
       73.25        62.79        19.79        29.95         0.56         4.87 
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-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-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-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       31.07        33.63        18.67         3.65        17.49        19.53 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17D TCGA-D1-A17F 
       30.15        18.02         1.58         7.00        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17Q TCGA-D1-A17U TCGA-D1-A1NU 
       28.01        28.08        26.37         1.78        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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            0.66             0.56 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          185.79           125.42 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          24.850           30.115 
[1] "0.7 - 185.8 (24.9)" "0.6 - 125.4 (30.1)"
[1] "hr=" "1.2"
D10V2, continuous
                  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"
D10V4, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    22  52
  CTNNB1 WILD-TYPE  64 110
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     22   52
  CTNNB1 WILD-TYPE   64  110
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO              22               64
  YES             52              110
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CTNNB1 MUTATED    54   4   1   3
  CTNNB1 WILD-TYPE 117   7   6  15
D10V5, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0             54              117
  R1              4                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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTNNB1 MUTATED                                  1     4
  CTNNB1 WILD-TYPE                                2     9
                  vv
clus               BLACK OR AFRICAN AMERICAN
  CTNNB1 MUTATED                           5
  CTNNB1 WILD-TYPE                        20
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTNNB1 MUTATED                                           3    59
  CTNNB1 WILD-TYPE                                         4   134
D10V6, multiclass
                                           clus
vv                                          CTNNB1 MUTATED CTNNB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       1                2
  ASIAN                                                  4                9
  BLACK OR AFRICAN AMERICAN                              5               20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              3                4
  WHITE                                                 59              134
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     1  47
  CTNNB1 WILD-TYPE   3 120
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      1   47
  CTNNB1 WILD-TYPE    3  120
                        clus
vv                       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             47              120
[1] 2 2
[1] FALSE

Clustering(11) Variable = FGFR2 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2               0   1
  FGFR2 MUTATED    29   2
  FGFR2 WILD-TYPE 195  22
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             31             217 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
              2              22 
$`FGFR2 MUTATED`
TCGA-A5-A0GQ TCGA-A5-A0GW TCGA-AP-A056 TCGA-AP-A0LM TCGA-AP-A0LP TCGA-AX-A063 
       38.37        23.21        86.07        27.12        61.64        66.58 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JR TCGA-B5-A0JT 
       34.98        27.39        40.11        65.88        56.91        43.13 
TCGA-B5-A0K1 TCGA-B5-A11E TCGA-B5-A11Y TCGA-B5-A121 TCGA-BG-A0LX TCGA-BG-A0M7 
       30.51         8.71        18.41        16.57        20.19        38.37 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BS-A0UV TCGA-D1-A15X 
       39.32        30.81        15.42        26.66        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        10.78 
TCGA-FI-A2EW 
       59.01 

$`FGFR2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       46.55        28.27        20.81        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.59        24.62        29.06        11.97        42.35        15.95 
TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A059 
        1.18        83.67        21.99         5.95        23.31         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        83.97        82.52        33.40 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       80.78        49.22        25.08        41.95        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A06B TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       53.92        60.66        35.01        28.54        37.78        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JS 
       13.55        36.39        71.24        19.36        80.38        46.75 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        32.55        28.64        28.34        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       17.88        13.74        17.10        17.85        11.01       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        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       19.50        19.59        17.36        50.89        11.87        18.61 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M8 
       19.33        20.94        35.21        34.98         7.92        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MT 
       28.27        41.52        48.56        23.47        43.04        21.17 
TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       20.28        24.39        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A165 
       21.99        39.48        30.08         3.68        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-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-A1NN 
       24.30         2.33        22.92        13.22        18.25        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EX 
       48.36        10.92        15.09         3.62        36.00         9.07 
TCGA-FI-A2F8 
       25.02 

  FGFR2 MUTATED FGFR2 WILD-TYPE 
           1.91            0.56 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
          86.07          185.79 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
          29.88           28.67 
[1] "1.9 - 86.1 (29.9)"  "0.6 - 185.8 (28.7)"
[1] "hr=" "1.6"
D11V2, continuous
                 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
D11V3, 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"
D11V4, binary
                 cls
clus                0   1
  FGFR2 MUTATED    11  20
  FGFR2 WILD-TYPE  75 142
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR2 MUTATED     11   20
  FGFR2 WILD-TYPE   75  142
     clus
vv    FGFR2 MUTATED FGFR2 WILD-TYPE
  NO             11              75
  YES            20             142
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FGFR2 MUTATED    23   1   0   0
  FGFR2 WILD-TYPE 148  10   7  18
D11V5, multiclass
    clus
vv   FGFR2 MUTATED FGFR2 WILD-TYPE
  R0            23             148
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FGFR2 MUTATED                                  1     1
  FGFR2 WILD-TYPE                                2    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  FGFR2 MUTATED                           2
  FGFR2 WILD-TYPE                        23
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FGFR2 MUTATED                                           1    25
  FGFR2 WILD-TYPE                                         6   168
D11V6, multiclass
                                           clus
vv                                          FGFR2 MUTATED FGFR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      1               2
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             2              23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                25             168
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                 cls
clus                0   1
  FGFR2 MUTATED     0  19
  FGFR2 WILD-TYPE   4 148
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR2 MUTATED      0   19
  FGFR2 WILD-TYPE    4  148
                        clus
vv                       FGFR2 MUTATED FGFR2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            19             148
[1] 2 2
[1] FALSE

Clustering(12) Variable = ZFHX3 MUTATION ANALYSIS
D12V1, survival
                 sevent
clus2               0   1
  ZFHX3 MUTATED    40   4
  ZFHX3 WILD-TYPE 184  20
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             44             204 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
              4              20 
$`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        20.81        83.67        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A0L9 TCGA-AP-A0LD 
       86.07         8.22        39.42         7.86       125.42       117.99 
TCGA-AP-A0LG TCGA-AP-A0LM TCGA-AP-A0LT TCGA-AX-A05Z TCGA-AX-A063 TCGA-AX-A06H 
       63.16        27.12        49.22        46.45        66.58        27.39 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JR TCGA-B5-A0JY TCGA-B5-A0K9 TCGA-B5-A11E 
       40.11        65.88        56.91        32.55        11.01         8.71 
TCGA-B5-A11Y TCGA-BG-A0VZ TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BS-A0TA TCGA-BS-A0TC 
       18.41        28.54        15.45        35.90        23.47        85.55 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UM TCGA-BS-A0UV TCGA-D1-A0ZS 
       88.34        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       46.95        37.02        17.85         3.22       105.37        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU 
       57.53        65.75        60.53        60.53        38.37        28.27 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        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        11.97        42.35        15.95         1.18        21.99 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05P TCGA-AP-A0L8 
        5.95        57.80        45.53        36.89        20.91        48.79 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37         3.39        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       45.99        34.98        53.92        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       37.78        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       80.38        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       17.85       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        43.96        40.50        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        19.59        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       34.29        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A2AE TCGA-BK-A0CA TCGA-BK-A0CB 
       14.73        14.01        15.45        23.70        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TD TCGA-BS-A0TE 
       10.22        10.16        24.99        46.95        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-A0UL TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       67.20        81.57        72.72        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74         4.44        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A165 
       30.08        29.88         1.91         3.68        29.33         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-A177 TCGA-D1-A17A 
       18.67         3.65        17.49        19.53        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
        7.00         0.99        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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
           1.28            0.56 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
         125.42          185.79 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
          32.68           28.44 
[1] "1.3 - 125.4 (32.7)" "0.6 - 185.8 (28.4)"
[1] "hr=" "1.3"
D12V2, continuous
                 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
D12V3, 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"
D12V4, binary
                 cls
clus                0   1
  ZFHX3 MUTATED    16  28
  ZFHX3 WILD-TYPE  70 134
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED     16   28
  ZFHX3 WILD-TYPE   70  134
     clus
vv    ZFHX3 MUTATED ZFHX3 WILD-TYPE
  NO             16              70
  YES            28             134
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZFHX3 MUTATED    34   3   0   2
  ZFHX3 WILD-TYPE 137   8   7  16
D12V5, multiclass
    clus
vv   ZFHX3 MUTATED ZFHX3 WILD-TYPE
  R0            34             137
  R1             3               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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFHX3 MUTATED                                  1     4
  ZFHX3 WILD-TYPE                                2     9
                 vv
clus              BLACK OR AFRICAN AMERICAN
  ZFHX3 MUTATED                           1
  ZFHX3 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZFHX3 MUTATED                                           2    35
  ZFHX3 WILD-TYPE                                         5   158
D12V6, multiclass
                                           clus
vv                                          ZFHX3 MUTATED ZFHX3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      1               2
  ASIAN                                                 4               9
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             2               5
  WHITE                                                35             158
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                 cls
clus                0   1
  ZFHX3 MUTATED     2  26
  ZFHX3 WILD-TYPE   2 141
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED      2   26
  ZFHX3 WILD-TYPE    2  141
                        clus
vv                       ZFHX3 MUTATED ZFHX3 WILD-TYPE
  HISPANIC OR LATINO                 2               2
  NOT HISPANIC OR LATINO            26             141
[1] 2 2
[1] FALSE

Clustering(13) Variable = TCP11L2 MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  TCP11L2 MUTATED    14   0
  TCP11L2 WILD-TYPE 210  24
  TCP11L2 MUTATED TCP11L2 WILD-TYPE 
               14               234 
  TCP11L2 MUTATED TCP11L2 WILD-TYPE 
                0                24 
$`TCP11L2 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 
       83.67        86.07         8.22        46.45        35.34        66.58 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A11E TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UV 
       40.11        65.88         8.71        88.34        85.84        73.25 
TCGA-D1-A167 TCGA-D1-A17Q 
       15.72         1.78 

$`TCP11L2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A062 
       13.58        19.82        29.69        68.35        72.03        45.99 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       34.98        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       37.78        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       80.38        56.91        46.75        43.13        40.67        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        17.85        11.01       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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-A0UJ TCGA-BS-A0UL 
       96.49        30.74        97.41        67.20        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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-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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  TCP11L2 MUTATED TCP11L2 WILD-TYPE 
             1.78              0.56 
  TCP11L2 MUTATED TCP11L2 WILD-TYPE 
            88.34            185.79 
  TCP11L2 MUTATED TCP11L2 WILD-TYPE 
           56.165            28.590 
[1] "1.8 - 88.3 (56.2)"  "0.6 - 185.8 (28.6)"
[1] "hr="     "7.5e+07"
D13V2, continuous
                   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
D13V3, 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"
D13V4, binary
                   cls
clus                  0   1
  TCP11L2 MUTATED     5   9
  TCP11L2 WILD-TYPE  81 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TCP11L2 MUTATED      5    9
  TCP11L2 WILD-TYPE   81  153
     clus
vv    TCP11L2 MUTATED TCP11L2 WILD-TYPE
  NO                5                81
  YES               9               153
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TCP11L2 MUTATED    11   2   0   0
  TCP11L2 WILD-TYPE 160   9   7  18
D13V5, multiclass
    clus
vv   TCP11L2 MUTATED TCP11L2 WILD-TYPE
  R0              11               160
  R1               2                 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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCP11L2 MUTATED                                  1     1
  TCP11L2 WILD-TYPE                                2    12
                   vv
clus                BLACK OR AFRICAN AMERICAN
  TCP11L2 MUTATED                           0
  TCP11L2 WILD-TYPE                        25
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TCP11L2 MUTATED                                           1    10
  TCP11L2 WILD-TYPE                                         6   183
D13V6, multiclass
                                           clus
vv                                          TCP11L2 MUTATED TCP11L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   1                12
  BLACK OR AFRICAN AMERICAN                               0                25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 6
  WHITE                                                  10               183
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                  0   1
  TCP11L2 MUTATED     1  10
  TCP11L2 WILD-TYPE   3 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TCP11L2 MUTATED      1   10
  TCP11L2 WILD-TYPE    3  157
                        clus
vv                       TCP11L2 MUTATED TCP11L2 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              10               157
[1] 2 2
[1] FALSE

Clustering(14) Variable = SPOP MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  SPOP MUTATED    20   1
  SPOP WILD-TYPE 204  23
  SPOP MUTATED SPOP WILD-TYPE 
            21            227 
  SPOP MUTATED SPOP WILD-TYPE 
             1             23 
$`SPOP MUTATED`
TCGA-A5-A0RA TCGA-AP-A059 TCGA-AP-A0L8 TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A063 
       29.06         8.22        48.79        46.45        45.99        66.58 
TCGA-B5-A0JY TCGA-B5-A0K0 TCGA-B5-A11Y TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BS-A0UF 
       32.55        28.34        18.41        35.21        38.37        85.84 
TCGA-BS-A0UT TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A103 TCGA-D1-A167 TCGA-D1-A168 
       72.72        19.79         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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0VO TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       20.91       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       34.98        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       37.78        40.11        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       40.67        28.64        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        17.85        11.01         8.71       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        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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-A0M4 TCGA-BG-A0M6 
       18.61        20.19        19.33        20.94        34.98         7.92 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        82.39        81.57        86.93 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       73.25        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
       29.95         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A169 TCGA-D1-A16B 
        3.68        29.33        32.58         0.66        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-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-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       13.22        18.25        16.31        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00         9.07        25.02 

  SPOP MUTATED SPOP WILD-TYPE 
          8.22           0.56 
  SPOP MUTATED SPOP WILD-TYPE 
         85.84         185.79 
  SPOP MUTATED SPOP WILD-TYPE 
         35.21          28.54 
[1] "8.2 - 85.8 (35.2)"  "0.6 - 185.8 (28.5)"
[1] "hr=" "2.4"
D14V2, continuous
                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
D14V3, 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"
D14V4, binary
                cls
clus               0   1
  SPOP MUTATED     8  13
  SPOP WILD-TYPE  78 149
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPOP MUTATED      8   13
  SPOP WILD-TYPE   78  149
     clus
vv    SPOP MUTATED SPOP WILD-TYPE
  NO             8             78
  YES           13            149
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SPOP MUTATED    17   1   0   0
  SPOP WILD-TYPE 154  10   7  18
D14V5, multiclass
    clus
vv   SPOP MUTATED SPOP WILD-TYPE
  R0           17            154
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPOP MUTATED                                  0     2
  SPOP WILD-TYPE                                3    11
                vv
clus             BLACK OR AFRICAN AMERICAN
  SPOP MUTATED                           2
  SPOP WILD-TYPE                        23
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPOP MUTATED                                           0    16
  SPOP WILD-TYPE                                         7   177
D14V6, multiclass
                                           clus
vv                                          SPOP MUTATED SPOP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                2             11
  BLACK OR AFRICAN AMERICAN                            2             23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              7
  WHITE                                               16            177
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                cls
clus               0   1
  SPOP MUTATED     1  14
  SPOP WILD-TYPE   3 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPOP MUTATED      1   14
  SPOP WILD-TYPE    3  153
                        clus
vv                       SPOP MUTATED SPOP WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           14            153
[1] 2 2
[1] FALSE

Clustering(15) Variable = RBMX MUTATION ANALYSIS
D15V1, survival
                sevent
clus2              0   1
  RBMX MUTATED    11   2
  RBMX WILD-TYPE 213  22
  RBMX MUTATED RBMX WILD-TYPE 
            13            235 
  RBMX MUTATED RBMX WILD-TYPE 
             2             22 
$`RBMX MUTATED`
TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AX-A05S TCGA-AX-A060 
       23.31         8.22       117.99       110.37        13.58        35.34 
TCGA-B5-A0JZ TCGA-BG-A0LX TCGA-BS-A0UF TCGA-BS-A0UM TCGA-D1-A0ZO TCGA-D1-A103 
       28.64        20.19        85.84        86.93        19.79        21.99 
TCGA-D1-A17Q 
        1.78 

$`RBMX WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91        48.79       125.42         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        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-A05T 
       61.64        80.78        49.22        25.08        41.95        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A063 
       29.69        68.35        72.03        46.45        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       34.98        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       37.78        40.11        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        32.55        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       17.88        13.74        17.10        17.85        11.01         8.71 
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 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        67.20        88.34 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       82.39        81.57        72.72        73.25        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       49.55        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-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  RBMX MUTATED RBMX WILD-TYPE 
          1.78           0.56 
  RBMX MUTATED RBMX WILD-TYPE 
        117.99         185.79 
  RBMX MUTATED RBMX WILD-TYPE 
         23.31          29.69 
[1] "1.8 - 118.0 (23.3)" "0.6 - 185.8 (29.7)"
[1] "hr=" "1.7"
D15V2, continuous
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  RBMX MUTATED                                        13
  RBMX WILD-TYPE                                     187
                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
D15V3, multiclass
                                         clus
vv                                        RBMX MUTATED RBMX 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"
D15V4, binary
                cls
clus               0   1
  RBMX MUTATED     7   6
  RBMX WILD-TYPE  79 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      7    6
  RBMX WILD-TYPE   79  156
     clus
vv    RBMX MUTATED RBMX WILD-TYPE
  NO             7             79
  YES            6            156
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RBMX MUTATED     9   2   1   0
  RBMX WILD-TYPE 162   9   6  18
D15V5, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  R0            9            162
  R1            2              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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBMX MUTATED                                  1     1
  RBMX WILD-TYPE                                2    12
                vv
clus             BLACK OR AFRICAN AMERICAN
  RBMX MUTATED                           0
  RBMX WILD-TYPE                        25
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RBMX MUTATED                                           0    11
  RBMX WILD-TYPE                                         7   182
D15V6, multiclass
                                           clus
vv                                          RBMX MUTATED RBMX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     1              2
  ASIAN                                                1             12
  BLACK OR AFRICAN AMERICAN                            0             25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              7
  WHITE                                               11            182
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                cls
clus               0   1
  RBMX MUTATED     0  10
  RBMX WILD-TYPE   4 157
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      0   10
  RBMX WILD-TYPE    4  157
                        clus
vv                       RBMX MUTATED RBMX WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           10            157
[1] 2 2
[1] FALSE

Clustering(16) Variable = SOX17 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  SOX17 MUTATED     7   0
  SOX17 WILD-TYPE 217  24
  SOX17 MUTATED SOX17 WILD-TYPE 
              7             241 
  SOX17 MUTATED SOX17 WILD-TYPE 
              0              24 
$`SOX17 MUTATED`
TCGA-AP-A05P TCGA-B5-A0K4 TCGA-BG-A0W1 TCGA-BG-A18A TCGA-BK-A13C TCGA-BS-A0UT 
       20.91        17.88        52.83        14.01        24.99        72.72 
TCGA-D1-A0ZR 
        0.56 

$`SOX17 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89         7.86        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       40.11        65.88        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        17.85        11.01         8.71       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        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       28.54        56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.22        10.16        46.95        23.47        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        67.20        88.34        85.84        82.39        81.57 
TCGA-BS-A0UM TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        73.25        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        19.79        29.95         8.55         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  SOX17 MUTATED SOX17 WILD-TYPE 
           0.56            0.66 
  SOX17 MUTATED SOX17 WILD-TYPE 
          72.72          185.79 
  SOX17 MUTATED SOX17 WILD-TYPE 
          20.91           29.69 
[1] "0.6 - 72.7 (20.9)"  "0.7 - 185.8 (29.7)"
[1] "hr="     "9300000"
D16V2, continuous
                 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
D16V3, 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"
D16V4, binary
                 cls
clus                0   1
  SOX17 MUTATED     1   6
  SOX17 WILD-TYPE  85 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SOX17 MUTATED      1    6
  SOX17 WILD-TYPE   85  156
     clus
vv    SOX17 MUTATED SOX17 WILD-TYPE
  NO              1              85
  YES             6             156
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SOX17 MUTATED     5   0   0   1
  SOX17 WILD-TYPE 166  11   7  17
D16V5, multiclass
    clus
vv   SOX17 MUTATED SOX17 WILD-TYPE
  R0             5             166
  R1             0              11
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SOX17 MUTATED                                  0     2
  SOX17 WILD-TYPE                                3    11
                 vv
clus              BLACK OR AFRICAN AMERICAN
  SOX17 MUTATED                           1
  SOX17 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SOX17 MUTATED                                           0     3
  SOX17 WILD-TYPE                                         7   190
D16V6, multiclass
                                           clus
vv                                          SOX17 MUTATED SOX17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 2              11
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                 3             190
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                 cls
clus                0   1
  SOX17 MUTATED     0   6
  SOX17 WILD-TYPE   4 161
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SOX17 MUTATED      0    6
  SOX17 WILD-TYPE    4  161
                        clus
vv                       SOX17 MUTATED SOX17 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             161
[1] 2 2
[1] FALSE

Clustering(17) Variable = NFE2L2 MUTATION ANALYSIS
D17V1, survival
                  sevent
clus2                0   1
  NFE2L2 MUTATED    14   1
  NFE2L2 WILD-TYPE 210  23
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              15              233 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               1               23 
$`NFE2L2 MUTATED`
TCGA-A5-A0G9 TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GW TCGA-AP-A059 TCGA-AX-A05W 
       83.51        74.10        46.55        23.21         8.22        68.35 
TCGA-B5-A0JT TCGA-B5-A11R TCGA-B5-A11Y TCGA-BG-A0M4 TCGA-BK-A0C9 TCGA-BS-A0U7 
       43.13        33.50        18.41        34.98        35.90        30.74 
TCGA-D1-A16E TCGA-D1-A17Q TCGA-D1-A17U 
       36.79         1.78        22.92 

$`NFE2L2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       46.95        37.02        17.85        32.78         3.22       105.37 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU 
       57.53        65.75        60.53        60.53        38.37        28.27 
TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       20.81        68.65        19.96        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        11.97        42.35        15.95         1.18        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D 
       21.99         5.95        23.31        86.07        39.42        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89         7.86        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        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        41.95        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       34.98        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       37.78        40.11        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JV 
       71.24        19.36        80.38        56.91        46.75        40.67 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       17.88        13.74        17.10        17.85        11.01         8.71 
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 
       43.96        40.50        32.09        27.35        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-A0M6 
       18.61        20.19        19.33        20.94        35.21         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51         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-A1NU TCGA-D1-A1NX 
        1.51        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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            1.78             0.56 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           83.51           185.79 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           34.98            28.64 
[1] "1.8 - 83.5 (35.0)"  "0.6 - 185.8 (28.6)"
[1] "hr=" "1.6"
D17V2, continuous
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  NFE2L2 MUTATED                                        15
  NFE2L2 WILD-TYPE                                     185
                  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
D17V3, multiclass
                                         clus
vv                                        NFE2L2 MUTATED NFE2L2 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"
D17V4, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     4  11
  NFE2L2 WILD-TYPE  82 151
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      4   11
  NFE2L2 WILD-TYPE   82  151
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  NO               4               82
  YES             11              151
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NFE2L2 MUTATED    12   0   0   0
  NFE2L2 WILD-TYPE 159  11   7  18
D17V5, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  R0             12              159
  R1              0               11
  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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFE2L2 MUTATED                                  0     2
  NFE2L2 WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  NFE2L2 MUTATED                           1
  NFE2L2 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NFE2L2 MUTATED                                           0    12
  NFE2L2 WILD-TYPE                                         7   181
D17V6, multiclass
                                           clus
vv                                          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                 12              181
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     0  11
  NFE2L2 WILD-TYPE   4 156
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      0   11
  NFE2L2 WILD-TYPE    4  156
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              156
[1] 2 2
[1] FALSE

Clustering(18) Variable = CCND1 MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2               0   1
  CCND1 MUTATED    13   1
  CCND1 WILD-TYPE 211  23
  CCND1 MUTATED CCND1 WILD-TYPE 
             14             234 
  CCND1 MUTATED CCND1 WILD-TYPE 
              1              23 
$`CCND1 MUTATED`
TCGA-AP-A054 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A0J0 
       23.31        27.12        46.45        45.99        66.58        40.11 
TCGA-B5-A0JV TCGA-BG-A0MQ TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-D1-A0ZO TCGA-D1-A0ZU 
       40.67        39.32        67.99        96.49        19.79        28.67 
TCGA-D1-A16D TCGA-D1-A17D 
       37.51        30.44 

$`CCND1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       35.34        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       28.54        37.78        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       17.88        13.74        17.10        17.85        11.01         8.71 
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 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MS TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        67.20        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       49.55        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        23.93        22.55         1.74         4.44        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-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-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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  CCND1 MUTATED CCND1 WILD-TYPE 
          19.79            0.56 
  CCND1 MUTATED CCND1 WILD-TYPE 
          96.49          185.79 
  CCND1 MUTATED CCND1 WILD-TYPE 
         39.715          28.540 
[1] "19.8 - 96.5 (39.7)" "0.6 - 185.8 (28.5)"
[1] "hr=" "1.7"
D18V2, continuous
                 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
D18V3, 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"
D18V4, binary
                 cls
clus                0   1
  CCND1 MUTATED     6   8
  CCND1 WILD-TYPE  80 154
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCND1 MUTATED      6    8
  CCND1 WILD-TYPE   80  154
     clus
vv    CCND1 MUTATED CCND1 WILD-TYPE
  NO              6              80
  YES             8             154
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CCND1 MUTATED    10   2   0   1
  CCND1 WILD-TYPE 161   9   7  17
D18V5, multiclass
    clus
vv   CCND1 MUTATED CCND1 WILD-TYPE
  R0            10             161
  R1             2               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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCND1 MUTATED                                  0     1
  CCND1 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  CCND1 MUTATED                           2
  CCND1 WILD-TYPE                        23
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCND1 MUTATED                                           0    10
  CCND1 WILD-TYPE                                         7   183
D18V6, multiclass
                                           clus
vv                                          CCND1 MUTATED CCND1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             2              23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                10             183
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                 cls
clus                0   1
  CCND1 MUTATED     1  10
  CCND1 WILD-TYPE   3 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCND1 MUTATED      1   10
  CCND1 WILD-TYPE    3  157
                        clus
vv                       CCND1 MUTATED CCND1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            10             157
[1] 2 2
[1] FALSE

Clustering(19) Variable = GNPTAB MUTATION ANALYSIS
D19V1, survival
                  sevent
clus2                0   1
  GNPTAB MUTATED    20   0
  GNPTAB WILD-TYPE 204  24
  GNPTAB MUTATED GNPTAB WILD-TYPE 
              20              228 
  GNPTAB MUTATED GNPTAB WILD-TYPE 
               0               24 
$`GNPTAB MUTATED`
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 
       86.07         8.22        27.12        46.45        40.11        65.88 
TCGA-B5-A0JY TCGA-B5-A0K4 TCGA-B5-A11E TCGA-B5-A11J TCGA-B5-A11N TCGA-BS-A0UF 
       32.55        17.88         8.71        54.44        43.96        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       35.01        28.54        37.78        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        17.85        11.01       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11M TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       88.34        75.72        44.78        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74         4.44        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 
        1.91        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-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-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       13.22        18.25        16.31        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  GNPTAB MUTATED GNPTAB WILD-TYPE 
            1.78             0.56 
  GNPTAB MUTATED GNPTAB WILD-TYPE 
           86.07           185.79 
  GNPTAB MUTATED GNPTAB WILD-TYPE 
          33.965           28.865 
[1] "1.8 - 86.1 (34.0)"  "0.6 - 185.8 (28.9)"
[1] "hr="     "7.6e+07"
D19V2, continuous
                  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
D19V3, 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"
D19V4, binary
                  cls
clus                 0   1
  GNPTAB MUTATED     5  15
  GNPTAB WILD-TYPE  81 147
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GNPTAB MUTATED      5   15
  GNPTAB WILD-TYPE   81  147
     clus
vv    GNPTAB MUTATED GNPTAB WILD-TYPE
  NO               5               81
  YES             15              147
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GNPTAB MUTATED    14   1   0   0
  GNPTAB WILD-TYPE 157  10   7  18
D19V5, multiclass
    clus
vv   GNPTAB MUTATED GNPTAB WILD-TYPE
  R0             14              157
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GNPTAB MUTATED                                  0     2
  GNPTAB WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  GNPTAB MUTATED                           1
  GNPTAB WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GNPTAB MUTATED                                           1    14
  GNPTAB WILD-TYPE                                         6   179
D19V6, multiclass
                                           clus
vv                                          GNPTAB MUTATED GNPTAB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                 14              179
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                  cls
clus                 0   1
  GNPTAB MUTATED     1  12
  GNPTAB WILD-TYPE   3 155
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GNPTAB MUTATED      1   12
  GNPTAB WILD-TYPE    3  155
                        clus
vv                       GNPTAB MUTATED GNPTAB WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             12              155
[1] 2 2
[1] FALSE

Clustering(20) Variable = ARID5B MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2                0   1
  ARID5B MUTATED    25   4
  ARID5B WILD-TYPE 199  20
  ARID5B MUTATED ARID5B WILD-TYPE 
              29              219 
  ARID5B MUTATED ARID5B WILD-TYPE 
               4               20 
$`ARID5B MUTATED`
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GP TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0RA 
       83.51        17.85        46.55        28.27        23.21        29.06 
TCGA-A5-A0VO TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A0LD 
       11.97        23.31        86.07         8.22         7.86       117.99 
TCGA-AP-A0LT TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A06H TCGA-B5-A0JT TCGA-B5-A11N 
       49.22        72.03        46.45        27.39        43.13        43.96 
TCGA-BG-A0M2 TCGA-BG-A0MC TCGA-BS-A0TC TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UF 
       20.94        41.52        85.55        30.74        97.41        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-D1-A0ZO TCGA-D1-A17F 
       82.39        81.57        73.25        19.79         1.28 

$`ARID5B WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       46.95        37.02        32.78         3.22       105.37        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GV 
       57.53        65.75        60.53        60.53        38.37        20.81 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0VP 
       68.65        19.96        17.59        19.59        24.62        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05A 
       15.95         1.18        83.67        21.99         5.95        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       57.80        45.53        36.89        20.91        48.79       125.42 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
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-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       25.08        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06L 
       35.34        45.99        66.58        34.98        53.92        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       35.01        28.54        37.78        40.11        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        40.67        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       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        40.50        32.09        33.50        27.35 
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-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       23.47        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       96.49        67.20        88.34        86.93        72.72        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        49.55        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        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-A17H TCGA-D1-A17K 
        1.58         7.00         0.99        30.44        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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  ARID5B MUTATED ARID5B WILD-TYPE 
            1.28             0.56 
  ARID5B MUTATED ARID5B WILD-TYPE 
          117.99           185.79 
  ARID5B MUTATED ARID5B WILD-TYPE 
           43.13            28.54 
[1] "1.3 - 118.0 (43.1)" "0.6 - 185.8 (28.5)"
[1] "hr=" "1.2"
D20V2, continuous
                  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
D20V3, 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"
D20V4, binary
                  cls
clus                 0   1
  ARID5B MUTATED    10  19
  ARID5B WILD-TYPE  76 143
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5B MUTATED     10   19
  ARID5B WILD-TYPE   76  143
     clus
vv    ARID5B MUTATED ARID5B WILD-TYPE
  NO              10               76
  YES             19              143
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ARID5B MUTATED    23   3   0   0
  ARID5B WILD-TYPE 148   8   7  18
D20V5, multiclass
    clus
vv   ARID5B MUTATED ARID5B WILD-TYPE
  R0             23              148
  R1              3                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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID5B MUTATED                                  1     5
  ARID5B WILD-TYPE                                2     8
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ARID5B MUTATED                           0
  ARID5B WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARID5B MUTATED                                           2    20
  ARID5B WILD-TYPE                                         5   173
D20V6, multiclass
                                           clus
vv                                          ARID5B MUTATED ARID5B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       1                2
  ASIAN                                                  5                8
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              2                5
  WHITE                                                 20              173
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                  cls
clus                 0   1
  ARID5B MUTATED     1  20
  ARID5B WILD-TYPE   3 147
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5B MUTATED      1   20
  ARID5B WILD-TYPE    3  147
                        clus
vv                       ARID5B MUTATED ARID5B WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             20              147
[1] 2 2
[1] FALSE

Clustering(21) Variable = DNER MUTATION ANALYSIS
D21V1, survival
                sevent
clus2              0   1
  DNER MUTATED    17   1
  DNER WILD-TYPE 207  23
  DNER MUTATED DNER WILD-TYPE 
            18            230 
  DNER MUTATED DNER WILD-TYPE 
             1             23 
$`DNER MUTATED`
TCGA-A5-A0GA TCGA-A5-A0GW TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J1 
       17.85        23.21        86.07        27.12        46.45        65.88 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A11E TCGA-B5-A11R TCGA-B5-A11W TCGA-BS-A0TC 
       32.55        28.64         8.71        33.50        19.50        85.55 
TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A0ZO TCGA-D1-A15X TCGA-D1-A16J TCGA-D1-A17Q 
       85.84        73.25        19.79        29.88        29.92         1.78 

$`DNER WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       46.95        37.02        83.51        32.78         3.22       105.37 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       38.37        28.27        20.81        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.59        24.62        29.06        11.97        42.35        15.95 
TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A059 
        1.18        83.67        21.99         5.95        23.31         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       28.54        37.78        40.11        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       40.67        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        17.85        11.01       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11X TCGA-B5-A11Y 
       32.09        27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE 
       10.16        24.99        46.95        23.47        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 
       67.20        88.34        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 
       62.79        63.58        49.55        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z 
        1.74         4.44        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-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       11.51        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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  DNER MUTATED DNER WILD-TYPE 
          1.78           0.56 
  DNER MUTATED DNER WILD-TYPE 
         86.07         185.79 
  DNER MUTATED DNER WILD-TYPE 
        29.900         28.865 
[1] "1.8 - 86.1 (29.9)"  "0.6 - 185.8 (28.9)"
[1] "hr=" "1.9"
D21V2, continuous
                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
D21V3, 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"
D21V4, binary
                cls
clus               0   1
  DNER MUTATED     8  10
  DNER WILD-TYPE  78 152
[1] "tbl2"
                cls
clus             [,1] [,2]
  DNER MUTATED      8   10
  DNER WILD-TYPE   78  152
     clus
vv    DNER MUTATED DNER WILD-TYPE
  NO             8             78
  YES           10            152
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  DNER MUTATED    12   1   0   0
  DNER WILD-TYPE 159  10   7  18
D21V5, multiclass
    clus
vv   DNER MUTATED DNER WILD-TYPE
  R0           12            159
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNER MUTATED                                  0     3
  DNER WILD-TYPE                                3    10
                vv
clus             BLACK OR AFRICAN AMERICAN
  DNER MUTATED                           2
  DNER WILD-TYPE                        23
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DNER MUTATED                                           1    11
  DNER WILD-TYPE                                         6   182
D21V6, multiclass
                                           clus
vv                                          DNER MUTATED DNER WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                3             10
  BLACK OR AFRICAN AMERICAN                            2             23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                               11            182
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                cls
clus               0   1
  DNER MUTATED     1  10
  DNER WILD-TYPE   3 157
[1] "tbl2"
                cls
clus             [,1] [,2]
  DNER MUTATED      1   10
  DNER WILD-TYPE    3  157
                        clus
vv                       DNER MUTATED DNER WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           10            157
[1] 2 2
[1] FALSE

Clustering(22) Variable = EP300 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2               0   1
  EP300 MUTATED    21   0
  EP300 WILD-TYPE 203  24
  EP300 MUTATED EP300 WILD-TYPE 
             21             227 
  EP300 MUTATED EP300 WILD-TYPE 
              0              24 
$`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        46.45        40.11        32.55 
TCGA-B5-A11E TCGA-B5-A11G TCGA-BG-A0LX TCGA-BG-A0MG TCGA-BG-A0MU TCGA-BG-A0RY 
        8.71       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        23.47        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        65.88        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        40.67        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N 
      185.79        88.34        75.72        54.44        44.78        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MI 
        7.92        38.37        36.49        28.27        41.52        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0VT TCGA-BG-A0VV 
       43.04        39.32        30.81        21.17        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        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        67.20        88.34 
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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A161 
       21.99        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-A16Y 
       31.07        33.63        10.65         0.69        18.67        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-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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  EP300 MUTATED EP300 WILD-TYPE 
           0.56            0.66 
  EP300 MUTATED EP300 WILD-TYPE 
         113.36          185.79 
  EP300 MUTATED EP300 WILD-TYPE 
          27.12           29.33 
[1] "0.6 - 113.4 (27.1)" "0.7 - 185.8 (29.3)"
[1] "hr="     "7.5e+07"
D22V2, continuous
                 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
D22V3, 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"
D22V4, binary
                 cls
clus                0   1
  EP300 MUTATED     6  15
  EP300 WILD-TYPE  80 147
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      6   15
  EP300 WILD-TYPE   80  147
     clus
vv    EP300 MUTATED EP300 WILD-TYPE
  NO              6              80
  YES            15             147
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EP300 MUTATED    16   1   0   1
  EP300 WILD-TYPE 155  10   7  17
D22V5, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  R0            16             155
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EP300 MUTATED                                  0     2
  EP300 WILD-TYPE                                3    11
                 vv
clus              BLACK OR AFRICAN AMERICAN
  EP300 MUTATED                           2
  EP300 WILD-TYPE                        23
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EP300 MUTATED                                           1    15
  EP300 WILD-TYPE                                         6   178
D22V6, multiclass
                                           clus
vv                                          EP300 MUTATED EP300 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 2              11
  BLACK OR AFRICAN AMERICAN                             2              23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                15             178
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                 cls
clus                0   1
  EP300 MUTATED     2  14
  EP300 WILD-TYPE   2 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      2   14
  EP300 WILD-TYPE    2  153
                        clus
vv                       EP300 MUTATED EP300 WILD-TYPE
  HISPANIC OR LATINO                 2               2
  NOT HISPANIC OR LATINO            14             153
[1] 2 2
[1] FALSE

Clustering(23) Variable = MAX MUTATION ANALYSIS
D23V1, survival
               sevent
clus2             0   1
  MAX MUTATED    10   1
  MAX WILD-TYPE 214  23
  MAX MUTATED MAX WILD-TYPE 
           11           237 
  MAX MUTATED MAX WILD-TYPE 
            1            23 
$`MAX MUTATED`
TCGA-A5-A0GI TCGA-AP-A059 TCGA-AX-A063 TCGA-AX-A0J0 TCGA-B5-A0K2 TCGA-B5-A11E 
       57.53         8.22        66.58        40.11        25.91         8.71 
TCGA-B5-A11O TCGA-BS-A0T9 TCGA-BS-A0UV TCGA-D1-A167 TCGA-D1-A17L 
       40.50        46.95        73.25        15.72        26.37 

$`MAX WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37        74.10        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       46.45        35.34        45.99        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       46.75        43.13        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       30.51        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       11.01       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       44.78        43.96        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        67.20        88.34 
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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-A168 
        1.91         3.68        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-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-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       28.08        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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  MAX MUTATED MAX WILD-TYPE 
         8.22          0.56 
  MAX MUTATED MAX WILD-TYPE 
        73.25        185.79 
  MAX MUTATED MAX WILD-TYPE 
        40.11         29.06 
[1] "8.2 - 73.2 (40.1)"  "0.6 - 185.8 (29.1)"
[1] "hr=" "1.2"
D23V2, continuous
               vv
clus            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MAX MUTATED                                        11
  MAX WILD-TYPE                                     189
               vv
clus            MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  MAX MUTATED                               0                                 0
  MAX WILD-TYPE                             4                                44
D23V3, multiclass
                                         clus
vv                                        MAX MUTATED MAX 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"
D23V4, binary
               cls
clus              0   1
  MAX MUTATED     3   8
  MAX WILD-TYPE  83 154
[1] "tbl2"
               cls
clus            [,1] [,2]
  MAX MUTATED      3    8
  MAX WILD-TYPE   83  154
     clus
vv    MAX MUTATED MAX WILD-TYPE
  NO            3            83
  YES           8           154
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MAX MUTATED     7   0   1   0
  MAX WILD-TYPE 164  11   6  18
D23V5, multiclass
    clus
vv   MAX MUTATED MAX WILD-TYPE
  R0           7           164
  R1           0            11
  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"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAX MUTATED                                  0     0
  MAX WILD-TYPE                                3    13
               vv
clus            BLACK OR AFRICAN AMERICAN
  MAX MUTATED                           0
  MAX WILD-TYPE                        25
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAX MUTATED                                           2     9
  MAX WILD-TYPE                                         5   184
D23V6, multiclass
                                           clus
vv                                          MAX MUTATED MAX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                    0             3
  ASIAN                                               0            13
  BLACK OR AFRICAN AMERICAN                           0            25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           2             5
  WHITE                                               9           184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
               cls
clus              0   1
  MAX MUTATED     0   8
  MAX WILD-TYPE   4 159
[1] "tbl2"
               cls
clus            [,1] [,2]
  MAX MUTATED      0    8
  MAX WILD-TYPE    4  159
                        clus
vv                       MAX MUTATED MAX WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           8           159
[1] 2 2
[1] FALSE

Clustering(24) Variable = SGK1 MUTATION ANALYSIS
D24V1, survival
                sevent
clus2              0   1
  SGK1 MUTATED    14   1
  SGK1 WILD-TYPE 210  23
  SGK1 MUTATED SGK1 WILD-TYPE 
            15            233 
  SGK1 MUTATED SGK1 WILD-TYPE 
             1             23 
$`SGK1 MUTATED`
TCGA-A5-A0GV TCGA-A5-A0R8 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LI TCGA-AP-A0LL 
       20.81        19.59        86.07         8.22        97.71        83.97 
TCGA-AX-A05S TCGA-AX-A060 TCGA-B5-A0JY TCGA-B5-A11E TCGA-BG-A0M7 TCGA-BG-A0RY 
       13.58        35.34        32.55         8.71        38.37        15.42 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A16X 
        4.44        21.99         3.65 

$`SGK1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       46.55        38.37        28.27        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        24.62        29.06        11.97        42.35        15.95 
TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A 
        1.18        83.67        21.99         5.95        23.31        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        45.53        36.89         7.86        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       49.22        25.08        41.95        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       72.03        46.45        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        35.01        28.54        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       65.88        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       80.38        56.91        46.75        43.13        40.67        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        17.85        11.01       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VV 
       39.32        30.81        21.17        20.28        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        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 
       67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  SGK1 MUTATED SGK1 WILD-TYPE 
          3.65           0.56 
  SGK1 MUTATED SGK1 WILD-TYPE 
         97.71         185.79 
  SGK1 MUTATED SGK1 WILD-TYPE 
         20.81          29.69 
[1] "3.6 - 97.7 (20.8)"  "0.6 - 185.8 (29.7)"
[1] "hr=" "1.2"
D24V2, continuous
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SGK1 MUTATED                                        14
  SGK1 WILD-TYPE                                     186
                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
D24V3, multiclass
                                         clus
vv                                        SGK1 MUTATED SGK1 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"
D24V4, binary
                cls
clus               0   1
  SGK1 MUTATED     8   7
  SGK1 WILD-TYPE  78 155
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK1 MUTATED      8    7
  SGK1 WILD-TYPE   78  155
     clus
vv    SGK1 MUTATED SGK1 WILD-TYPE
  NO             8             78
  YES            7            155
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SGK1 MUTATED     9   1   2   1
  SGK1 WILD-TYPE 162  10   5  17
D24V5, multiclass
    clus
vv   SGK1 MUTATED SGK1 WILD-TYPE
  R0            9            162
  R1            1             10
  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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SGK1 MUTATED                                  1     0
  SGK1 WILD-TYPE                                2    13
                vv
clus             BLACK OR AFRICAN AMERICAN
  SGK1 MUTATED                           1
  SGK1 WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SGK1 MUTATED                                           0    13
  SGK1 WILD-TYPE                                         7   180
D24V6, multiclass
                                           clus
vv                                          SGK1 MUTATED SGK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     1              2
  ASIAN                                                0             13
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              7
  WHITE                                               13            180
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                cls
clus               0   1
  SGK1 MUTATED     0  10
  SGK1 WILD-TYPE   4 157
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK1 MUTATED      0   10
  SGK1 WILD-TYPE    4  157
                        clus
vv                       SGK1 MUTATED SGK1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           10            157
[1] 2 2
[1] FALSE

Clustering(25) Variable = NRAS MUTATION ANALYSIS
D25V1, survival
                sevent
clus2              0   1
  NRAS MUTATED     9   0
  NRAS WILD-TYPE 215  24
  NRAS MUTATED NRAS WILD-TYPE 
             9            239 
  NRAS MUTATED NRAS WILD-TYPE 
             0             24 
$`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        40.67        78.21 
TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A17F 
       82.39        73.25         1.28 

$`NRAS WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        1.18        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       20.91        48.79       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TE 
       10.16        24.99        46.95        23.47        85.55         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 
       67.20        88.34        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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-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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  NRAS MUTATED NRAS WILD-TYPE 
          1.28           0.56 
  NRAS MUTATED NRAS WILD-TYPE 
        125.42         185.79 
  NRAS MUTATED NRAS WILD-TYPE 
         73.25          28.64 
[1] "1.3 - 125.4 (73.2)" "0.6 - 185.8 (28.6)"
[1] "hr="     "2.7e+07"
D25V2, continuous
                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
D25V3, 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"
D25V4, binary
                cls
clus               0   1
  NRAS MUTATED     2   7
  NRAS WILD-TYPE  84 155
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      2    7
  NRAS WILD-TYPE   84  155
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             2             84
  YES            7            155
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NRAS MUTATED     8   0   0   0
  NRAS WILD-TYPE 163  11   7  18
D25V5, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  R0            8            163
  R1            0             11
  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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NRAS MUTATED                                  0     2
  NRAS WILD-TYPE                                3    11
                vv
clus             BLACK OR AFRICAN AMERICAN
  NRAS MUTATED                           1
  NRAS WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NRAS MUTATED                                           1     4
  NRAS WILD-TYPE                                         6   189
D25V6, multiclass
                                           clus
vv                                          NRAS MUTATED NRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                2             11
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                                4            189
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                cls
clus               0   1
  NRAS MUTATED     1   6
  NRAS WILD-TYPE   3 161
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      1    6
  NRAS WILD-TYPE    3  161
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            6            161
[1] 2 2
[1] FALSE

Clustering(26) Variable = KLHL8 MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2               0   1
  KLHL8 MUTATED    12   0
  KLHL8 WILD-TYPE 212  24
  KLHL8 MUTATED KLHL8 WILD-TYPE 
             12             236 
  KLHL8 MUTATED KLHL8 WILD-TYPE 
              0              24 
$`KLHL8 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY 
       83.67         8.22        46.45        40.11        65.88        32.55 
TCGA-B5-A0K9 TCGA-B5-A11Q TCGA-BG-A0VX TCGA-BG-A18B TCGA-BS-A0UV TCGA-D1-A17Q 
       11.01        32.09        34.29        15.45        73.25         1.78 

$`KLHL8 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 
       60.66        35.01        28.54        37.78        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        40.67        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A11E 
       23.01        17.88        13.74        17.10        17.85         8.71 
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-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       43.96        40.50        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VZ 
       20.28        15.42        24.39        26.66        16.34        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       14.01        15.45        23.70        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  KLHL8 MUTATED KLHL8 WILD-TYPE 
           1.78            0.56 
  KLHL8 MUTATED KLHL8 WILD-TYPE 
          83.67          185.79 
  KLHL8 MUTATED KLHL8 WILD-TYPE 
         33.420          28.655 
[1] "1.8 - 83.7 (33.4)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.6e+07"
D26V2, continuous
                 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
D26V3, 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"
D26V4, binary
                 cls
clus                0   1
  KLHL8 MUTATED     4   8
  KLHL8 WILD-TYPE  82 154
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL8 MUTATED      4    8
  KLHL8 WILD-TYPE   82  154
     clus
vv    KLHL8 MUTATED KLHL8 WILD-TYPE
  NO              4              82
  YES             8             154
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KLHL8 MUTATED     6   1   0   2
  KLHL8 WILD-TYPE 165  10   7  16
D26V5, multiclass
    clus
vv   KLHL8 MUTATED KLHL8 WILD-TYPE
  R0             6             165
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLHL8 MUTATED                                  0     0
  KLHL8 WILD-TYPE                                3    13
                 vv
clus              BLACK OR AFRICAN AMERICAN
  KLHL8 MUTATED                           0
  KLHL8 WILD-TYPE                        25
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KLHL8 MUTATED                                           1    10
  KLHL8 WILD-TYPE                                         6   183
D26V6, multiclass
                                           clus
vv                                          KLHL8 MUTATED KLHL8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 0              13
  BLACK OR AFRICAN AMERICAN                             0              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                10             183
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                 cls
clus                0   1
  KLHL8 MUTATED     1   7
  KLHL8 WILD-TYPE   3 160
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL8 MUTATED      1    7
  KLHL8 WILD-TYPE    3  160
                        clus
vv                       KLHL8 MUTATED KLHL8 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             7             160
[1] 2 2
[1] FALSE

Clustering(27) Variable = MORC4 MUTATION ANALYSIS
D27V1, survival
                 sevent
clus2               0   1
  MORC4 MUTATED    20   0
  MORC4 WILD-TYPE 204  24
  MORC4 MUTATED MORC4 WILD-TYPE 
             20             228 
  MORC4 MUTATED MORC4 WILD-TYPE 
              0              24 
$`MORC4 MUTATED`
TCGA-A5-A0GN TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0L9 TCGA-AP-A0LG TCGA-AP-A0LM 
       60.53        86.07         8.22       125.42        63.16        27.12 
TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11Y 
       46.45        40.11        65.88        32.55         8.71        18.41 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BS-A0UF TCGA-BS-A0V7 TCGA-D1-A163 TCGA-D1-A16Q 
       34.29        28.54        85.84        63.58        32.58        10.65 
TCGA-D1-A16X TCGA-D1-A177 
        3.65        18.02 

$`MORC4 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP 
      105.37        74.10        57.53        65.75        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LH TCGA-AP-A0LI 
       48.79       117.99       110.37         3.39        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        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        41.95        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       68.35        72.03        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z 
       27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       16.34        52.83        56.58        14.83        12.56        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        67.20        88.34 
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        62.79 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
        3.68        29.33         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-A16R TCGA-D1-A16S TCGA-D1-A16Y 
       29.92        31.07        33.63         0.69        18.67        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-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  MORC4 MUTATED MORC4 WILD-TYPE 
           3.65            0.56 
  MORC4 MUTATED MORC4 WILD-TYPE 
         125.42          185.79 
  MORC4 MUTATED MORC4 WILD-TYPE 
         33.435          28.655 
[1] "3.6 - 125.4 (33.4)" "0.6 - 185.8 (28.7)"
[1] "hr="     "7.7e+07"
D27V2, continuous
                 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
D27V3, 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"
D27V4, binary
                 cls
clus                0   1
  MORC4 MUTATED     7  13
  MORC4 WILD-TYPE  79 149
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC4 MUTATED      7   13
  MORC4 WILD-TYPE   79  149
     clus
vv    MORC4 MUTATED MORC4 WILD-TYPE
  NO              7              79
  YES            13             149
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MORC4 MUTATED    15   1   0   1
  MORC4 WILD-TYPE 156  10   7  17
D27V5, multiclass
    clus
vv   MORC4 MUTATED MORC4 WILD-TYPE
  R0            15             156
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MORC4 MUTATED                                  0     1
  MORC4 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  MORC4 MUTATED                           1
  MORC4 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MORC4 MUTATED                                           1    16
  MORC4 WILD-TYPE                                         6   177
D27V6, multiclass
                                           clus
vv                                          MORC4 MUTATED MORC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                16             177
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                 cls
clus                0   1
  MORC4 MUTATED     1  12
  MORC4 WILD-TYPE   3 155
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC4 MUTATED      1   12
  MORC4 WILD-TYPE    3  155
                        clus
vv                       MORC4 MUTATED MORC4 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            12             155
[1] 2 2
[1] FALSE

Clustering(28) Variable = ZNF781 MUTATION ANALYSIS
D28V1, survival
                  sevent
clus2                0   1
  ZNF781 MUTATED    10   0
  ZNF781 WILD-TYPE 214  24
  ZNF781 MUTATED ZNF781 WILD-TYPE 
              10              238 
  ZNF781 MUTATED ZNF781 WILD-TYPE 
               0               24 
$`ZNF781 MUTATED`
TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A11N TCGA-BS-A0UF 
       86.07        27.12        46.45        32.55        43.96        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        37.78        40.11        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         8.71       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        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74         4.44        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-A174 TCGA-D1-A176 
       33.63        10.65         0.69        18.67        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  ZNF781 MUTATED ZNF781 WILD-TYPE 
            1.78             0.56 
  ZNF781 MUTATED ZNF781 WILD-TYPE 
           86.07           185.79 
  ZNF781 MUTATED ZNF781 WILD-TYPE 
          29.835           29.195 
[1] "1.8 - 86.1 (29.8)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "2.6e+07"
D28V2, continuous
                  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
D28V3, 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"
D28V4, binary
                  cls
clus                 0   1
  ZNF781 MUTATED     2   8
  ZNF781 WILD-TYPE  84 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF781 MUTATED      2    8
  ZNF781 WILD-TYPE   84  154
     clus
vv    ZNF781 MUTATED ZNF781 WILD-TYPE
  NO               2               84
  YES              8              154
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF781 MUTATED     6   1   0   1
  ZNF781 WILD-TYPE 165  10   7  17
D28V5, multiclass
    clus
vv   ZNF781 MUTATED ZNF781 WILD-TYPE
  R0              6              165
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF781 MUTATED                                  0     1
  ZNF781 WILD-TYPE                                3    12
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ZNF781 MUTATED                           1
  ZNF781 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF781 MUTATED                                           0     7
  ZNF781 WILD-TYPE                                         7   186
D28V6, multiclass
                                           clus
vv                                          ZNF781 MUTATED ZNF781 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  1               12
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                  7              186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                  cls
clus                 0   1
  ZNF781 MUTATED     1   5
  ZNF781 WILD-TYPE   3 162
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF781 MUTATED      1    5
  ZNF781 WILD-TYPE    3  162
                        clus
vv                       ZNF781 MUTATED ZNF781 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              5              162
[1] 2 2
[1] FALSE

Clustering(29) Variable = MKI67 MUTATION ANALYSIS
D29V1, survival
                 sevent
clus2               0   1
  MKI67 MUTATED    28   1
  MKI67 WILD-TYPE 196  23
  MKI67 MUTATED MKI67 WILD-TYPE 
             29             219 
  MKI67 MUTATED MKI67 WILD-TYPE 
              1              23 
$`MKI67 MUTATED`
TCGA-A5-A0GB TCGA-A5-A0GH TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       32.78        74.10        83.67        23.31        86.07         8.22 
TCGA-AP-A0LG TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A064 
       63.16        27.12        46.45        35.34        66.58        34.98 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-BG-A0M0 
       40.11        65.88        32.55         8.71        43.96        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GE 
       46.95        37.02        83.51        17.85         3.22       105.37 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.59        24.62        29.06        11.97        42.35        15.95 
TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
        1.18        21.99         5.95        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89         7.86        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37         3.39        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A062 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       45.99        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       37.78        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       80.38        56.91        46.75        43.13        40.67        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        17.85        11.01       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        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       24.99        46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 
       88.34        81.57        86.93        72.72        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51         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-A176 
       31.07        33.63        10.65         0.69        18.67        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-A17N TCGA-D1-A17R TCGA-D1-A17S 
       28.01        28.08        26.37         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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  MKI67 MUTATED MKI67 WILD-TYPE 
           1.78            0.56 
  MKI67 MUTATED MKI67 WILD-TYPE 
          86.07          185.79 
  MKI67 MUTATED MKI67 WILD-TYPE 
          35.34           28.54 
[1] "1.8 - 86.1 (35.3)"  "0.6 - 185.8 (28.5)"
[1] "hr=" "3.6"
D29V2, continuous
                 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
D29V3, 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"
D29V4, binary
                 cls
clus                0   1
  MKI67 MUTATED     9  20
  MKI67 WILD-TYPE  77 142
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED      9   20
  MKI67 WILD-TYPE   77  142
     clus
vv    MKI67 MUTATED MKI67 WILD-TYPE
  NO              9              77
  YES            20             142
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MKI67 MUTATED    21   3   0   1
  MKI67 WILD-TYPE 150   8   7  17
D29V5, multiclass
    clus
vv   MKI67 MUTATED MKI67 WILD-TYPE
  R0            21             150
  R1             3               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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MKI67 MUTATED                                  1     3
  MKI67 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN
  MKI67 MUTATED                           1
  MKI67 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MKI67 MUTATED                                           1    22
  MKI67 WILD-TYPE                                         6   171
D29V6, multiclass
                                           clus
vv                                          MKI67 MUTATED MKI67 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      1               2
  ASIAN                                                 3              10
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                22             171
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                 cls
clus                0   1
  MKI67 MUTATED     1  19
  MKI67 WILD-TYPE   3 148
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED      1   19
  MKI67 WILD-TYPE    3  148
                        clus
vv                       MKI67 MUTATED MKI67 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            19             148
[1] 2 2
[1] FALSE

Clustering(30) Variable = ING1 MUTATION ANALYSIS
D30V1, survival
                sevent
clus2              0   1
  ING1 MUTATED    13   0
  ING1 WILD-TYPE 211  24
  ING1 MUTATED ING1 WILD-TYPE 
            13            235 
  ING1 MUTATED ING1 WILD-TYPE 
             0             24 
$`ING1 MUTATED`
TCGA-A5-A0VP TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-B5-A0JY TCGA-B5-A11E 
       42.35        86.07         8.22        27.12        32.55         8.71 
TCGA-B5-A11W TCGA-BG-A0M9 TCGA-BS-A0TC TCGA-D1-A168 TCGA-D1-A17C TCGA-D1-A17D 
       19.50        28.27        85.55        36.10         0.99        30.44 
TCGA-D1-A17Q 
        1.78 

$`ING1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       35.01        28.54        37.78        40.11        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        40.67        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       11.01       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        43.96        40.50        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0MC 
       35.21        34.98         7.92        38.37        36.49        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       23.47        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        67.20        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-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-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        1.58         7.00         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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  ING1 MUTATED ING1 WILD-TYPE 
          0.99           0.56 
  ING1 MUTATED ING1 WILD-TYPE 
         86.07         185.79 
  ING1 MUTATED ING1 WILD-TYPE 
         28.27          29.33 
[1] "1.0 - 86.1 (28.3)"  "0.6 - 185.8 (29.3)"
[1] "hr="     "2.6e+07"
D30V2, continuous
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ING1 MUTATED                                        13
  ING1 WILD-TYPE                                     187
                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
D30V3, multiclass
                                         clus
vv                                        ING1 MUTATED ING1 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"
D30V4, binary
                cls
clus               0   1
  ING1 MUTATED     7   6
  ING1 WILD-TYPE  79 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING1 MUTATED      7    6
  ING1 WILD-TYPE   79  156
     clus
vv    ING1 MUTATED ING1 WILD-TYPE
  NO             7             79
  YES            6            156
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ING1 MUTATED    10   0   0   0
  ING1 WILD-TYPE 161  11   7  18
D30V5, multiclass
    clus
vv   ING1 MUTATED ING1 WILD-TYPE
  R0           10            161
  R1            0             11
  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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ING1 MUTATED                                  0     1
  ING1 WILD-TYPE                                3    12
                vv
clus             BLACK OR AFRICAN AMERICAN
  ING1 MUTATED                           1
  ING1 WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ING1 MUTATED                                           0    11
  ING1 WILD-TYPE                                         7   182
D30V6, multiclass
                                           clus
vv                                          ING1 MUTATED ING1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                1             12
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              7
  WHITE                                               11            182
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                cls
clus               0   1
  ING1 MUTATED     0   8
  ING1 WILD-TYPE   4 159
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING1 MUTATED      0    8
  ING1 WILD-TYPE    4  159
                        clus
vv                       ING1 MUTATED ING1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            159
[1] 2 2
[1] FALSE

Clustering(31) Variable = INTS7 MUTATION ANALYSIS
D31V1, survival
                 sevent
clus2               0   1
  INTS7 MUTATED     8   0
  INTS7 WILD-TYPE 216  24
  INTS7 MUTATED INTS7 WILD-TYPE 
              8             240 
  INTS7 MUTATED INTS7 WILD-TYPE 
              0              24 
$`INTS7 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-BS-A0UF 
       83.67        86.07        46.45        40.11        32.55        85.84 
TCGA-BS-A0UJ TCGA-D1-A167 
       82.39        15.72 

$`INTS7 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        40.67        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  INTS7 MUTATED INTS7 WILD-TYPE 
          15.72            0.56 
  INTS7 MUTATED INTS7 WILD-TYPE 
          86.07          185.79 
  INTS7 MUTATED INTS7 WILD-TYPE 
          64.42           28.59 
[1] "15.7 - 86.1 (64.4)" "0.6 - 185.8 (28.6)"
[1] "hr="     "2.6e+07"
D31V2, continuous
                 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
D31V3, 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"
D31V4, binary
                 cls
clus                0   1
  INTS7 MUTATED     3   5
  INTS7 WILD-TYPE  83 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS7 MUTATED      3    5
  INTS7 WILD-TYPE   83  157
     clus
vv    INTS7 MUTATED INTS7 WILD-TYPE
  NO              3              83
  YES             5             157
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  INTS7 MUTATED     6   1   0   0
  INTS7 WILD-TYPE 165  10   7  18
D31V5, multiclass
    clus
vv   INTS7 MUTATED INTS7 WILD-TYPE
  R0             6             165
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  INTS7 MUTATED                                  0     2
  INTS7 WILD-TYPE                                3    11
                 vv
clus              BLACK OR AFRICAN AMERICAN
  INTS7 MUTATED                           0
  INTS7 WILD-TYPE                        25
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  INTS7 MUTATED                                           0     5
  INTS7 WILD-TYPE                                         7   188
D31V6, multiclass
                                           clus
vv                                          INTS7 MUTATED INTS7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 2              11
  BLACK OR AFRICAN AMERICAN                             0              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                 5             188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                 cls
clus                0   1
  INTS7 MUTATED     1   4
  INTS7 WILD-TYPE   3 163
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS7 MUTATED      1    4
  INTS7 WILD-TYPE    3  163
                        clus
vv                       INTS7 MUTATED INTS7 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             4             163
[1] 2 2
[1] FALSE

Clustering(32) Variable = CCDC6 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2               0   1
  CCDC6 MUTATED     6   0
  CCDC6 WILD-TYPE 218  24
  CCDC6 MUTATED CCDC6 WILD-TYPE 
              6             242 
  CCDC6 MUTATED CCDC6 WILD-TYPE 
              0              24 
$`CCDC6 MUTATED`
TCGA-AP-A059 TCGA-BS-A0UF TCGA-D1-A15V TCGA-D1-A17B TCGA-D1-A17Q TCGA-FI-A2EX 
        8.22        85.84        39.48         7.00         1.78         9.07 

$`CCDC6 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       40.11        65.88        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       17.88        13.74        17.10        17.85        11.01         8.71 
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 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74         4.44        21.99        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-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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2F8 
       59.01        25.02 

  CCDC6 MUTATED CCDC6 WILD-TYPE 
           1.78            0.56 
  CCDC6 MUTATED CCDC6 WILD-TYPE 
          85.84          185.79 
  CCDC6 MUTATED CCDC6 WILD-TYPE 
          8.645          29.510 
[1] "1.8 - 85.8 (8.6)"   "0.6 - 185.8 (29.5)"
[1] "hr="     "9100000"
D32V2, continuous
                 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
D32V3, 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"
D32V4, binary
                 cls
clus                0   1
  CCDC6 MUTATED     2   4
  CCDC6 WILD-TYPE  84 158
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC6 MUTATED      2    4
  CCDC6 WILD-TYPE   84  158
     clus
vv    CCDC6 MUTATED CCDC6 WILD-TYPE
  NO              2              84
  YES             4             158
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CCDC6 MUTATED     6   0   0   0
  CCDC6 WILD-TYPE 165  11   7  18
D32V5, multiclass
    clus
vv   CCDC6 MUTATED CCDC6 WILD-TYPE
  R0             6             165
  R1             0              11
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC6 MUTATED                                  0     1
  CCDC6 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  CCDC6 MUTATED                           0
  CCDC6 WILD-TYPE                        25
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC6 MUTATED                                           0     5
  CCDC6 WILD-TYPE                                         7   188
D32V6, multiclass
                                           clus
vv                                          CCDC6 MUTATED CCDC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             0              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                 5             188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                 cls
clus                0   1
  CCDC6 MUTATED     0   6
  CCDC6 WILD-TYPE   4 161
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC6 MUTATED      0    6
  CCDC6 WILD-TYPE    4  161
                        clus
vv                       CCDC6 MUTATED CCDC6 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             161
[1] 2 2
[1] FALSE

Clustering(33) Variable = EIF2S2 MUTATION ANALYSIS
D33V1, survival
                  sevent
clus2                0   1
  EIF2S2 MUTATED     9   0
  EIF2S2 WILD-TYPE 215  24
  EIF2S2 MUTATED EIF2S2 WILD-TYPE 
               9              239 
  EIF2S2 MUTATED EIF2S2 WILD-TYPE 
               0               24 
$`EIF2S2 MUTATED`
TCGA-AP-A059 TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11N TCGA-BG-A187 
        8.22        46.45        40.11        32.55        43.96        14.73 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-D1-A16Y 
       85.84        82.39        17.49 

$`EIF2S2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       72.03        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        35.01        28.54        37.78        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         8.71       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        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        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-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       67.20        88.34        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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-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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  EIF2S2 MUTATED EIF2S2 WILD-TYPE 
            8.22             0.56 
  EIF2S2 MUTATED EIF2S2 WILD-TYPE 
           85.84           185.79 
  EIF2S2 MUTATED EIF2S2 WILD-TYPE 
           40.11            28.67 
[1] "8.2 - 85.8 (40.1)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.6e+07"
D33V2, continuous
                  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
D33V3, 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"
D33V4, binary
                  cls
clus                 0   1
  EIF2S2 MUTATED     1   8
  EIF2S2 WILD-TYPE  85 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2S2 MUTATED      1    8
  EIF2S2 WILD-TYPE   85  154
     clus
vv    EIF2S2 MUTATED EIF2S2 WILD-TYPE
  NO               1               85
  YES              8              154
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  EIF2S2 MUTATED     5   1   0   1
  EIF2S2 WILD-TYPE 166  10   7  17
D33V5, multiclass
    clus
vv   EIF2S2 MUTATED EIF2S2 WILD-TYPE
  R0              5              166
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EIF2S2 MUTATED                                  0     2
  EIF2S2 WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  EIF2S2 MUTATED                           0
  EIF2S2 WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EIF2S2 MUTATED                                           0     6
  EIF2S2 WILD-TYPE                                         7   187
D33V6, multiclass
                                           clus
vv                                          EIF2S2 MUTATED EIF2S2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                  6              187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                  cls
clus                 0   1
  EIF2S2 MUTATED     1   6
  EIF2S2 WILD-TYPE   3 161
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2S2 MUTATED      1    6
  EIF2S2 WILD-TYPE    3  161
                        clus
vv                       EIF2S2 MUTATED EIF2S2 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              6              161
[1] 2 2
[1] FALSE

Clustering(34) Variable = RBBP6 MUTATION ANALYSIS
D34V1, survival
                 sevent
clus2               0   1
  RBBP6 MUTATED    21   1
  RBBP6 WILD-TYPE 203  23
  RBBP6 MUTATED RBBP6 WILD-TYPE 
             22             226 
  RBBP6 MUTATED RBBP6 WILD-TYPE 
              1              23 
$`RBBP6 MUTATED`
TCGA-A5-A0GM TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       60.53        42.35        83.67        23.31        86.07         8.22 
TCGA-AP-A0LM TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-BS-A0TJ 
       27.12        65.88        32.55         8.71        43.96        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37        74.10        57.53        65.75        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        15.95 
TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
        1.18        21.99         5.95        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89         7.86        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       40.11        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       80.38        56.91        46.75        43.13        40.67        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        17.85        11.01       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        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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 
       67.20        88.34        81.57        86.93        72.72        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       29.33        32.58        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-A17A TCGA-D1-A17B TCGA-D1-A17D TCGA-D1-A17F 
       19.53        30.15         1.58         7.00        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  RBBP6 MUTATED RBBP6 WILD-TYPE 
           0.66            0.56 
  RBBP6 MUTATED RBBP6 WILD-TYPE 
          86.07          185.79 
  RBBP6 MUTATED RBBP6 WILD-TYPE 
         29.835          29.195 
[1] "0.7 - 86.1 (29.8)"  "0.6 - 185.8 (29.2)"
[1] "hr=" "2.4"
D34V2, continuous
                 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
D34V3, 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"
D34V4, binary
                 cls
clus                0   1
  RBBP6 MUTATED     8  14
  RBBP6 WILD-TYPE  78 148
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP6 MUTATED      8   14
  RBBP6 WILD-TYPE   78  148
     clus
vv    RBBP6 MUTATED RBBP6 WILD-TYPE
  NO              8              78
  YES            14             148
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RBBP6 MUTATED    18   1   0   0
  RBBP6 WILD-TYPE 153  10   7  18
D34V5, multiclass
    clus
vv   RBBP6 MUTATED RBBP6 WILD-TYPE
  R0            18             153
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBBP6 MUTATED                                  0     3
  RBBP6 WILD-TYPE                                3    10
                 vv
clus              BLACK OR AFRICAN AMERICAN
  RBBP6 MUTATED                           1
  RBBP6 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RBBP6 MUTATED                                           1    17
  RBBP6 WILD-TYPE                                         6   176
D34V6, multiclass
                                           clus
vv                                          RBBP6 MUTATED RBBP6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 3              10
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                17             176
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                 cls
clus                0   1
  RBBP6 MUTATED     0  16
  RBBP6 WILD-TYPE   4 151
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP6 MUTATED      0   16
  RBBP6 WILD-TYPE    4  151
                        clus
vv                       RBBP6 MUTATED RBBP6 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            16             151
[1] 2 2
[1] FALSE

Clustering(35) Variable = SOS1 MUTATION ANALYSIS
D35V1, survival
                sevent
clus2              0   1
  SOS1 MUTATED    12   0
  SOS1 WILD-TYPE 212  24
  SOS1 MUTATED SOS1 WILD-TYPE 
            12            236 
  SOS1 MUTATED SOS1 WILD-TYPE 
             0             24 
$`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         8.22        31.73        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        32.55        15.42        30.15 

$`SOS1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        29.06        11.97        42.35        15.95 
TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A 
        1.18        83.67        21.99         5.95        23.31        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        45.53        36.89         7.86        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       65.88        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       80.38        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         8.71       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VT 
       43.04        39.32        30.81        21.17        20.28        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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-A177 TCGA-D1-A17A TCGA-D1-A17B 
        3.65        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-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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  SOS1 MUTATED SOS1 WILD-TYPE 
          8.22           0.56 
  SOS1 MUTATED SOS1 WILD-TYPE 
         86.07         185.79 
  SOS1 MUTATED SOS1 WILD-TYPE 
        32.140         28.655 
[1] "8.2 - 86.1 (32.1)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.6e+07"
D35V2, continuous
                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
D35V3, 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"
D35V4, binary
                cls
clus               0   1
  SOS1 MUTATED     5   7
  SOS1 WILD-TYPE  81 155
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS1 MUTATED      5    7
  SOS1 WILD-TYPE   81  155
     clus
vv    SOS1 MUTATED SOS1 WILD-TYPE
  NO             5             81
  YES            7            155
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SOS1 MUTATED    10   0   0   0
  SOS1 WILD-TYPE 161  11   7  18
D35V5, multiclass
    clus
vv   SOS1 MUTATED SOS1 WILD-TYPE
  R0           10            161
  R1            0             11
  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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SOS1 MUTATED                                  0     1
  SOS1 WILD-TYPE                                3    12
                vv
clus             BLACK OR AFRICAN AMERICAN
  SOS1 MUTATED                           1
  SOS1 WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SOS1 MUTATED                                           0    10
  SOS1 WILD-TYPE                                         7   183
D35V6, multiclass
                                           clus
vv                                          SOS1 MUTATED SOS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                1             12
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              7
  WHITE                                               10            183
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                cls
clus               0   1
  SOS1 MUTATED     0   6
  SOS1 WILD-TYPE   4 161
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS1 MUTATED      0    6
  SOS1 WILD-TYPE    4  161
                        clus
vv                       SOS1 MUTATED SOS1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            161
[1] 2 2
[1] FALSE

Clustering(36) Variable = NAT1 MUTATION ANALYSIS
D36V1, survival
                sevent
clus2              0   1
  NAT1 MUTATED     6   1
  NAT1 WILD-TYPE 218  23
  NAT1 MUTATED NAT1 WILD-TYPE 
             7            241 
  NAT1 MUTATED NAT1 WILD-TYPE 
             1             23 
$`NAT1 MUTATED`
TCGA-A5-A0GB TCGA-AP-A054 TCGA-B5-A0JZ TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 
       32.78        23.31        28.64        85.84        73.25        21.99 
TCGA-D1-A17Q 
        1.78 

$`NAT1 WILD-TYPE`
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         3.22       105.37 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A056 
       15.95         1.18        83.67        21.99         5.95        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        35.01        28.54        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       65.88        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       80.38        56.91        46.75        43.13        40.67        32.55 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         8.71       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  NAT1 MUTATED NAT1 WILD-TYPE 
          1.78           0.56 
  NAT1 MUTATED NAT1 WILD-TYPE 
         85.84         185.79 
  NAT1 MUTATED NAT1 WILD-TYPE 
         28.64          29.33 
[1] "1.8 - 85.8 (28.6)"  "0.6 - 185.8 (29.3)"
[1] "hr=" "1.5"
D36V2, continuous
                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
D36V3, 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"
D36V4, binary
                cls
clus               0   1
  NAT1 MUTATED     2   5
  NAT1 WILD-TYPE  84 157
[1] "tbl2"
                cls
clus             [,1] [,2]
  NAT1 MUTATED      2    5
  NAT1 WILD-TYPE   84  157
     clus
vv    NAT1 MUTATED NAT1 WILD-TYPE
  NO             2             84
  YES            5            157
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  NAT1 MUTATED     5   1   0   0
  NAT1 WILD-TYPE 166  10   7  18
D36V5, multiclass
    clus
vv   NAT1 MUTATED NAT1 WILD-TYPE
  R0            5            166
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NAT1 MUTATED                                  0     1
  NAT1 WILD-TYPE                                3    12
                vv
clus             BLACK OR AFRICAN AMERICAN
  NAT1 MUTATED                           0
  NAT1 WILD-TYPE                        25
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NAT1 MUTATED                                           1     5
  NAT1 WILD-TYPE                                         6   188
D36V6, multiclass
                                           clus
vv                                          NAT1 MUTATED NAT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                1             12
  BLACK OR AFRICAN AMERICAN                            0             25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                                5            188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                cls
clus               0   1
  NAT1 MUTATED     0   5
  NAT1 WILD-TYPE   4 162
[1] "tbl2"
                cls
clus             [,1] [,2]
  NAT1 MUTATED      0    5
  NAT1 WILD-TYPE    4  162
                        clus
vv                       NAT1 MUTATED NAT1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            162
[1] 2 2
[1] FALSE

Clustering(37) Variable = ADNP MUTATION ANALYSIS
D37V1, survival
                sevent
clus2              0   1
  ADNP MUTATED    13   1
  ADNP WILD-TYPE 211  23
  ADNP MUTATED ADNP WILD-TYPE 
            14            234 
  ADNP MUTATED ADNP WILD-TYPE 
             1             23 
$`ADNP MUTATED`
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LJ TCGA-AP-A0LM 
       17.85        32.78        83.67         8.22        31.73        27.12 
TCGA-AX-A05Z TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11Y TCGA-BS-A0TC 
       46.45        65.88        32.55         8.71        18.41        85.55 
TCGA-D1-A103 TCGA-D1-A167 
       21.99        15.72 

$`ADNP WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       46.95        37.02        83.51         3.22       105.37        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.59        24.62        29.06        11.97        42.35        15.95 
TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A 
        1.18        21.99         5.95        23.31        86.07        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        45.53        36.89         7.86        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       97.71        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        41.95        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       68.35        72.03        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       40.11        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       80.38        56.91        46.75        43.13        40.67        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        17.85        11.01       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE 
       10.16        24.99        46.95        23.47        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 
       67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74         4.44        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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  ADNP MUTATED ADNP WILD-TYPE 
          8.22           0.56 
  ADNP MUTATED ADNP WILD-TYPE 
         85.55         185.79 
  ADNP MUTATED ADNP WILD-TYPE 
        29.425         29.195 
[1] "8.2 - 85.5 (29.4)"  "0.6 - 185.8 (29.2)"
[1] "hr=" "1.3"
D37V2, continuous
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ADNP MUTATED                                        14
  ADNP WILD-TYPE                                     186
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  ADNP MUTATED                               0
  ADNP WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  ADNP MUTATED                                   0
  ADNP WILD-TYPE                                44
D37V3, multiclass
                                         clus
vv                                        ADNP MUTATED ADNP 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"
D37V4, binary
                cls
clus               0   1
  ADNP MUTATED     5   9
  ADNP WILD-TYPE  81 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADNP MUTATED      5    9
  ADNP WILD-TYPE   81  153
     clus
vv    ADNP MUTATED ADNP WILD-TYPE
  NO             5             81
  YES            9            153
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ADNP MUTATED    10   1   0   0
  ADNP WILD-TYPE 161  10   7  18
D37V5, multiclass
    clus
vv   ADNP MUTATED ADNP WILD-TYPE
  R0           10            161
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADNP MUTATED                                  0     1
  ADNP WILD-TYPE                                3    12
                vv
clus             BLACK OR AFRICAN AMERICAN
  ADNP MUTATED                           1
  ADNP WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ADNP MUTATED                                           0    11
  ADNP WILD-TYPE                                         7   182
D37V6, multiclass
                                           clus
vv                                          ADNP MUTATED ADNP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                1             12
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              7
  WHITE                                               11            182
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                cls
clus               0   1
  ADNP MUTATED     1   6
  ADNP WILD-TYPE   3 161
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADNP MUTATED      1    6
  ADNP WILD-TYPE    3  161
                        clus
vv                       ADNP MUTATED ADNP WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            6            161
[1] 2 2
[1] FALSE

Clustering(38) Variable = VPS11 MUTATION ANALYSIS
D38V1, survival
                 sevent
clus2               0   1
  VPS11 MUTATED    11   1
  VPS11 WILD-TYPE 213  23
  VPS11 MUTATED VPS11 WILD-TYPE 
             12             236 
  VPS11 MUTATED VPS11 WILD-TYPE 
              1              23 
$`VPS11 MUTATED`
TCGA-A5-A0GA TCGA-A5-A0VP TCGA-AP-A051 TCGA-AX-A0J1 TCGA-B5-A11E TCGA-B5-A11Y 
       17.85        42.35        83.67        65.88         8.71        18.41 
TCGA-BG-A0MQ TCGA-BG-A0YV TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A15X TCGA-D1-A17Q 
       39.32        12.56        85.84        73.25        29.88         1.78 

$`VPS11 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       46.95        37.02        83.51        32.78         3.22       105.37 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        15.95 
TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        1.18        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        40.11        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       46.75        43.13        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z 
       27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MS 
       28.27        41.52        48.56        23.47        43.04        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        28.54        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        67.20        88.34 
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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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-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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  VPS11 MUTATED VPS11 WILD-TYPE 
           1.78            0.56 
  VPS11 MUTATED VPS11 WILD-TYPE 
          85.84          185.79 
  VPS11 MUTATED VPS11 WILD-TYPE 
         34.600          28.865 
[1] "1.8 - 85.8 (34.6)"  "0.6 - 185.8 (28.9)"
[1] "hr=" "1.3"
D38V2, continuous
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  VPS11 MUTATED                                        10
  VPS11 WILD-TYPE                                     190
                 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
D38V3, multiclass
                                         clus
vv                                        VPS11 MUTATED VPS11 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"
D38V4, binary
                 cls
clus                0   1
  VPS11 MUTATED     3   9
  VPS11 WILD-TYPE  83 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS11 MUTATED      3    9
  VPS11 WILD-TYPE   83  153
     clus
vv    VPS11 MUTATED VPS11 WILD-TYPE
  NO              3              83
  YES             9             153
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  VPS11 MUTATED    10   0   0   0
  VPS11 WILD-TYPE 161  11   7  18
D38V5, multiclass
    clus
vv   VPS11 MUTATED VPS11 WILD-TYPE
  R0            10             161
  R1             0              11
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VPS11 MUTATED                                  0     1
  VPS11 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  VPS11 MUTATED                           0
  VPS11 WILD-TYPE                        25
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  VPS11 MUTATED                                           1    10
  VPS11 WILD-TYPE                                         6   183
D38V6, multiclass
                                           clus
vv                                          VPS11 MUTATED VPS11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             0              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                10             183
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                 cls
clus                0   1
  VPS11 MUTATED     0   9
  VPS11 WILD-TYPE   4 158
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS11 MUTATED      0    9
  VPS11 WILD-TYPE    4  158
                        clus
vv                       VPS11 MUTATED VPS11 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             158
[1] 2 2
[1] FALSE

Clustering(39) Variable = L1TD1 MUTATION ANALYSIS
D39V1, survival
                 sevent
clus2               0   1
  L1TD1 MUTATED    16   0
  L1TD1 WILD-TYPE 208  24
  L1TD1 MUTATED L1TD1 WILD-TYPE 
             16             232 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
              0              24 
$`L1TD1 MUTATED`
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY 
       86.07         8.22        27.12        46.45        40.11        32.55 
TCGA-B5-A11E TCGA-B5-A11N TCGA-BG-A0VX TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UV 
        8.71        43.96        34.29        85.55        85.84        73.25 
TCGA-D1-A0ZO TCGA-D1-A103 TCGA-D1-A167 TCGA-D1-A17Q 
       19.79        21.99        15.72         1.78 

$`L1TD1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        65.88        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        40.67        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
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 
       40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VZ 
       20.28        15.42        24.39        26.66        16.34        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79        63.58        49.55        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-A102 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  L1TD1 MUTATED L1TD1 WILD-TYPE 
           1.78            0.56 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
          86.07          185.79 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
         33.420          28.865 
[1] "1.8 - 86.1 (33.4)"  "0.6 - 185.8 (28.9)"
[1] "hr="     "2.7e+07"
D39V2, continuous
                 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
D39V3, 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"
D39V4, binary
                 cls
clus                0   1
  L1TD1 MUTATED     4  12
  L1TD1 WILD-TYPE  82 150
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1TD1 MUTATED      4   12
  L1TD1 WILD-TYPE   82  150
     clus
vv    L1TD1 MUTATED L1TD1 WILD-TYPE
  NO              4              82
  YES            12             150
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  L1TD1 MUTATED    11   1   0   1
  L1TD1 WILD-TYPE 160  10   7  17
D39V5, multiclass
    clus
vv   L1TD1 MUTATED L1TD1 WILD-TYPE
  R0            11             160
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  L1TD1 MUTATED                                  0     2
  L1TD1 WILD-TYPE                                3    11
                 vv
clus              BLACK OR AFRICAN AMERICAN
  L1TD1 MUTATED                           1
  L1TD1 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  L1TD1 MUTATED                                           1    11
  L1TD1 WILD-TYPE                                         6   182
D39V6, multiclass
                                           clus
vv                                          L1TD1 MUTATED L1TD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 2              11
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                11             182
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                 cls
clus                0   1
  L1TD1 MUTATED     1  10
  L1TD1 WILD-TYPE   3 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1TD1 MUTATED      1   10
  L1TD1 WILD-TYPE    3  157
                        clus
vv                       L1TD1 MUTATED L1TD1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            10             157
[1] 2 2
[1] FALSE

Clustering(40) Variable = MARK3 MUTATION ANALYSIS
D40V1, survival
                 sevent
clus2               0   1
  MARK3 MUTATED    10   1
  MARK3 WILD-TYPE 214  23
  MARK3 MUTATED MARK3 WILD-TYPE 
             11             237 
  MARK3 MUTATED MARK3 WILD-TYPE 
              1              23 
$`MARK3 MUTATED`
TCGA-A5-A0GW TCGA-AP-A051 TCGA-AP-A056 TCGA-AX-A05S TCGA-AX-A05Z TCGA-AX-A0J0 
       23.21        83.67        86.07        13.58        46.45        40.11 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11H TCGA-BS-A0UV TCGA-D1-A17Q 
       32.55         8.71        88.34        73.25         1.78 

$`MARK3 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 
       46.55        38.37        28.27        20.81        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A059 
       15.95         1.18        21.99         5.95        23.31         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       28.54        37.78        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       17.88        13.74        17.10        17.85        11.01       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  MARK3 MUTATED MARK3 WILD-TYPE 
           1.78            0.56 
  MARK3 MUTATED MARK3 WILD-TYPE 
          88.34          185.79 
  MARK3 MUTATED MARK3 WILD-TYPE 
          40.11           28.67 
[1] "1.8 - 88.3 (40.1)"  "0.6 - 185.8 (28.7)"
[1] "hr=" "1.3"
D40V2, continuous
                 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
D40V3, 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"
D40V4, binary
                 cls
clus                0   1
  MARK3 MUTATED     4   7
  MARK3 WILD-TYPE  82 155
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MARK3 MUTATED      4    7
  MARK3 WILD-TYPE   82  155
     clus
vv    MARK3 MUTATED MARK3 WILD-TYPE
  NO              4              82
  YES             7             155
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MARK3 MUTATED     6   1   1   0
  MARK3 WILD-TYPE 165  10   6  18
D40V5, multiclass
    clus
vv   MARK3 MUTATED MARK3 WILD-TYPE
  R0             6             165
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MARK3 MUTATED                                  0     1
  MARK3 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  MARK3 MUTATED                           0
  MARK3 WILD-TYPE                        25
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MARK3 MUTATED                                           1     8
  MARK3 WILD-TYPE                                         6   185
D40V6, multiclass
                                           clus
vv                                          MARK3 MUTATED MARK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             0              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                 8             185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                 cls
clus                0   1
  MARK3 MUTATED     1   5
  MARK3 WILD-TYPE   3 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MARK3 MUTATED      1    5
  MARK3 WILD-TYPE    3  162
                        clus
vv                       MARK3 MUTATED MARK3 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             5             162
[1] 2 2
[1] FALSE

Clustering(41) Variable = CTNND1 MUTATION ANALYSIS
D41V1, survival
                  sevent
clus2                0   1
  CTNND1 MUTATED    17   2
  CTNND1 WILD-TYPE 207  22
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              19              229 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
               2               22 
$`CTNND1 MUTATED`
TCGA-A5-A0GA TCGA-A5-A0R8 TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM 
       17.85        19.59        83.67        86.07         8.22        27.12 
TCGA-AX-A05S TCGA-AX-A05T TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0TC TCGA-BS-A0UA 
       13.58        19.82        32.55         8.71        85.55        88.34 
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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       46.95        37.02        83.51        32.78         3.22       105.37 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        24.62        29.06        11.97        42.35        15.95 
TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D 
        1.18        21.99         5.95        23.31        39.42        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89         7.86        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        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        41.95        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        35.01        28.54        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       65.88        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       80.38        56.91        46.75        43.13        40.67        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        17.85        11.01       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD 
       10.22        10.16        24.99        46.95        23.47        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-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       97.41        67.20        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A168 
       29.88         1.91         3.68        29.33        32.58        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-E6-A1LZ TCGA-EO-A1Y5 
        2.33        22.92        13.22        18.25        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  CTNND1 MUTATED CTNND1 WILD-TYPE 
            0.66             0.56 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
           88.34           185.79 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
           19.82            29.69 
[1] "0.7 - 88.3 (19.8)"  "0.6 - 185.8 (29.7)"
[1] "hr=" "1.2"
D41V2, continuous
                  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
D41V3, 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"
D41V4, binary
                  cls
clus                 0   1
  CTNND1 MUTATED     8  11
  CTNND1 WILD-TYPE  78 151
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED      8   11
  CTNND1 WILD-TYPE   78  151
     clus
vv    CTNND1 MUTATED CTNND1 WILD-TYPE
  NO               8               78
  YES             11              151
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CTNND1 MUTATED    15   1   1   0
  CTNND1 WILD-TYPE 156  10   6  18
D41V5, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  R0             15              156
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTNND1 MUTATED                                  0     2
  CTNND1 WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  CTNND1 MUTATED                           1
  CTNND1 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTNND1 MUTATED                                           1    15
  CTNND1 WILD-TYPE                                         6   178
D41V6, multiclass
                                           clus
vv                                          CTNND1 MUTATED CTNND1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                 15              178
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                  cls
clus                 0   1
  CTNND1 MUTATED     0  13
  CTNND1 WILD-TYPE   4 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED      0   13
  CTNND1 WILD-TYPE    4  154
                        clus
vv                       CTNND1 MUTATED CTNND1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             13              154
[1] 2 2
[1] FALSE

Clustering(42) Variable = GFAP MUTATION ANALYSIS
D42V1, survival
                sevent
clus2              0   1
  GFAP MUTATED     9   0
  GFAP WILD-TYPE 215  24
  GFAP MUTATED GFAP WILD-TYPE 
             9            239 
  GFAP MUTATED GFAP WILD-TYPE 
             0             24 
$`GFAP MUTATED`
TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A11E 
        8.22        27.12        46.45        32.55        28.64         8.71 
TCGA-BS-A0UV TCGA-D1-A101 TCGA-D1-A103 
       73.25         1.74        21.99 

$`GFAP WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        37.78        40.11        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0K0 TCGA-B5-A0K1 
       56.91        46.75        43.13        40.67        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       11.01       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        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 
       67.20        88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93        22.55         4.44        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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  GFAP MUTATED GFAP WILD-TYPE 
          1.74           0.56 
  GFAP MUTATED GFAP WILD-TYPE 
         73.25         185.79 
  GFAP MUTATED GFAP WILD-TYPE 
         27.12          29.69 
[1] "1.7 - 73.2 (27.1)"  "0.6 - 185.8 (29.7)"
[1] "hr="     "2.5e+07"
D42V2, continuous
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  GFAP MUTATED                                         9
  GFAP WILD-TYPE                                     191
                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
D42V3, multiclass
                                         clus
vv                                        GFAP MUTATED GFAP 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"
D42V4, binary
                cls
clus               0   1
  GFAP MUTATED     3   6
  GFAP WILD-TYPE  83 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  GFAP MUTATED      3    6
  GFAP WILD-TYPE   83  156
     clus
vv    GFAP MUTATED GFAP WILD-TYPE
  NO             3             83
  YES            6            156
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GFAP MUTATED     4   1   0   1
  GFAP WILD-TYPE 167  10   7  17
D42V5, multiclass
    clus
vv   GFAP MUTATED GFAP WILD-TYPE
  R0            4            167
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GFAP MUTATED                                  0     0
  GFAP WILD-TYPE                                3    13
                vv
clus             BLACK OR AFRICAN AMERICAN
  GFAP MUTATED                           1
  GFAP WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GFAP MUTATED                                           1     6
  GFAP WILD-TYPE                                         6   187
D42V6, multiclass
                                           clus
vv                                          GFAP MUTATED GFAP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                0             13
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                                6            187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                cls
clus               0   1
  GFAP MUTATED     1   4
  GFAP WILD-TYPE   3 163
[1] "tbl2"
                cls
clus             [,1] [,2]
  GFAP MUTATED      1    4
  GFAP WILD-TYPE    3  163
                        clus
vv                       GFAP MUTATED GFAP WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            4            163
[1] 2 2
[1] FALSE

Clustering(43) Variable = PPP2R1A MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  PPP2R1A MUTATED    24   3
  PPP2R1A WILD-TYPE 200  21
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               27               221 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
                3                21 
$`PPP2R1A MUTATED`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D 
       46.95        37.02        83.67        86.07         8.22        57.80 
TCGA-AP-A0LM TCGA-AP-A1DQ TCGA-AX-A063 TCGA-AX-A0J1 TCGA-AX-A1C8 TCGA-B5-A0JY 
       27.12        41.95        66.58        65.88        13.55        32.55 
TCGA-B5-A0K6 TCGA-B5-A0K8 TCGA-B5-A11G TCGA-BG-A0M6 TCGA-BG-A0VW TCGA-BK-A0CC 
       13.74        17.85       113.36         7.92        16.34        10.22 
TCGA-BS-A0UM TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16S 
       86.93         4.44        39.48        15.72        37.32        18.67 
TCGA-EO-A1Y8 TCGA-EY-A212 TCGA-FI-A2D2 
       10.78         3.62        36.00 

$`PPP2R1A WILD-TYPE`
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78         3.22       105.37        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.59        24.62        29.06        11.97        42.35        15.95 
TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H 
        1.18        21.99         5.95        23.31        39.42        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89         7.86        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
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        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       46.45        35.34        45.99        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        40.11        16.96 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        40.67        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       23.01        17.88        17.10        11.01         8.71       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       24.39        26.66        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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-A139 
       15.45        23.70        35.90        34.98         6.21        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        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-A0UT 
       67.20        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       73.25        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        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-A163 TCGA-D1-A165 TCGA-D1-A168 
        1.91         3.68        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-A16X 
       29.92        31.07        33.63        10.65         0.69         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        48.36 
TCGA-EO-A1Y5 TCGA-EY-A1GS TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       10.92        15.09        59.01         9.07        25.02 

  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
             3.62              0.56 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
           113.36            185.79 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
            32.55             29.06 
[1] "3.6 - 113.4 (32.5)" "0.6 - 185.8 (29.1)"
[1] "hr=" "1.2"
D43V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PPP2R1A MUTATED                                        14
  PPP2R1A WILD-TYPE                                     186
                   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
D43V3, multiclass
                                         clus
vv                                        PPP2R1A MUTATED PPP2R1A WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              14               186
  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"
D43V4, binary
                   cls
clus                  0   1
  PPP2R1A MUTATED    11  16
  PPP2R1A WILD-TYPE  75 146
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R1A MUTATED     11   16
  PPP2R1A WILD-TYPE   75  146
     clus
vv    PPP2R1A MUTATED PPP2R1A WILD-TYPE
  NO               11                75
  YES              16               146
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PPP2R1A MUTATED    20   1   0   2
  PPP2R1A WILD-TYPE 151  10   7  16
D43V5, multiclass
    clus
vv   PPP2R1A MUTATED PPP2R1A WILD-TYPE
  R0              20               151
  R1               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPP2R1A MUTATED                                  0     0
  PPP2R1A WILD-TYPE                                3    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  PPP2R1A MUTATED                           5
  PPP2R1A WILD-TYPE                        20
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPP2R1A MUTATED                                           0    21
  PPP2R1A WILD-TYPE                                         7   172
D43V6, multiclass
                                           clus
vv                                          PPP2R1A MUTATED PPP2R1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   0                13
  BLACK OR AFRICAN AMERICAN                               5                20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 7
  WHITE                                                  21               172
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                   cls
clus                  0   1
  PPP2R1A MUTATED     1  14
  PPP2R1A WILD-TYPE   3 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R1A MUTATED      1   14
  PPP2R1A WILD-TYPE    3  153
                        clus
vv                       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              14               153
[1] 2 2
[1] FALSE

Clustering(44) Variable = C9ORF102 MUTATION ANALYSIS
D44V1, survival
                    sevent
clus2                  0   1
  C9ORF102 MUTATED    16   0
  C9ORF102 WILD-TYPE 208  24
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
                16                232 
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
                 0                 24 
$`C9ORF102 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       83.67        86.07         8.22        27.12        46.45        40.11 
TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-BG-A0MQ TCGA-BS-A0UF TCGA-BS-A0UJ 
       65.88        32.55         8.71        39.32        85.84        82.39 
TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A16X TCGA-D1-A17Q 
       73.25        21.99         3.65         1.78 

$`C9ORF102 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       28.54        37.78        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        17.85        11.01       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
              1.78               0.56 
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
             86.07             185.79 
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
            39.715             28.655 
[1] "1.8 - 86.1 (39.7)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "7.5e+07"
D44V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  C9ORF102 MUTATED                                        16
  C9ORF102 WILD-TYPE                                     184
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  C9ORF102 MUTATED                               0
  C9ORF102 WILD-TYPE                             4
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  C9ORF102 MUTATED                                   0
  C9ORF102 WILD-TYPE                                44
D44V3, multiclass
                                         clus
vv                                        C9ORF102 MUTATED C9ORF102 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"
D44V4, binary
                    cls
clus                   0   1
  C9ORF102 MUTATED     4  12
  C9ORF102 WILD-TYPE  82 150
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF102 MUTATED      4   12
  C9ORF102 WILD-TYPE   82  150
     clus
vv    C9ORF102 MUTATED C9ORF102 WILD-TYPE
  NO                 4                 82
  YES               12                150
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C9ORF102 MUTATED    13   1   0   0
  C9ORF102 WILD-TYPE 158  10   7  18
D44V5, multiclass
    clus
vv   C9ORF102 MUTATED C9ORF102 WILD-TYPE
  R0               13                158
  R1                1                 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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C9ORF102 MUTATED                                  0     2
  C9ORF102 WILD-TYPE                                3    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  C9ORF102 MUTATED                           1
  C9ORF102 WILD-TYPE                        24
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C9ORF102 MUTATED                                           1    11
  C9ORF102 WILD-TYPE                                         6   182
D44V6, multiclass
                                           clus
vv                                          C9ORF102 MUTATED C9ORF102 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    2                 11
  BLACK OR AFRICAN AMERICAN                                1                 24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  6
  WHITE                                                   11                182
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                    cls
clus                   0   1
  C9ORF102 MUTATED     1  10
  C9ORF102 WILD-TYPE   3 157
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF102 MUTATED      1   10
  C9ORF102 WILD-TYPE    3  157
                        clus
vv                       C9ORF102 MUTATED C9ORF102 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               10                157
[1] 2 2
[1] FALSE

Clustering(45) Variable = EIF4A2 MUTATION ANALYSIS
D45V1, survival
                  sevent
clus2                0   1
  EIF4A2 MUTATED     7   0
  EIF4A2 WILD-TYPE 217  24
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
               7              241 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
               0               24 
$`EIF4A2 MUTATED`
TCGA-AP-A059 TCGA-AX-A064 TCGA-AX-A0J1 TCGA-B5-A11E TCGA-B5-A11Z TCGA-BS-A0UF 
        8.22        34.98        65.88         8.71        17.36        85.84 
TCGA-BS-A0UJ 
       82.39 

$`EIF4A2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A06B 
       72.03        46.45        35.34        45.99        66.58        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        35.01        28.54        37.78        40.11 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        46.75        43.13        40.67        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        17.85        11.01       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       18.41        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
            8.22             0.56 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
           85.84           185.79 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
           34.98            29.06 
[1] "8.2 - 85.8 (35.0)"  "0.6 - 185.8 (29.1)"
[1] "hr="     "2.6e+07"
D45V2, continuous
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  EIF4A2 MUTATED                                         7
  EIF4A2 WILD-TYPE                                     193
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  EIF4A2 MUTATED                               0
  EIF4A2 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  EIF4A2 MUTATED                                   0
  EIF4A2 WILD-TYPE                                44
D45V3, multiclass
                                         clus
vv                                        EIF4A2 MUTATED EIF4A2 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"
D45V4, binary
                  cls
clus                 0   1
  EIF4A2 MUTATED     1   6
  EIF4A2 WILD-TYPE  85 156
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4A2 MUTATED      1    6
  EIF4A2 WILD-TYPE   85  156
     clus
vv    EIF4A2 MUTATED EIF4A2 WILD-TYPE
  NO               1               85
  YES              6              156
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  EIF4A2 MUTATED     4   0   0   0
  EIF4A2 WILD-TYPE 167  11   7  18
D45V5, multiclass
    clus
vv   EIF4A2 MUTATED EIF4A2 WILD-TYPE
  R0              4              167
  R1              0               11
  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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EIF4A2 MUTATED                                  0     2
  EIF4A2 WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  EIF4A2 MUTATED                           0
  EIF4A2 WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EIF4A2 MUTATED                                           0     5
  EIF4A2 WILD-TYPE                                         7   188
D45V6, multiclass
                                           clus
vv                                          EIF4A2 MUTATED EIF4A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                  5              188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                  cls
clus                 0   1
  EIF4A2 MUTATED     0   4
  EIF4A2 WILD-TYPE   4 163
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4A2 MUTATED      0    4
  EIF4A2 WILD-TYPE    4  163
                        clus
vv                       EIF4A2 MUTATED EIF4A2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              163
[1] 2 2
[1] FALSE

Clustering(46) Variable = ZNF471 MUTATION ANALYSIS
D46V1, survival
                  sevent
clus2                0   1
  ZNF471 MUTATED    13   2
  ZNF471 WILD-TYPE 211  22
  ZNF471 MUTATED ZNF471 WILD-TYPE 
              15              233 
  ZNF471 MUTATED ZNF471 WILD-TYPE 
               2               22 
$`ZNF471 MUTATED`
TCGA-A5-A0GP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       46.55        83.67        86.07        27.12        46.45        40.11 
TCGA-B5-A0JY TCGA-BS-A0T9 TCGA-BS-A0U7 TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 
       32.55        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A059 
       15.95         1.18        21.99         5.95        23.31         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       28.54        37.78        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       17.88        13.74        17.10        17.85        11.01         8.71 
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 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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-A0UJ 
       67.99        96.49        97.41        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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-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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  ZNF471 MUTATED ZNF471 WILD-TYPE 
            1.78             0.56 
  ZNF471 MUTATED ZNF471 WILD-TYPE 
           86.07           185.79 
  ZNF471 MUTATED ZNF471 WILD-TYPE 
           40.11            28.64 
[1] "1.8 - 86.1 (40.1)"  "0.6 - 185.8 (28.6)"
[1] "hr=" "1.2"
D46V2, continuous
                  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
D46V3, 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"
D46V4, binary
                  cls
clus                 0   1
  ZNF471 MUTATED     4  11
  ZNF471 WILD-TYPE  82 151
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF471 MUTATED      4   11
  ZNF471 WILD-TYPE   82  151
     clus
vv    ZNF471 MUTATED ZNF471 WILD-TYPE
  NO               4               82
  YES             11              151
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF471 MUTATED    12   1   1   0
  ZNF471 WILD-TYPE 159  10   6  18
D46V5, multiclass
    clus
vv   ZNF471 MUTATED ZNF471 WILD-TYPE
  R0             12              159
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF471 MUTATED                                  0     2
  ZNF471 WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ZNF471 MUTATED                           1
  ZNF471 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF471 MUTATED                                           2     9
  ZNF471 WILD-TYPE                                         5   184
D46V6, multiclass
                                           clus
vv                                          ZNF471 MUTATED ZNF471 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              2                5
  WHITE                                                  9              184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                  cls
clus                 0   1
  ZNF471 MUTATED     1  10
  ZNF471 WILD-TYPE   3 157
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF471 MUTATED      1   10
  ZNF471 WILD-TYPE    3  157
                        clus
vv                       ZNF471 MUTATED ZNF471 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             10              157
[1] 2 2
[1] FALSE

Clustering(47) Variable = CDK17 MUTATION ANALYSIS
D47V1, survival
                 sevent
clus2               0   1
  CDK17 MUTATED    13   1
  CDK17 WILD-TYPE 211  23
  CDK17 MUTATED CDK17 WILD-TYPE 
             14             234 
  CDK17 MUTATED CDK17 WILD-TYPE 
              1              23 
$`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        46.45        66.58        56.91 
TCGA-B5-A11E TCGA-B5-A11G TCGA-BG-A0M0 TCGA-BS-A0UV TCGA-D1-A163 TCGA-D1-A16Y 
        8.71       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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
        3.39        63.16        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       28.54        37.78        40.11        65.88        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JT 
       36.39        71.24        19.36        80.38        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       40.67        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N 
      185.79        88.34        75.72        54.44        44.78        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       11.87        18.61        20.19        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
        3.68        29.33         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-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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  CDK17 MUTATED CDK17 WILD-TYPE 
           1.78            0.56 
  CDK17 MUTATED CDK17 WILD-TYPE 
         113.36          185.79 
  CDK17 MUTATED CDK17 WILD-TYPE 
         41.405          28.655 
[1] "1.8 - 113.4 (41.4)" "0.6 - 185.8 (28.7)"
[1] "hr=" "1.6"
D47V2, continuous
                 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
D47V3, 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"
D47V4, binary
                 cls
clus                0   1
  CDK17 MUTATED     4  10
  CDK17 WILD-TYPE  82 152
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK17 MUTATED      4   10
  CDK17 WILD-TYPE   82  152
     clus
vv    CDK17 MUTATED CDK17 WILD-TYPE
  NO              4              82
  YES            10             152
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDK17 MUTATED     8   1   1   1
  CDK17 WILD-TYPE 163  10   6  17
D47V5, multiclass
    clus
vv   CDK17 MUTATED CDK17 WILD-TYPE
  R0             8             163
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDK17 MUTATED                                  0     1
  CDK17 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  CDK17 MUTATED                           2
  CDK17 WILD-TYPE                        23
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDK17 MUTATED                                           1     9
  CDK17 WILD-TYPE                                         6   184
D47V6, multiclass
                                           clus
vv                                          CDK17 MUTATED CDK17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             2              23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                 9             184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                 cls
clus                0   1
  CDK17 MUTATED     1   9
  CDK17 WILD-TYPE   3 158
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK17 MUTATED      1    9
  CDK17 WILD-TYPE    3  158
                        clus
vv                       CDK17 MUTATED CDK17 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             9             158
[1] 2 2
[1] FALSE

Clustering(48) Variable = SIN3A MUTATION ANALYSIS
D48V1, survival
                 sevent
clus2               0   1
  SIN3A MUTATED    20   1
  SIN3A WILD-TYPE 204  23
  SIN3A MUTATED SIN3A WILD-TYPE 
             21             227 
  SIN3A MUTATED SIN3A WILD-TYPE 
              1              23 
$`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        65.88 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11R TCGA-B5-A11X 
       32.55         8.71       185.79        88.34        33.50        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 
       46.55        38.37        28.27        20.81        68.65        19.96 
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        11.97        15.95 
TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        1.18        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       35.01        28.54        37.78        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11G 
       17.88        13.74        17.10        17.85        11.01       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        43.96        40.50        32.09 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       16.34        28.54        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BK-A0C9 
       13.78        14.73        14.01        15.45        15.45        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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-A0UJ 
       96.49        30.74        97.41        67.20        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
        4.44        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-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-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX 
        1.78        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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  SIN3A MUTATED SIN3A WILD-TYPE 
           8.71            0.56 
  SIN3A MUTATED SIN3A WILD-TYPE 
         185.79          125.42 
  SIN3A MUTATED SIN3A WILD-TYPE 
          32.55           28.67 
[1] "8.7 - 185.8 (32.5)" "0.6 - 125.4 (28.7)"
[1] "hr=" "2.3"
D48V2, continuous
                 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
D48V3, 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"
D48V4, binary
                 cls
clus                0   1
  SIN3A MUTATED     8  13
  SIN3A WILD-TYPE  78 149
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIN3A MUTATED      8   13
  SIN3A WILD-TYPE   78  149
     clus
vv    SIN3A MUTATED SIN3A WILD-TYPE
  NO              8              78
  YES            13             149
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SIN3A MUTATED    12   1   0   1
  SIN3A WILD-TYPE 159  10   7  17
D48V5, multiclass
    clus
vv   SIN3A MUTATED SIN3A WILD-TYPE
  R0            12             159
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SIN3A MUTATED                                  1     3
  SIN3A WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN
  SIN3A MUTATED                           3
  SIN3A WILD-TYPE                        22
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SIN3A MUTATED                                           0    14
  SIN3A WILD-TYPE                                         7   179
D48V6, multiclass
                                           clus
vv                                          SIN3A MUTATED SIN3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      1               2
  ASIAN                                                 3              10
  BLACK OR AFRICAN AMERICAN                             3              22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                14             179
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                 cls
clus                0   1
  SIN3A MUTATED     0  14
  SIN3A WILD-TYPE   4 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIN3A MUTATED      0   14
  SIN3A WILD-TYPE    4  153
                        clus
vv                       SIN3A MUTATED SIN3A WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            14             153
[1] 2 2
[1] FALSE

Clustering(49) Variable = ZNF485 MUTATION ANALYSIS
D49V1, survival
                  sevent
clus2                0   1
  ZNF485 MUTATED     8   1
  ZNF485 WILD-TYPE 216  23
  ZNF485 MUTATED ZNF485 WILD-TYPE 
               9              239 
  ZNF485 MUTATED ZNF485 WILD-TYPE 
               1               23 
$`ZNF485 MUTATED`
TCGA-A5-A0GP TCGA-AP-A054 TCGA-AP-A059 TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY 
       46.55        23.31         8.22        46.45        40.11        32.55 
TCGA-BS-A0TC TCGA-D1-A103 TCGA-D1-A16Y 
       85.55        21.99        17.49 

$`ZNF485 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A056 
       15.95         1.18        83.67        21.99         5.95        86.07 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        65.88        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        40.67        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       24.99        46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        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-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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  ZNF485 MUTATED ZNF485 WILD-TYPE 
            8.22             0.56 
  ZNF485 MUTATED ZNF485 WILD-TYPE 
           85.55           185.79 
  ZNF485 MUTATED ZNF485 WILD-TYPE 
           32.55            29.06 
[1] "8.2 - 85.5 (32.5)"  "0.6 - 185.8 (29.1)"
[1] "hr=" "1.1"
D49V2, continuous
                  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
D49V3, 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"
D49V4, binary
                  cls
clus                 0   1
  ZNF485 MUTATED     1   8
  ZNF485 WILD-TYPE  85 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF485 MUTATED      1    8
  ZNF485 WILD-TYPE   85  154
     clus
vv    ZNF485 MUTATED ZNF485 WILD-TYPE
  NO               1               85
  YES              8              154
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF485 MUTATED     5   2   0   1
  ZNF485 WILD-TYPE 166   9   7  17
D49V5, multiclass
    clus
vv   ZNF485 MUTATED ZNF485 WILD-TYPE
  R0              5              166
  R1              2                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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF485 MUTATED                                  0     2
  ZNF485 WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ZNF485 MUTATED                           0
  ZNF485 WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF485 MUTATED                                           0     6
  ZNF485 WILD-TYPE                                         7   187
D49V6, multiclass
                                           clus
vv                                          ZNF485 MUTATED ZNF485 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                  6              187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                  cls
clus                 0   1
  ZNF485 MUTATED     1   7
  ZNF485 WILD-TYPE   3 160
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF485 MUTATED      1    7
  ZNF485 WILD-TYPE    3  160
                        clus
vv                       ZNF485 MUTATED ZNF485 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              7              160
[1] 2 2
[1] FALSE

Clustering(50) Variable = RSBN1L MUTATION ANALYSIS
D50V1, survival
                  sevent
clus2                0   1
  RSBN1L MUTATED    12   0
  RSBN1L WILD-TYPE 212  24
  RSBN1L MUTATED RSBN1L WILD-TYPE 
              12              236 
  RSBN1L MUTATED RSBN1L WILD-TYPE 
               0               24 
$`RSBN1L MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A0J0 TCGA-B5-A11E 
       83.67        86.07        46.45        35.34        40.11         8.71 
TCGA-BG-A0M0 TCGA-BS-A0TC TCGA-BS-A0U9 TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A15X 
       19.33        85.55        67.20        85.84        73.25        29.88 

$`RSBN1L WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        65.88        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       43.13        40.67        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       11.01       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        23.47        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UJ 
       67.99        96.49        30.74        97.41        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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-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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  RSBN1L MUTATED RSBN1L WILD-TYPE 
            8.71             0.56 
  RSBN1L MUTATED RSBN1L WILD-TYPE 
           86.07           185.79 
  RSBN1L MUTATED RSBN1L WILD-TYPE 
          56.825           28.540 
[1] "8.7 - 86.1 (56.8)"  "0.6 - 185.8 (28.5)"
[1] "hr="     "2.7e+07"
D50V2, continuous
                  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
D50V3, 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"
D50V4, binary
                  cls
clus                 0   1
  RSBN1L MUTATED     4   8
  RSBN1L WILD-TYPE  82 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RSBN1L MUTATED      4    8
  RSBN1L WILD-TYPE   82  154
     clus
vv    RSBN1L MUTATED RSBN1L WILD-TYPE
  NO               4               82
  YES              8              154
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RSBN1L MUTATED     8   2   0   1
  RSBN1L WILD-TYPE 163   9   7  17
D50V5, multiclass
    clus
vv   RSBN1L MUTATED RSBN1L WILD-TYPE
  R0              8              163
  R1              2                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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RSBN1L MUTATED                                  1     2
  RSBN1L WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  RSBN1L MUTATED                           0
  RSBN1L WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RSBN1L MUTATED                                           2     6
  RSBN1L WILD-TYPE                                         5   187
D50V6, multiclass
                                           clus
vv                                          RSBN1L MUTATED RSBN1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       1                2
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              2                5
  WHITE                                                  6              187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                  cls
clus                 0   1
  RSBN1L MUTATED     1   8
  RSBN1L WILD-TYPE   3 159
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RSBN1L MUTATED      1    8
  RSBN1L WILD-TYPE    3  159
                        clus
vv                       RSBN1L MUTATED RSBN1L WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              8              159
[1] 2 2
[1] FALSE

Clustering(51) Variable = CUX1 MUTATION ANALYSIS
D51V1, survival
                sevent
clus2              0   1
  CUX1 MUTATED    22   1
  CUX1 WILD-TYPE 202  23
  CUX1 MUTATED CUX1 WILD-TYPE 
            23            225 
  CUX1 MUTATED CUX1 WILD-TYPE 
             1             23 
$`CUX1 MUTATED`
TCGA-A5-A0GI TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A0LM 
       57.53        83.67        86.07         8.22         7.86        27.12 
TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11J TCGA-B5-A11Z TCGA-BG-A0M2 
       65.88        32.55         8.71        54.44        17.36        20.94 
TCGA-BG-A18B TCGA-BS-A0TJ TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A0ZV TCGA-D1-A103 
       15.45        67.99        85.84        73.25        23.93        21.99 
TCGA-D1-A15X TCGA-D1-A160 TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A17Q 
       29.88         3.68        17.49        19.53         1.78 

$`CUX1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37        74.10        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A 
       15.95         1.18        21.99         5.95        23.31        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       57.80        45.53        36.89        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        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        41.95        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       34.98        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       37.78        40.11        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        17.85        11.01       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX 
       18.41        16.57        50.89        11.87        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       19.33        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18C TCGA-BG-A2AE 
       12.56        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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        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        67.20        88.34 
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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        0.56         4.87        28.67        22.55         1.74         4.44 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       39.48        30.08         1.91        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-A176 TCGA-D1-A177 
       10.65         0.69        18.67         3.65        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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  CUX1 MUTATED CUX1 WILD-TYPE 
          1.78           0.56 
  CUX1 MUTATED CUX1 WILD-TYPE 
         86.07         185.79 
  CUX1 MUTATED CUX1 WILD-TYPE 
         23.93          29.69 
[1] "1.8 - 86.1 (23.9)"  "0.6 - 185.8 (29.7)"
[1] "hr=" "2.4"
D51V2, continuous
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CUX1 MUTATED                                        22
  CUX1 WILD-TYPE                                     178
                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
D51V3, multiclass
                                         clus
vv                                        CUX1 MUTATED CUX1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           22            178
  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"
D51V4, binary
                cls
clus               0   1
  CUX1 MUTATED    10  13
  CUX1 WILD-TYPE  76 149
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUX1 MUTATED     10   13
  CUX1 WILD-TYPE   76  149
     clus
vv    CUX1 MUTATED CUX1 WILD-TYPE
  NO            10             76
  YES           13            149
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CUX1 MUTATED    17   0   0   2
  CUX1 WILD-TYPE 154  11   7  16
D51V5, multiclass
    clus
vv   CUX1 MUTATED CUX1 WILD-TYPE
  R0           17            154
  R1            0             11
  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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CUX1 MUTATED                                  0     2
  CUX1 WILD-TYPE                                3    11
                vv
clus             BLACK OR AFRICAN AMERICAN
  CUX1 MUTATED                           1
  CUX1 WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CUX1 MUTATED                                           1    19
  CUX1 WILD-TYPE                                         6   174
D51V6, multiclass
                                           clus
vv                                          CUX1 MUTATED CUX1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                2             11
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                               19            174
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                cls
clus               0   1
  CUX1 MUTATED     0  15
  CUX1 WILD-TYPE   4 152
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUX1 MUTATED      0   15
  CUX1 WILD-TYPE    4  152
                        clus
vv                       CUX1 MUTATED CUX1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           15            152
[1] 2 2
[1] FALSE

Clustering(52) Variable = BCOR MUTATION ANALYSIS
D52V1, survival
                sevent
clus2              0   1
  BCOR MUTATED    30   0
  BCOR WILD-TYPE 194  24
  BCOR MUTATED BCOR WILD-TYPE 
            30            218 
  BCOR MUTATED BCOR WILD-TYPE 
             0             24 
$`BCOR MUTATED`
TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LL TCGA-AX-A06H 
       42.35        83.67        86.07         8.22        83.97        27.39 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0K6 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11H 
       40.11        65.88        13.74        11.01         8.71        88.34 
TCGA-B5-A11N TCGA-BG-A0M4 TCGA-BG-A0MU TCGA-BG-A0VW TCGA-BS-A0TC TCGA-BS-A0TJ 
       43.96        34.98        20.28        16.34        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A 
       15.95         1.18        21.99         5.95        23.31        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        45.53        36.89         7.86        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        31.73        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        41.95        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       66.58        34.98        53.92        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       37.78        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       80.38        56.91        46.75        43.13        40.67        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J 
       17.10        17.85       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        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       35.21         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        24.39        26.66        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD 
       10.22        10.16        24.99        46.95        23.47        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U9 
        4.80        77.95        61.87        96.49        30.74        67.20 
TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 
       88.34        81.57        86.93        72.72        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZS 
       49.55        66.48        19.79        29.95         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74         4.44        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-A16G 
        0.66        36.10        37.32        36.36        37.51        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-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        7.00        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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  BCOR MUTATED BCOR WILD-TYPE 
          0.99           0.56 
  BCOR MUTATED BCOR WILD-TYPE 
         97.41         185.79 
  BCOR MUTATED BCOR WILD-TYPE 
        35.885         28.865 
[1] "1.0 - 97.4 (35.9)"  "0.6 - 185.8 (28.9)"
[1] "hr="     "8.4e+07"
D52V2, continuous
                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
D52V3, 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"
D52V4, binary
                cls
clus               0   1
  BCOR MUTATED    10  20
  BCOR WILD-TYPE  76 142
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     10   20
  BCOR WILD-TYPE   76  142
     clus
vv    BCOR MUTATED BCOR WILD-TYPE
  NO            10             76
  YES           20            142
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BCOR MUTATED    23   1   0   0
  BCOR WILD-TYPE 148  10   7  18
D52V5, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  R0           23            148
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCOR MUTATED                                  1     4
  BCOR WILD-TYPE                                2     9
                vv
clus             BLACK OR AFRICAN AMERICAN
  BCOR MUTATED                           0
  BCOR WILD-TYPE                        25
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BCOR MUTATED                                           1    24
  BCOR WILD-TYPE                                         6   169
D52V6, multiclass
                                           clus
vv                                          BCOR MUTATED BCOR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     1              2
  ASIAN                                                4              9
  BLACK OR AFRICAN AMERICAN                            0             25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                               24            169
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                cls
clus               0   1
  BCOR MUTATED     0  22
  BCOR WILD-TYPE   4 145
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED      0   22
  BCOR WILD-TYPE    4  145
                        clus
vv                       BCOR MUTATED BCOR WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           22            145
[1] 2 2
[1] FALSE

Clustering(53) Variable = WDR45 MUTATION ANALYSIS
D53V1, survival
                 sevent
clus2               0   1
  WDR45 MUTATED    10   1
  WDR45 WILD-TYPE 214  23
  WDR45 MUTATED WDR45 WILD-TYPE 
             11             237 
  WDR45 MUTATED WDR45 WILD-TYPE 
              1              23 
$`WDR45 MUTATED`
TCGA-AP-A051 TCGA-AP-A0LE TCGA-AP-A0LM TCGA-AX-A060 TCGA-B5-A0K3 TCGA-B5-A11E 
       83.67       110.37        27.12        35.34        23.01         8.71 
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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LF 
        7.86        20.91        48.79       125.42       117.99         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       35.01        28.54        37.78        40.11        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       46.75        43.13        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       30.51        25.91        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       11.01       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       23.47        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        67.20        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  WDR45 MUTATED WDR45 WILD-TYPE 
           1.58            0.56 
  WDR45 MUTATED WDR45 WILD-TYPE 
         110.37          185.79 
  WDR45 MUTATED WDR45 WILD-TYPE 
          23.01           29.69 
[1] "1.6 - 110.4 (23.0)" "0.6 - 185.8 (29.7)"
[1] "hr=" "1.1"
D53V2, continuous
                 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
D53V3, 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"
D53V4, binary
                 cls
clus                0   1
  WDR45 MUTATED     5   6
  WDR45 WILD-TYPE  81 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR45 MUTATED      5    6
  WDR45 WILD-TYPE   81  156
     clus
vv    WDR45 MUTATED WDR45 WILD-TYPE
  NO              5              81
  YES             6             156
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  WDR45 MUTATED     6   1   0   0
  WDR45 WILD-TYPE 165  10   7  18
D53V5, multiclass
    clus
vv   WDR45 MUTATED WDR45 WILD-TYPE
  R0             6             165
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WDR45 MUTATED                                  1     1
  WDR45 WILD-TYPE                                2    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  WDR45 MUTATED                           3
  WDR45 WILD-TYPE                        22
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WDR45 MUTATED                                           0     6
  WDR45 WILD-TYPE                                         7   187
D53V6, multiclass
                                           clus
vv                                          WDR45 MUTATED WDR45 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      1               2
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             3              22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                 6             187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                 cls
clus                0   1
  WDR45 MUTATED     0   4
  WDR45 WILD-TYPE   4 163
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR45 MUTATED      0    4
  WDR45 WILD-TYPE    4  163
                        clus
vv                       WDR45 MUTATED WDR45 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             163
[1] 2 2
[1] FALSE

Clustering(54) Variable = CAB39L MUTATION ANALYSIS
D54V1, survival
                  sevent
clus2                0   1
  CAB39L MUTATED     8   0
  CAB39L WILD-TYPE 216  24
  CAB39L MUTATED CAB39L WILD-TYPE 
               8              240 
  CAB39L MUTATED CAB39L WILD-TYPE 
               0               24 
$`CAB39L MUTATED`
TCGA-A5-A0GP TCGA-AX-A05T TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-BG-A0M3 TCGA-BS-A0UF 
       46.55        19.82        40.11        32.55        35.21        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UV 
       82.39        73.25 

$`CAB39L WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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        41.95        13.58        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        35.01        28.54        37.78        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         8.71       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 TCGA-BG-A0M7 
       20.19        19.33        20.94        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  CAB39L MUTATED CAB39L WILD-TYPE 
           19.82             0.56 
  CAB39L MUTATED CAB39L WILD-TYPE 
           85.84           185.79 
  CAB39L MUTATED CAB39L WILD-TYPE 
           43.33            28.59 
[1] "19.8 - 85.8 (43.3)" "0.6 - 185.8 (28.6)"
[1] "hr="     "2.6e+07"
D54V2, continuous
                  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
D54V3, 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"
D54V4, binary
                  cls
clus                 0   1
  CAB39L MUTATED     1   7
  CAB39L WILD-TYPE  85 155
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      1    7
  CAB39L WILD-TYPE   85  155
     clus
vv    CAB39L MUTATED CAB39L WILD-TYPE
  NO               1               85
  YES              7              155
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CAB39L MUTATED     6   1   0   0
  CAB39L WILD-TYPE 165  10   7  18
D54V5, multiclass
    clus
vv   CAB39L MUTATED CAB39L WILD-TYPE
  R0              6              165
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CAB39L MUTATED                                  0     3
  CAB39L WILD-TYPE                                3    10
                  vv
clus               BLACK OR AFRICAN AMERICAN
  CAB39L MUTATED                           0
  CAB39L WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CAB39L MUTATED                                           1     4
  CAB39L WILD-TYPE                                         6   189
D54V6, multiclass
                                           clus
vv                                          CAB39L MUTATED CAB39L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  3               10
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  4              189
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                  cls
clus                 0   1
  CAB39L MUTATED     0   6
  CAB39L WILD-TYPE   4 161
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      0    6
  CAB39L WILD-TYPE    4  161
                        clus
vv                       CAB39L MUTATED CAB39L WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              161
[1] 2 2
[1] FALSE

Clustering(55) Variable = TAB3 MUTATION ANALYSIS
D55V1, survival
                sevent
clus2              0   1
  TAB3 MUTATED    18   0
  TAB3 WILD-TYPE 206  24
  TAB3 MUTATED TAB3 WILD-TYPE 
            18            230 
  TAB3 MUTATED TAB3 WILD-TYPE 
             0             24 
$`TAB3 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A063 TCGA-AX-A06H 
       83.67         8.22        27.12        46.45        66.58        27.39 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-BS-A0UF TCGA-BS-A0UL TCGA-BS-A0UV 
       40.11        65.88        32.55        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       45.99        34.98        53.92        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       37.78        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       80.38        56.91        46.75        43.13        40.67        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         8.71       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        82.39 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-D1-A0ZN 
       86.93        72.72        62.79        63.58        49.55        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74         4.44        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-A176 TCGA-D1-A177 
        0.69        18.67         3.65        17.49        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-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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  TAB3 MUTATED TAB3 WILD-TYPE 
          1.78           0.56 
  TAB3 MUTATED TAB3 WILD-TYPE 
         85.84         185.79 
  TAB3 MUTATED TAB3 WILD-TYPE 
        36.330         28.655 
[1] "1.8 - 85.8 (36.3)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "7.7e+07"
D55V2, continuous
                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
D55V3, 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"
D55V4, binary
                cls
clus               0   1
  TAB3 MUTATED     5  13
  TAB3 WILD-TYPE  81 149
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB3 MUTATED      5   13
  TAB3 WILD-TYPE   81  149
     clus
vv    TAB3 MUTATED TAB3 WILD-TYPE
  NO             5             81
  YES           13            149
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TAB3 MUTATED    15   2   0   0
  TAB3 WILD-TYPE 156   9   7  18
D55V5, multiclass
    clus
vv   TAB3 MUTATED TAB3 WILD-TYPE
  R0           15            156
  R1            2              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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAB3 MUTATED                                  1     2
  TAB3 WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN
  TAB3 MUTATED                           1
  TAB3 WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TAB3 MUTATED                                           2    11
  TAB3 WILD-TYPE                                         5   182
D55V6, multiclass
                                           clus
vv                                          TAB3 MUTATED TAB3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     1              2
  ASIAN                                                2             11
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            2              5
  WHITE                                               11            182
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                cls
clus               0   1
  TAB3 MUTATED     1  14
  TAB3 WILD-TYPE   3 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB3 MUTATED      1   14
  TAB3 WILD-TYPE    3  153
                        clus
vv                       TAB3 MUTATED TAB3 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           14            153
[1] 2 2
[1] FALSE

Clustering(56) Variable = OAZ3 MUTATION ANALYSIS
D56V1, survival
                sevent
clus2              0   1
  OAZ3 MUTATED     8   0
  OAZ3 WILD-TYPE 216  24
  OAZ3 MUTATED OAZ3 WILD-TYPE 
             8            240 
  OAZ3 MUTATED OAZ3 WILD-TYPE 
             0             24 
$`OAZ3 MUTATED`
TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A11E 
       42.35        83.67        27.12        46.45        40.11         8.71 
TCGA-BS-A0UV TCGA-E6-A1LZ 
       73.25        48.36 

$`OAZ3 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
       15.95         1.18        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        65.88        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       43.13        40.67        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       11.01       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        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 
       67.20        88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        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-EO-A1Y5 TCGA-EO-A1Y8 
       13.22        18.25        16.31        35.38        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  OAZ3 MUTATED OAZ3 WILD-TYPE 
          8.71           0.56 
  OAZ3 MUTATED OAZ3 WILD-TYPE 
         83.67         185.79 
  OAZ3 MUTATED OAZ3 WILD-TYPE 
        44.400         28.655 
[1] "8.7 - 83.7 (44.4)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.6e+07"
D56V2, continuous
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  OAZ3 MUTATED                                         7
  OAZ3 WILD-TYPE                                     193
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  OAZ3 MUTATED                               0
  OAZ3 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  OAZ3 MUTATED                                   1
  OAZ3 WILD-TYPE                                43
D56V3, multiclass
                                         clus
vv                                        OAZ3 MUTATED OAZ3 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"
D56V4, binary
                cls
clus               0   1
  OAZ3 MUTATED     4   4
  OAZ3 WILD-TYPE  82 158
[1] "tbl2"
                cls
clus             [,1] [,2]
  OAZ3 MUTATED      4    4
  OAZ3 WILD-TYPE   82  158
     clus
vv    OAZ3 MUTATED OAZ3 WILD-TYPE
  NO             4             82
  YES            4            158
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  OAZ3 MUTATED     6   1   0   0
  OAZ3 WILD-TYPE 165  10   7  18
D56V5, multiclass
    clus
vv   OAZ3 MUTATED OAZ3 WILD-TYPE
  R0            6            165
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OAZ3 MUTATED                                  0     0
  OAZ3 WILD-TYPE                                3    13
                vv
clus             BLACK OR AFRICAN AMERICAN
  OAZ3 MUTATED                           2
  OAZ3 WILD-TYPE                        23
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OAZ3 MUTATED                                           1     4
  OAZ3 WILD-TYPE                                         6   189
D56V6, multiclass
                                           clus
vv                                          OAZ3 MUTATED OAZ3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                0             13
  BLACK OR AFRICAN AMERICAN                            2             23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                                4            189
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                cls
clus               0   1
  OAZ3 MUTATED     1   4
  OAZ3 WILD-TYPE   3 163
[1] "tbl2"
                cls
clus             [,1] [,2]
  OAZ3 MUTATED      1    4
  OAZ3 WILD-TYPE    3  163
                        clus
vv                       OAZ3 MUTATED OAZ3 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            4            163
[1] 2 2
[1] FALSE

Clustering(57) Variable = AHCYL1 MUTATION ANALYSIS
D57V1, survival
                  sevent
clus2                0   1
  AHCYL1 MUTATED     6   0
  AHCYL1 WILD-TYPE 218  24
  AHCYL1 MUTATED AHCYL1 WILD-TYPE 
               6              242 
  AHCYL1 MUTATED AHCYL1 WILD-TYPE 
               0               24 
$`AHCYL1 MUTATED`
TCGA-AP-A051 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-B5-A11Y TCGA-BS-A0UV TCGA-D1-A17Q 
       83.67        27.12        46.45        18.41        73.25         1.78 

$`AHCYL1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        37.78        40.11        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        46.75        43.13        40.67        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         8.71       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  AHCYL1 MUTATED AHCYL1 WILD-TYPE 
            1.78             0.56 
  AHCYL1 MUTATED AHCYL1 WILD-TYPE 
           83.67           185.79 
  AHCYL1 MUTATED AHCYL1 WILD-TYPE 
          36.785           29.195 
[1] "1.8 - 83.7 (36.8)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "2.5e+07"
D57V2, continuous
                  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
D57V3, 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"
D57V4, binary
                  cls
clus                 0   1
  AHCYL1 MUTATED     2   4
  AHCYL1 WILD-TYPE  84 158
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCYL1 MUTATED      2    4
  AHCYL1 WILD-TYPE   84  158
     clus
vv    AHCYL1 MUTATED AHCYL1 WILD-TYPE
  NO               2               84
  YES              4              158
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  AHCYL1 MUTATED     4   1   0   0
  AHCYL1 WILD-TYPE 167  10   7  18
D57V5, multiclass
    clus
vv   AHCYL1 MUTATED AHCYL1 WILD-TYPE
  R0              4              167
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AHCYL1 MUTATED                                  0     0
  AHCYL1 WILD-TYPE                                3    13
                  vv
clus               BLACK OR AFRICAN AMERICAN
  AHCYL1 MUTATED                           1
  AHCYL1 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AHCYL1 MUTATED                                           1     3
  AHCYL1 WILD-TYPE                                         6   190
D57V6, multiclass
                                           clus
vv                                          AHCYL1 MUTATED AHCYL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  0               13
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  3              190
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                  cls
clus                 0   1
  AHCYL1 MUTATED     1   2
  AHCYL1 WILD-TYPE   3 165
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCYL1 MUTATED      1    2
  AHCYL1 WILD-TYPE    3  165
                        clus
vv                       AHCYL1 MUTATED AHCYL1 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              2              165
[1] 2 2
[1] FALSE

Clustering(58) Variable = ATM MUTATION ANALYSIS
D58V1, survival
               sevent
clus2             0   1
  ATM MUTATED    29   0
  ATM WILD-TYPE 195  24
  ATM MUTATED ATM WILD-TYPE 
           29           219 
  ATM MUTATED ATM WILD-TYPE 
            0            24 
$`ATM MUTATED`
TCGA-A5-A0GB TCGA-A5-A0GP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM 
       32.78        46.55        83.67        86.07         8.22        27.12 
TCGA-AP-A0LT TCGA-AX-A05Z TCGA-AX-A063 TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JR 
       49.22        46.45        66.58        40.11        65.88        56.91 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11G TCGA-B5-A11U TCGA-BG-A0M4 TCGA-BG-A0MT 
       32.55         8.71       113.36        16.73        34.98        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GE 
       46.95        37.02        83.51        17.85         3.22       105.37 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GQ 
       74.10        57.53        65.75        60.53        60.53        38.37 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.59        24.62        29.06        11.97        42.35        15.95 
TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D 
        1.18        21.99         5.95        23.31        39.42        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89         7.86        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       72.03        35.34        45.99        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 
       60.66        35.01        28.54        37.78        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JT 
       36.39        71.24        19.36        80.38        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       17.88        13.74        17.10        17.85        11.01       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       39.32        30.81        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        13.78        14.73        14.01        15.45        15.45 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        23.47        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        67.20        88.34 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       81.57        72.72        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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-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-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-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
       24.30        22.92        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  ATM MUTATED ATM WILD-TYPE 
         1.78          0.56 
  ATM MUTATED ATM WILD-TYPE 
       113.36        185.79 
  ATM MUTATED ATM WILD-TYPE 
        40.11         28.54 
[1] "1.8 - 113.4 (40.1)" "0.6 - 185.8 (28.5)"
[1] "hr="     "8.5e+07"
D58V2, continuous
               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
D58V3, 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"
D58V4, binary
               cls
clus              0   1
  ATM MUTATED     8  21
  ATM WILD-TYPE  78 141
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      8   21
  ATM WILD-TYPE   78  141
     clus
vv    ATM MUTATED ATM WILD-TYPE
  NO            8            78
  YES          21           141
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  ATM MUTATED    21   1   0   1
  ATM WILD-TYPE 150  10   7  17
D58V5, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  R0          21           150
  R1           1            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"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATM MUTATED                                  0     4
  ATM WILD-TYPE                                3     9
               vv
clus            BLACK OR AFRICAN AMERICAN
  ATM MUTATED                           3
  ATM WILD-TYPE                        22
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATM MUTATED                                           1    20
  ATM WILD-TYPE                                         6   173
D58V6, multiclass
                                           clus
vv                                          ATM MUTATED ATM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                    0             3
  ASIAN                                               4             9
  BLACK OR AFRICAN AMERICAN                           3            22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           1             6
  WHITE                                              20           173
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
               cls
clus              0   1
  ATM MUTATED     1  18
  ATM WILD-TYPE   3 149
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      1   18
  ATM WILD-TYPE    3  149
                        clus
vv                       ATM MUTATED ATM WILD-TYPE
  HISPANIC OR LATINO               1             3
  NOT HISPANIC OR LATINO          18           149
[1] 2 2
[1] FALSE

Clustering(59) Variable = MSH4 MUTATION ANALYSIS
D59V1, survival
                sevent
clus2              0   1
  MSH4 MUTATED    15   0
  MSH4 WILD-TYPE 209  24
  MSH4 MUTATED MSH4 WILD-TYPE 
            15            233 
  MSH4 MUTATED MSH4 WILD-TYPE 
             0             24 
$`MSH4 MUTATED`
TCGA-A5-A0GI TCGA-A5-A0GP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM 
       57.53        46.55        83.67        86.07         8.22        27.12 
TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UV 
       46.45        32.55         8.71        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GQ 
      105.37        74.10        65.75        60.53        60.53        38.37 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.59        24.62        29.06        11.97        42.35        15.95 
TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D 
        1.18        21.99         5.95        23.31        39.42        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89         7.86        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        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        41.95        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       68.35        72.03        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       40.11        65.88        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        17.85        11.01       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74         4.44        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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  MSH4 MUTATED MSH4 WILD-TYPE 
          1.78           0.56 
  MSH4 MUTATED MSH4 WILD-TYPE 
         86.07         185.79 
  MSH4 MUTATED MSH4 WILD-TYPE 
         46.45          28.67 
[1] "1.8 - 86.1 (46.5)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.7e+07"
D59V2, continuous
                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
D59V3, 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"
D59V4, binary
                cls
clus               0   1
  MSH4 MUTATED     5  10
  MSH4 WILD-TYPE  81 152
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH4 MUTATED      5   10
  MSH4 WILD-TYPE   81  152
     clus
vv    MSH4 MUTATED MSH4 WILD-TYPE
  NO             5             81
  YES           10            152
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MSH4 MUTATED    12   1   0   0
  MSH4 WILD-TYPE 159  10   7  18
D59V5, multiclass
    clus
vv   MSH4 MUTATED MSH4 WILD-TYPE
  R0           12            159
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MSH4 MUTATED                                  0     3
  MSH4 WILD-TYPE                                3    10
                vv
clus             BLACK OR AFRICAN AMERICAN
  MSH4 MUTATED                           1
  MSH4 WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MSH4 MUTATED                                           1     9
  MSH4 WILD-TYPE                                         6   184
D59V6, multiclass
                                           clus
vv                                          MSH4 MUTATED MSH4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                3             10
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                                9            184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                cls
clus               0   1
  MSH4 MUTATED     1   9
  MSH4 WILD-TYPE   3 158
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH4 MUTATED      1    9
  MSH4 WILD-TYPE    3  158
                        clus
vv                       MSH4 MUTATED MSH4 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            9            158
[1] 2 2
[1] FALSE

Clustering(60) Variable = FAM65B MUTATION ANALYSIS
D60V1, survival
                  sevent
clus2                0   1
  FAM65B MUTATED    16   0
  FAM65B WILD-TYPE 208  24
  FAM65B MUTATED FAM65B WILD-TYPE 
              16              232 
  FAM65B MUTATED FAM65B WILD-TYPE 
               0               24 
$`FAM65B MUTATED`
TCGA-A5-A0VQ TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-B5-A0JY 
       15.95        86.07         8.22        27.12        40.11        32.55 
TCGA-B5-A11E TCGA-B5-A11N TCGA-B5-A11R TCGA-BS-A0TC TCGA-BS-A0UA TCGA-BS-A0UF 
        8.71        43.96        33.50        85.55        88.34        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        65.88        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        40.67        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
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-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       40.50        32.09        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       30.74        97.41        67.20        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        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-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17R 
        1.28        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  FAM65B MUTATED FAM65B WILD-TYPE 
            1.78             0.56 
  FAM65B MUTATED FAM65B WILD-TYPE 
           88.34           185.79 
  FAM65B MUTATED FAM65B WILD-TYPE 
          33.025           28.655 
[1] "1.8 - 88.3 (33.0)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "7.4e+07"
D60V2, continuous
                  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
D60V3, 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"
D60V4, binary
                  cls
clus                 0   1
  FAM65B MUTATED     6  10
  FAM65B WILD-TYPE  80 152
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65B MUTATED      6   10
  FAM65B WILD-TYPE   80  152
     clus
vv    FAM65B MUTATED FAM65B WILD-TYPE
  NO               6               80
  YES             10              152
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAM65B MUTATED    12   0   0   0
  FAM65B WILD-TYPE 159  11   7  18
D60V5, multiclass
    clus
vv   FAM65B MUTATED FAM65B WILD-TYPE
  R0             12              159
  R1              0               11
  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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM65B MUTATED                                  0     2
  FAM65B WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  FAM65B MUTATED                           2
  FAM65B WILD-TYPE                        23
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM65B MUTATED                                           1    10
  FAM65B WILD-TYPE                                         6   183
D60V6, multiclass
                                           clus
vv                                          FAM65B MUTATED FAM65B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              2               23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                 10              183
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                  cls
clus                 0   1
  FAM65B MUTATED     1   9
  FAM65B WILD-TYPE   3 158
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65B MUTATED      1    9
  FAM65B WILD-TYPE    3  158
                        clus
vv                       FAM65B MUTATED FAM65B WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              9              158
[1] 2 2
[1] FALSE

Clustering(61) Variable = FN1 MUTATION ANALYSIS
D61V1, survival
               sevent
clus2             0   1
  FN1 MUTATED    23   1
  FN1 WILD-TYPE 201  23
  FN1 MUTATED FN1 WILD-TYPE 
           24           224 
  FN1 MUTATED FN1 WILD-TYPE 
            1            23 
$`FN1 MUTATED`
TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM 
       42.35        83.67        23.31        86.07         8.22        27.12 
TCGA-AX-A05Z TCGA-AX-A0J1 TCGA-B5-A0JR TCGA-B5-A0JY TCGA-B5-A11N TCGA-B5-A11Y 
       46.45        65.88        56.91        32.55        43.96        18.41 
TCGA-BG-A0M4 TCGA-BG-A0MQ TCGA-BG-A0VW TCGA-BG-A18C TCGA-BS-A0UF TCGA-BS-A0UV 
       34.98        39.32        16.34        15.45        85.84        73.25 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A174 TCGA-D1-A17D TCGA-D1-A17Q TCGA-DI-A0WH 
        1.74        21.99        19.53        30.44         1.78        16.31 

$`FN1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D 
       15.95         1.18        21.99         5.95        39.42        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89         7.86        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        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        41.95        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       68.35        72.03        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       40.11        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       80.38        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         8.71       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        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z 
       27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       20.94        35.21         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MS TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        24.39        26.66        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       14.01        15.45        23.70        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W 
       28.67        23.93        22.55         4.44        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-A1NN TCGA-E6-A1LZ 
        2.33        22.92        13.22        18.25        35.38        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  FN1 MUTATED FN1 WILD-TYPE 
         1.74          0.56 
  FN1 MUTATED FN1 WILD-TYPE 
        86.07        185.79 
  FN1 MUTATED FN1 WILD-TYPE 
       31.495        28.865 
[1] "1.7 - 86.1 (31.5)"  "0.6 - 185.8 (28.9)"
[1] "hr=" "2.6"
D61V2, continuous
               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
D61V3, 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"
D61V4, binary
               cls
clus              0   1
  FN1 MUTATED     8  16
  FN1 WILD-TYPE  78 146
[1] "tbl2"
               cls
clus            [,1] [,2]
  FN1 MUTATED      8   16
  FN1 WILD-TYPE   78  146
     clus
vv    FN1 MUTATED FN1 WILD-TYPE
  NO            8            78
  YES          16           146
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  FN1 MUTATED    16   2   0   2
  FN1 WILD-TYPE 155   9   7  16
D61V5, multiclass
    clus
vv   FN1 MUTATED FN1 WILD-TYPE
  R0          16           155
  R1           2             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"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FN1 MUTATED                                  0     1
  FN1 WILD-TYPE                                3    12
               vv
clus            BLACK OR AFRICAN AMERICAN
  FN1 MUTATED                           1
  FN1 WILD-TYPE                        24
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FN1 MUTATED                                           1    20
  FN1 WILD-TYPE                                         6   173
D61V6, multiclass
                                           clus
vv                                          FN1 MUTATED FN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                    0             3
  ASIAN                                               1            12
  BLACK OR AFRICAN AMERICAN                           1            24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           1             6
  WHITE                                              20           173
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
               cls
clus              0   1
  FN1 MUTATED     1  16
  FN1 WILD-TYPE   3 151
[1] "tbl2"
               cls
clus            [,1] [,2]
  FN1 MUTATED      1   16
  FN1 WILD-TYPE    3  151
                        clus
vv                       FN1 MUTATED FN1 WILD-TYPE
  HISPANIC OR LATINO               1             3
  NOT HISPANIC OR LATINO          16           151
[1] 2 2
[1] FALSE

Clustering(62) Variable = JAKMIP2 MUTATION ANALYSIS
D62V1, survival
                   sevent
clus2                 0   1
  JAKMIP2 MUTATED    11   1
  JAKMIP2 WILD-TYPE 213  23
  JAKMIP2 MUTATED JAKMIP2 WILD-TYPE 
               12               236 
  JAKMIP2 MUTATED JAKMIP2 WILD-TYPE 
                1                23 
$`JAKMIP2 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       83.67        86.07         8.22        27.12        46.45        40.11 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0TC TCGA-BS-A0TE TCGA-BS-A0UF TCGA-BS-A0UV 
       32.55         8.71        85.55         4.80        85.84        73.25 

$`JAKMIP2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       28.54        37.78        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       17.88        13.74        17.10        17.85        11.01       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        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  JAKMIP2 MUTATED JAKMIP2 WILD-TYPE 
             4.80              0.56 
  JAKMIP2 MUTATED JAKMIP2 WILD-TYPE 
            86.07            185.79 
  JAKMIP2 MUTATED JAKMIP2 WILD-TYPE 
           43.280            28.655 
[1] "4.8 - 86.1 (43.3)"  "0.6 - 185.8 (28.7)"
[1] "hr=" "1.5"
D62V2, continuous
                   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
D62V3, 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"
D62V4, binary
                   cls
clus                  0   1
  JAKMIP2 MUTATED     4   8
  JAKMIP2 WILD-TYPE  82 154
[1] "tbl2"
                   cls
clus                [,1] [,2]
  JAKMIP2 MUTATED      4    8
  JAKMIP2 WILD-TYPE   82  154
     clus
vv    JAKMIP2 MUTATED JAKMIP2 WILD-TYPE
  NO                4                82
  YES               8               154
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  JAKMIP2 MUTATED     8   1   1   0
  JAKMIP2 WILD-TYPE 163  10   6  18
D62V5, multiclass
    clus
vv   JAKMIP2 MUTATED JAKMIP2 WILD-TYPE
  R0               8               163
  R1               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  JAKMIP2 MUTATED                                  0     3
  JAKMIP2 WILD-TYPE                                3    10
                   vv
clus                BLACK OR AFRICAN AMERICAN
  JAKMIP2 MUTATED                           1
  JAKMIP2 WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  JAKMIP2 MUTATED                                           1     6
  JAKMIP2 WILD-TYPE                                         6   187
D62V6, multiclass
                                           clus
vv                                          JAKMIP2 MUTATED JAKMIP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   3                10
  BLACK OR AFRICAN AMERICAN                               1                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 6
  WHITE                                                   6               187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                   cls
clus                  0   1
  JAKMIP2 MUTATED     1   6
  JAKMIP2 WILD-TYPE   3 161
[1] "tbl2"
                   cls
clus                [,1] [,2]
  JAKMIP2 MUTATED      1    6
  JAKMIP2 WILD-TYPE    3  161
                        clus
vv                       JAKMIP2 MUTATED JAKMIP2 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               6               161
[1] 2 2
[1] FALSE

Clustering(63) Variable = WBP4 MUTATION ANALYSIS
D63V1, survival
                sevent
clus2              0   1
  WBP4 MUTATED     8   0
  WBP4 WILD-TYPE 216  24
  WBP4 MUTATED WBP4 WILD-TYPE 
             8            240 
  WBP4 MUTATED WBP4 WILD-TYPE 
             0             24 
$`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        32.55         8.71        21.99 
TCGA-D1-A160 TCGA-D1-A17Q 
        3.68         1.78 

$`WBP4 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        35.01        28.54        37.78        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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-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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  WBP4 MUTATED WBP4 WILD-TYPE 
          1.78           0.56 
  WBP4 MUTATED WBP4 WILD-TYPE 
         86.07         185.79 
  WBP4 MUTATED WBP4 WILD-TYPE 
        24.555         29.510 
[1] "1.8 - 86.1 (24.6)"  "0.6 - 185.8 (29.5)"
[1] "hr="     "9300000"
D63V2, continuous
                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
D63V3, 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"
D63V4, binary
                cls
clus               0   1
  WBP4 MUTATED     2   6
  WBP4 WILD-TYPE  84 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  WBP4 MUTATED      2    6
  WBP4 WILD-TYPE   84  156
     clus
vv    WBP4 MUTATED WBP4 WILD-TYPE
  NO             2             84
  YES            6            156
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  WBP4 MUTATED     6   0   0   0
  WBP4 WILD-TYPE 165  11   7  18
D63V5, multiclass
    clus
vv   WBP4 MUTATED WBP4 WILD-TYPE
  R0            6            165
  R1            0             11
  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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WBP4 MUTATED                                  0     0
  WBP4 WILD-TYPE                                3    13
                vv
clus             BLACK OR AFRICAN AMERICAN
  WBP4 MUTATED                           1
  WBP4 WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WBP4 MUTATED                                           0     7
  WBP4 WILD-TYPE                                         7   186
D63V6, multiclass
                                           clus
vv                                          WBP4 MUTATED WBP4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                0             13
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              7
  WHITE                                                7            186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                cls
clus               0   1
  WBP4 MUTATED     0   4
  WBP4 WILD-TYPE   4 163
[1] "tbl2"
                cls
clus             [,1] [,2]
  WBP4 MUTATED      0    4
  WBP4 WILD-TYPE    4  163
                        clus
vv                       WBP4 MUTATED WBP4 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            4            163
[1] 2 2
[1] FALSE

Clustering(64) Variable = RASA1 MUTATION ANALYSIS
D64V1, survival
                 sevent
clus2               0   1
  RASA1 MUTATED    22   0
  RASA1 WILD-TYPE 202  24
  RASA1 MUTATED RASA1 WILD-TYPE 
             22             226 
  RASA1 MUTATED RASA1 WILD-TYPE 
              0              24 
$`RASA1 MUTATED`
TCGA-A5-A0VQ TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z 
       15.95        83.67        86.07         8.22        27.12        46.45 
TCGA-AX-A0IU TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JR TCGA-B5-A0JY TCGA-B5-A11N 
       28.54        40.11        65.88        56.91        32.55        43.96 
TCGA-BG-A0VW TCGA-BG-A0VZ TCGA-BK-A0C9 TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0UF 
       16.34        28.54        35.90        85.55        78.21        85.84 
TCGA-BS-A0UJ TCGA-D1-A15X TCGA-D1-A16Y TCGA-D1-A17Q 
       82.39        29.88        17.49         1.78 

$`RASA1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A 
       42.35         1.18        21.99         5.95        23.31        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        45.53        36.89         7.86        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        31.73        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        41.95        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        68.35        72.03        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW 
       34.98        53.92        27.39        60.66        35.01        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        40.67        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       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        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VX TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       34.29        52.83        56.58        14.83        12.56        13.78 
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-A0T9 TCGA-BS-A0TA 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        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-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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  RASA1 MUTATED RASA1 WILD-TYPE 
           1.78            0.56 
  RASA1 MUTATED RASA1 WILD-TYPE 
          86.07          185.79 
  RASA1 MUTATED RASA1 WILD-TYPE 
         38.005          28.490 
[1] "1.8 - 86.1 (38.0)"  "0.6 - 185.8 (28.5)"
[1] "hr="     "7.9e+07"
D64V2, continuous
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  RASA1 MUTATED                                        20
  RASA1 WILD-TYPE                                     180
                 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
D64V3, multiclass
                                         clus
vv                                        RASA1 MUTATED RASA1 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            20             180
  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"
D64V4, binary
                 cls
clus                0   1
  RASA1 MUTATED     6  16
  RASA1 WILD-TYPE  80 146
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      6   16
  RASA1 WILD-TYPE   80  146
     clus
vv    RASA1 MUTATED RASA1 WILD-TYPE
  NO              6              80
  YES            16             146
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RASA1 MUTATED    17   1   0   1
  RASA1 WILD-TYPE 154  10   7  17
D64V5, multiclass
    clus
vv   RASA1 MUTATED RASA1 WILD-TYPE
  R0            17             154
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RASA1 MUTATED                                  0     4
  RASA1 WILD-TYPE                                3     9
                 vv
clus              BLACK OR AFRICAN AMERICAN
  RASA1 MUTATED                           2
  RASA1 WILD-TYPE                        23
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RASA1 MUTATED                                           0    14
  RASA1 WILD-TYPE                                         7   179
D64V6, multiclass
                                           clus
vv                                          RASA1 MUTATED RASA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 4               9
  BLACK OR AFRICAN AMERICAN                             2              23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                14             179
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                 cls
clus                0   1
  RASA1 MUTATED     2  14
  RASA1 WILD-TYPE   2 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      2   14
  RASA1 WILD-TYPE    2  153
                        clus
vv                       RASA1 MUTATED RASA1 WILD-TYPE
  HISPANIC OR LATINO                 2               2
  NOT HISPANIC OR LATINO            14             153
[1] 2 2
[1] FALSE

Clustering(65) Variable = ALPK2 MUTATION ANALYSIS
D65V1, survival
                 sevent
clus2               0   1
  ALPK2 MUTATED    19   0
  ALPK2 WILD-TYPE 205  24
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             19             229 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
              0              24 
$`ALPK2 MUTATED`
TCGA-A5-A0GB TCGA-A5-A0GH TCGA-A5-A0GI TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LM 
       32.78        74.10        57.53        83.67         8.22        27.12 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11G TCGA-B5-A11J 
       46.45        35.34        40.11        32.55       113.36        54.44 
TCGA-B5-A11R TCGA-BS-A0U8 TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-D1-A103 TCGA-D1-A15X 
       33.50        97.41        85.84        82.39        21.99        29.88 
TCGA-D1-A17Q 
        1.78 

$`ALPK2 WILD-TYPE`
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         3.22       105.37 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       65.75        60.53        60.53        46.55        38.37        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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        11.97        42.35        15.95         1.18 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D 
       21.99         5.95        23.31        86.07        39.42        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89         7.86        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        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        41.95        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       68.35        72.03        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        35.01        28.54        37.78        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01         8.71       185.79        88.34        75.72 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U 
       44.78        43.96        40.50        32.09        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20        88.34 
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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
        4.44        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-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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  ALPK2 MUTATED ALPK2 WILD-TYPE 
           1.78            0.56 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
         113.36          185.79 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
          40.11           28.34 
[1] "1.8 - 113.4 (40.1)" "0.6 - 185.8 (28.3)"
[1] "hr="     "7.8e+07"
D65V2, continuous
                 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
D65V3, 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"
D65V4, binary
                 cls
clus                0   1
  ALPK2 MUTATED     9  10
  ALPK2 WILD-TYPE  77 152
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED      9   10
  ALPK2 WILD-TYPE   77  152
     clus
vv    ALPK2 MUTATED ALPK2 WILD-TYPE
  NO              9              77
  YES            10             152
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ALPK2 MUTATED    12   2   0   0
  ALPK2 WILD-TYPE 159   9   7  18
D65V5, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  R0            12             159
  R1             2               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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALPK2 MUTATED                                  1     2
  ALPK2 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN
  ALPK2 MUTATED                           3
  ALPK2 WILD-TYPE                        22
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ALPK2 MUTATED                                           0    12
  ALPK2 WILD-TYPE                                         7   181
D65V6, multiclass
                                           clus
vv                                          ALPK2 MUTATED ALPK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      1               2
  ASIAN                                                 2              11
  BLACK OR AFRICAN AMERICAN                             3              22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                12             181
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                 cls
clus                0   1
  ALPK2 MUTATED     1  11
  ALPK2 WILD-TYPE   3 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED      1   11
  ALPK2 WILD-TYPE    3  156
                        clus
vv                       ALPK2 MUTATED ALPK2 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            11             156
[1] 2 2
[1] FALSE

Clustering(66) Variable = POLE MUTATION ANALYSIS
D66V1, survival
                sevent
clus2              0   1
  POLE MUTATED    25   2
  POLE WILD-TYPE 199  22
  POLE MUTATED POLE WILD-TYPE 
            27            221 
  POLE MUTATED POLE WILD-TYPE 
             2             22 
$`POLE MUTATED`
TCGA-A5-A0GP TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       46.55        42.35        83.67        23.31        86.07         8.22 
TCGA-AP-A0LM TCGA-AP-A1DQ TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY 
       27.12        41.95        46.45        40.11        65.88        32.55 
TCGA-B5-A11E TCGA-B5-A11H TCGA-B5-A11N TCGA-B5-A11Y TCGA-BG-A0LX TCGA-BG-A0VX 
        8.71        88.34        43.96        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        15.95 
TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
        1.18        21.99         5.95        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89         7.86        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
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        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 
       60.66        35.01        28.54        37.78        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        40.67        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O 
      185.79       113.36        75.72        54.44        44.78        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       26.66        16.34        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE 
       12.56        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-BK-A13C 
       35.90        34.98         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        23.47        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        67.20        88.34 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       82.39        81.57        72.72        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  POLE MUTATED POLE WILD-TYPE 
          1.78           0.56 
  POLE MUTATED POLE WILD-TYPE 
         88.34         185.79 
  POLE MUTATED POLE WILD-TYPE 
         40.11          28.64 
[1] "1.8 - 88.3 (40.1)"  "0.6 - 185.8 (28.6)"
[1] "hr=" "1.6"
D66V2, continuous
                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
D66V3, 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"
D66V4, binary
                cls
clus               0   1
  POLE MUTATED     6  21
  POLE WILD-TYPE  80 141
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLE MUTATED      6   21
  POLE WILD-TYPE   80  141
     clus
vv    POLE MUTATED POLE WILD-TYPE
  NO             6             80
  YES           21            141
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  POLE MUTATED    17   2   0   3
  POLE WILD-TYPE 154   9   7  15
D66V5, multiclass
    clus
vv   POLE MUTATED POLE WILD-TYPE
  R0           17            154
  R1            2              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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POLE MUTATED                                  0     3
  POLE WILD-TYPE                                3    10
                vv
clus             BLACK OR AFRICAN AMERICAN
  POLE MUTATED                           1
  POLE WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  POLE MUTATED                                           1    21
  POLE WILD-TYPE                                         6   172
D66V6, multiclass
                                           clus
vv                                          POLE MUTATED POLE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                3             10
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                               21            172
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                cls
clus               0   1
  POLE MUTATED     1  17
  POLE WILD-TYPE   3 150
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLE MUTATED      1   17
  POLE WILD-TYPE    3  150
                        clus
vv                       POLE MUTATED POLE WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           17            150
[1] 2 2
[1] FALSE

Clustering(67) Variable = KIF20B MUTATION ANALYSIS
D67V1, survival
                  sevent
clus2                0   1
  KIF20B MUTATED    21   0
  KIF20B WILD-TYPE 203  24
  KIF20B MUTATED KIF20B WILD-TYPE 
              21              227 
  KIF20B MUTATED KIF20B WILD-TYPE 
               0               24 
$`KIF20B MUTATED`
TCGA-A5-A0GP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z 
       46.55        83.67        86.07         8.22        27.12        46.45 
TCGA-AX-A063 TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11H 
       66.58        40.11        32.55        11.01         8.71        88.34 
TCGA-B5-A11N TCGA-B5-A11Y TCGA-BG-A186 TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A0ZS 
       43.96        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A 
       15.95         1.18        21.99         5.95        23.31        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        45.53        36.89         7.86        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        31.73        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        41.95        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A064 
       29.69        68.35        72.03        35.34        45.99        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       65.88        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       80.38        56.91        46.75        43.13        40.67        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J 
       17.10        17.85       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        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A187 
       28.54        52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74         4.44        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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  KIF20B MUTATED KIF20B WILD-TYPE 
            1.78             0.56 
  KIF20B MUTATED KIF20B WILD-TYPE 
           88.34           185.79 
  KIF20B MUTATED KIF20B WILD-TYPE 
           32.55            29.06 
[1] "1.8 - 88.3 (32.5)"  "0.6 - 185.8 (29.1)"
[1] "hr="     "7.6e+07"
D67V2, continuous
                  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
D67V3, 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"
D67V4, binary
                  cls
clus                 0   1
  KIF20B MUTATED     6  15
  KIF20B WILD-TYPE  80 147
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF20B MUTATED      6   15
  KIF20B WILD-TYPE   80  147
     clus
vv    KIF20B MUTATED KIF20B WILD-TYPE
  NO               6               80
  YES             15              147
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  KIF20B MUTATED    13   1   0   1
  KIF20B WILD-TYPE 158  10   7  17
D67V5, multiclass
    clus
vv   KIF20B MUTATED KIF20B WILD-TYPE
  R0             13              158
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIF20B MUTATED                                  0     2
  KIF20B WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  KIF20B MUTATED                           2
  KIF20B WILD-TYPE                        23
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIF20B MUTATED                                           1    15
  KIF20B WILD-TYPE                                         6   178
D67V6, multiclass
                                           clus
vv                                          KIF20B MUTATED KIF20B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              2               23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                 15              178
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                  cls
clus                 0   1
  KIF20B MUTATED     1  11
  KIF20B WILD-TYPE   3 156
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF20B MUTATED      1   11
  KIF20B WILD-TYPE    3  156
                        clus
vv                       KIF20B MUTATED KIF20B WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             11              156
[1] 2 2
[1] FALSE

Clustering(68) Variable = C14ORF166B MUTATION ANALYSIS
D68V1, survival
                      sevent
clus2                    0   1
  C14ORF166B MUTATED    10   0
  C14ORF166B WILD-TYPE 214  24
  C14ORF166B MUTATED C14ORF166B WILD-TYPE 
                  10                  238 
  C14ORF166B MUTATED C14ORF166B WILD-TYPE 
                   0                   24 
$`C14ORF166B MUTATED`
TCGA-AP-A056 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-BG-A0VW TCGA-BS-A0TC 
       86.07        32.55         8.71        43.96        16.34        85.55 
TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A17Q 
       85.84        73.25        21.99         1.78 

$`C14ORF166B WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       40.11        65.88        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        17.85        11.01       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        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       24.39        26.66        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE 
       10.16        24.99        46.95        23.47        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 
       67.20        88.34        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74         4.44        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  C14ORF166B MUTATED C14ORF166B WILD-TYPE 
                1.78                 0.56 
  C14ORF166B MUTATED C14ORF166B WILD-TYPE 
               86.07               185.79 
  C14ORF166B MUTATED C14ORF166B WILD-TYPE 
              38.255               28.865 
[1] "1.8 - 86.1 (38.3)"  "0.6 - 185.8 (28.9)"
[1] "hr="     "2.6e+07"
D68V2, continuous
                      vv
clus                   ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  C14ORF166B MUTATED                                        10
  C14ORF166B WILD-TYPE                                     190
                      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
D68V3, multiclass
                                         clus
vv                                        C14ORF166B MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                 10
  MIXED SEROUS AND ENDOMETRIOID                            0
  SEROUS ENDOMETRIAL ADENOCARCINOMA                        0
                                         clus
vv                                        C14ORF166B WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                  190
  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"
D68V4, binary
                      cls
clus                     0   1
  C14ORF166B MUTATED     1   9
  C14ORF166B WILD-TYPE  85 153
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  C14ORF166B MUTATED      1    9
  C14ORF166B WILD-TYPE   85  153
     clus
vv    C14ORF166B MUTATED C14ORF166B WILD-TYPE
  NO                   1                   85
  YES                  9                  153
[1] 2 2
[1] FALSE
                      vv
clus                    R0  R1  R2  RX
  C14ORF166B MUTATED     7   0   0   0
  C14ORF166B WILD-TYPE 164  11   7  18
D68V5, multiclass
    clus
vv   C14ORF166B MUTATED C14ORF166B WILD-TYPE
  R0                  7                  164
  R1                  0                   11
  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"
                      vv
clus                   AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF166B MUTATED                                  0     2
  C14ORF166B WILD-TYPE                                3    11
                      vv
clus                   BLACK OR AFRICAN AMERICAN
  C14ORF166B MUTATED                           0
  C14ORF166B WILD-TYPE                        25
                      vv
clus                   NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C14ORF166B MUTATED                                           1     7
  C14ORF166B WILD-TYPE                                         6   186
D68V6, multiclass
                                           clus
vv                                          C14ORF166B MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                  1
  WHITE                                                      7
                                           clus
vv                                          C14ORF166B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             3
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                   25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                    6
  WHITE                                                      186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                      cls
clus                     0   1
  C14ORF166B MUTATED     0   6
  C14ORF166B WILD-TYPE   4 161
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  C14ORF166B MUTATED      0    6
  C14ORF166B WILD-TYPE    4  161
                        clus
vv                       C14ORF166B MUTATED C14ORF166B WILD-TYPE
  HISPANIC OR LATINO                      0                    4
  NOT HISPANIC OR LATINO                  6                  161
[1] 2 2
[1] FALSE

Clustering(69) Variable = SLC26A8 MUTATION ANALYSIS
D69V1, survival
                   sevent
clus2                 0   1
  SLC26A8 MUTATED    12   0
  SLC26A8 WILD-TYPE 212  24
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
               12               236 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
                0                24 
$`SLC26A8 MUTATED`
TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY 
        8.22        27.12        46.45        40.11        65.88        32.55 
TCGA-B5-A11E TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A167 TCGA-D1-A16X TCGA-D1-A17Q 
        8.71        85.84        73.25        15.72         3.65         1.78 

$`SLC26A8 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 
       60.66        35.01        28.54        37.78        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        40.67        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
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 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       88.34        82.39        81.57        86.93        72.72        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-A168 
        1.91         3.68        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-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
             1.78              0.56 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
            85.84            185.79 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
           29.835            29.195 
[1] "1.8 - 85.8 (29.8)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "2.6e+07"
D69V2, continuous
                   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
D69V3, 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"
D69V4, binary
                   cls
clus                  0   1
  SLC26A8 MUTATED     3   9
  SLC26A8 WILD-TYPE  83 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A8 MUTATED      3    9
  SLC26A8 WILD-TYPE   83  153
     clus
vv    SLC26A8 MUTATED SLC26A8 WILD-TYPE
  NO                3                83
  YES               9               153
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC26A8 MUTATED     9   1   0   0
  SLC26A8 WILD-TYPE 162  10   7  18
D69V5, multiclass
    clus
vv   SLC26A8 MUTATED SLC26A8 WILD-TYPE
  R0               9               162
  R1               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC26A8 MUTATED                                  0     1
  SLC26A8 WILD-TYPE                                3    12
                   vv
clus                BLACK OR AFRICAN AMERICAN
  SLC26A8 MUTATED                           1
  SLC26A8 WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC26A8 MUTATED                                           1     8
  SLC26A8 WILD-TYPE                                         6   185
D69V6, multiclass
                                           clus
vv                                          SLC26A8 MUTATED SLC26A8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                12
  BLACK OR AFRICAN AMERICAN                               1                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 6
  WHITE                                                   8               185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                   cls
clus                  0   1
  SLC26A8 MUTATED     1   8
  SLC26A8 WILD-TYPE   3 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A8 MUTATED      1    8
  SLC26A8 WILD-TYPE    3  159
                        clus
vv                       SLC26A8 MUTATED SLC26A8 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               8               159
[1] 2 2
[1] FALSE

Clustering(70) Variable = ZNF334 MUTATION ANALYSIS
D70V1, survival
                  sevent
clus2                0   1
  ZNF334 MUTATED    16   1
  ZNF334 WILD-TYPE 208  23
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              17              231 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
               1               23 
$`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         8.22        27.12        46.45 
TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-BS-A0UV TCGA-D1-A103 
       40.11        32.55         8.71        43.96        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        29.06        11.97        42.35        15.95 
TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A 
        1.18        83.67        21.99         5.95        23.31        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        45.53        36.89         7.86        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        31.73        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        41.95        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        68.35        72.03        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       34.98        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       37.78        65.88        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        17.85        11.01       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        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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-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-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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  ZNF334 MUTATED ZNF334 WILD-TYPE 
            1.78             0.56 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
           86.07           185.79 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
           27.12            29.33 
[1] "1.8 - 86.1 (27.1)"  "0.6 - 185.8 (29.3)"
[1] "hr=" "1.4"
D70V2, continuous
                  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
D70V3, 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"
D70V4, binary
                  cls
clus                 0   1
  ZNF334 MUTATED     6  11
  ZNF334 WILD-TYPE  80 151
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED      6   11
  ZNF334 WILD-TYPE   80  151
     clus
vv    ZNF334 MUTATED ZNF334 WILD-TYPE
  NO               6               80
  YES             11              151
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF334 MUTATED    13   1   0   0
  ZNF334 WILD-TYPE 158  10   7  18
D70V5, multiclass
    clus
vv   ZNF334 MUTATED ZNF334 WILD-TYPE
  R0             13              158
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF334 MUTATED                                  0     1
  ZNF334 WILD-TYPE                                3    12
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ZNF334 MUTATED                           1
  ZNF334 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF334 MUTATED                                           1    13
  ZNF334 WILD-TYPE                                         6   180
D70V6, multiclass
                                           clus
vv                                          ZNF334 MUTATED ZNF334 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  1               12
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                 13              180
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                  cls
clus                 0   1
  ZNF334 MUTATED     1  11
  ZNF334 WILD-TYPE   3 156
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED      1   11
  ZNF334 WILD-TYPE    3  156
                        clus
vv                       ZNF334 MUTATED ZNF334 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             11              156
[1] 2 2
[1] FALSE

Clustering(71) Variable = RRAS2 MUTATION ANALYSIS
D71V1, survival
                 sevent
clus2               0   1
  RRAS2 MUTATED     4   0
  RRAS2 WILD-TYPE 220  24
  RRAS2 MUTATED RRAS2 WILD-TYPE 
              4             244 
  RRAS2 MUTATED RRAS2 WILD-TYPE 
              0              24 
$`RRAS2 MUTATED`
TCGA-B5-A0K4 TCGA-BG-A0M4 TCGA-BG-A0YU TCGA-D1-A17U 
       17.88        34.98        14.83        22.92 

$`RRAS2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89         7.86        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
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        41.95        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       34.98        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       37.78        40.11        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       40.67        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       23.01        13.74        17.10        17.85        11.01         8.71 
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 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       35.21         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       28.54        52.83        56.58        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  RRAS2 MUTATED RRAS2 WILD-TYPE 
          14.83            0.56 
  RRAS2 MUTATED RRAS2 WILD-TYPE 
          34.98          185.79 
  RRAS2 MUTATED RRAS2 WILD-TYPE 
          20.40           29.51 
[1] "14.8 - 35.0 (20.4)" "0.6 - 185.8 (29.5)"
[1] "hr="     "9100000"
D71V2, continuous
                 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
D71V3, 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"
D71V4, binary
                 cls
clus                0   1
  RRAS2 MUTATED     2   2
  RRAS2 WILD-TYPE  84 160
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRAS2 MUTATED      2    2
  RRAS2 WILD-TYPE   84  160
     clus
vv    RRAS2 MUTATED RRAS2 WILD-TYPE
  NO              2              84
  YES             2             160
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RRAS2 MUTATED     2   0   0   1
  RRAS2 WILD-TYPE 169  11   7  17
D71V5, multiclass
    clus
vv   RRAS2 MUTATED RRAS2 WILD-TYPE
  R0             2             169
  R1             0              11
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RRAS2 MUTATED                                  0     0
  RRAS2 WILD-TYPE                                3    13
                 vv
clus              BLACK OR AFRICAN AMERICAN
  RRAS2 MUTATED                           0
  RRAS2 WILD-TYPE                        25
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RRAS2 MUTATED                                           0     3
  RRAS2 WILD-TYPE                                         7   190
D71V6, multiclass
                                           clus
vv                                          RRAS2 MUTATED RRAS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 0              13
  BLACK OR AFRICAN AMERICAN                             0              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                 3             190
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                 cls
clus                0   1
  RRAS2 MUTATED     0   3
  RRAS2 WILD-TYPE   4 164
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRAS2 MUTATED      0    3
  RRAS2 WILD-TYPE    4  164
                        clus
vv                       RRAS2 MUTATED RRAS2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             164
[1] 2 2
[1] FALSE

Clustering(72) Variable = PPM1N MUTATION ANALYSIS
D72V1, survival
                 sevent
clus2               0   1
  PPM1N MUTATED     7   0
  PPM1N WILD-TYPE 217  24
  PPM1N MUTATED PPM1N WILD-TYPE 
              7             241 
  PPM1N MUTATED PPM1N WILD-TYPE 
              0              24 
$`PPM1N MUTATED`
TCGA-AP-A051 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J1 TCGA-BS-A0UF TCGA-D1-A103 
       83.67        27.12        46.45        65.88        85.84        21.99 
TCGA-D1-A16Y 
       17.49 

$`PPM1N WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        40.11        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       46.75        43.13        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         8.71       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  PPM1N MUTATED PPM1N WILD-TYPE 
          17.49            0.56 
  PPM1N MUTATED PPM1N WILD-TYPE 
          85.84          185.79 
  PPM1N MUTATED PPM1N WILD-TYPE 
          46.45           29.06 
[1] "17.5 - 85.8 (46.5)" "0.6 - 185.8 (29.1)"
[1] "hr="     "2.6e+07"
D72V2, continuous
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PPM1N MUTATED                                         7
  PPM1N WILD-TYPE                                     193
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  PPM1N MUTATED                               0
  PPM1N WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  PPM1N MUTATED                                   0
  PPM1N WILD-TYPE                                44
D72V3, multiclass
                                         clus
vv                                        PPM1N MUTATED PPM1N 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"
D72V4, binary
                 cls
clus                0   1
  PPM1N MUTATED     2   5
  PPM1N WILD-TYPE  84 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1N MUTATED      2    5
  PPM1N WILD-TYPE   84  157
     clus
vv    PPM1N MUTATED PPM1N WILD-TYPE
  NO              2              84
  YES             5             157
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PPM1N MUTATED     5   1   0   1
  PPM1N WILD-TYPE 166  10   7  17
D72V5, multiclass
    clus
vv   PPM1N MUTATED PPM1N WILD-TYPE
  R0             5             166
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPM1N MUTATED                                  0     1
  PPM1N WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  PPM1N MUTATED                           1
  PPM1N WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPM1N MUTATED                                           0     4
  PPM1N WILD-TYPE                                         7   189
D72V6, multiclass
                                           clus
vv                                          PPM1N MUTATED PPM1N WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                 4             189
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                 cls
clus                0   1
  PPM1N MUTATED     1   4
  PPM1N WILD-TYPE   3 163
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1N MUTATED      1    4
  PPM1N WILD-TYPE    3  163
                        clus
vv                       PPM1N MUTATED PPM1N WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             4             163
[1] 2 2
[1] FALSE

Clustering(73) Variable = FCN1 MUTATION ANALYSIS
D73V1, survival
                sevent
clus2              0   1
  FCN1 MUTATED     7   1
  FCN1 WILD-TYPE 217  23
  FCN1 MUTATED FCN1 WILD-TYPE 
             8            240 
  FCN1 MUTATED FCN1 WILD-TYPE 
             1             23 
$`FCN1 MUTATED`
TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-B5-A11N TCGA-BG-A0MI TCGA-BS-A0TC 
        8.22        27.12        40.11        43.96        23.47        85.55 
TCGA-BS-A0UV TCGA-D1-A103 
       73.25        21.99 

$`FCN1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        35.01        28.54        37.78        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        46.75        43.13        40.67        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         8.71       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        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MO 
       38.37        36.49        28.27        41.52        48.56        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE 
       10.16        24.99        46.95        23.47        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 
       67.20        88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  FCN1 MUTATED FCN1 WILD-TYPE 
          8.22           0.56 
  FCN1 MUTATED FCN1 WILD-TYPE 
         85.55         185.79 
  FCN1 MUTATED FCN1 WILD-TYPE 
        33.615         29.195 
[1] "8.2 - 85.5 (33.6)"  "0.6 - 185.8 (29.2)"
[1] "hr=" "1.1"
D73V2, continuous
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  FCN1 MUTATED                                         8
  FCN1 WILD-TYPE                                     192
                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
D73V3, multiclass
                                         clus
vv                                        FCN1 MUTATED FCN1 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"
D73V4, binary
                cls
clus               0   1
  FCN1 MUTATED     2   6
  FCN1 WILD-TYPE  84 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  FCN1 MUTATED      2    6
  FCN1 WILD-TYPE   84  156
     clus
vv    FCN1 MUTATED FCN1 WILD-TYPE
  NO             2             84
  YES            6            156
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FCN1 MUTATED     7   0   0   0
  FCN1 WILD-TYPE 164  11   7  18
D73V5, multiclass
    clus
vv   FCN1 MUTATED FCN1 WILD-TYPE
  R0            7            164
  R1            0             11
  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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FCN1 MUTATED                                  0     1
  FCN1 WILD-TYPE                                3    12
                vv
clus             BLACK OR AFRICAN AMERICAN
  FCN1 MUTATED                           1
  FCN1 WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FCN1 MUTATED                                           1     5
  FCN1 WILD-TYPE                                         6   188
D73V6, multiclass
                                           clus
vv                                          FCN1 MUTATED FCN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                1             12
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                                5            188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                cls
clus               0   1
  FCN1 MUTATED     0   6
  FCN1 WILD-TYPE   4 161
[1] "tbl2"
                cls
clus             [,1] [,2]
  FCN1 MUTATED      0    6
  FCN1 WILD-TYPE    4  161
                        clus
vv                       FCN1 MUTATED FCN1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            161
[1] 2 2
[1] FALSE

Clustering(74) Variable = TIAL1 MUTATION ANALYSIS
D74V1, survival
                 sevent
clus2               0   1
  TIAL1 MUTATED    10   0
  TIAL1 WILD-TYPE 214  24
  TIAL1 MUTATED TIAL1 WILD-TYPE 
             10             238 
  TIAL1 MUTATED TIAL1 WILD-TYPE 
              0              24 
$`TIAL1 MUTATED`
TCGA-A5-A0GB TCGA-AP-A051 TCGA-AP-A059 TCGA-AX-A06H TCGA-AX-A0J1 TCGA-B5-A11E 
       32.78        83.67         8.22        27.39        65.88         8.71 
TCGA-B5-A11N TCGA-BS-A0UF TCGA-D1-A103 TCGA-D1-A17Q 
       43.96        85.84        21.99         1.78 

$`TIAL1 WILD-TYPE`
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         3.22       105.37 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
       15.95         1.18        21.99         5.95        23.31        86.07 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06L 
       35.34        45.99        66.58        34.98        53.92        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        40.11        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       43.13        40.67        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       11.01       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        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74         4.44        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  TIAL1 MUTATED TIAL1 WILD-TYPE 
           1.78            0.56 
  TIAL1 MUTATED TIAL1 WILD-TYPE 
          85.84          185.79 
  TIAL1 MUTATED TIAL1 WILD-TYPE 
         30.085          29.195 
[1] "1.8 - 85.8 (30.1)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "2.6e+07"
D74V2, continuous
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  TIAL1 MUTATED                                        10
  TIAL1 WILD-TYPE                                     190
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  TIAL1 MUTATED                               0
  TIAL1 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  TIAL1 MUTATED                                   0
  TIAL1 WILD-TYPE                                44
D74V3, multiclass
                                         clus
vv                                        TIAL1 MUTATED TIAL1 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"
D74V4, binary
                 cls
clus                0   1
  TIAL1 MUTATED     3   7
  TIAL1 WILD-TYPE  83 155
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIAL1 MUTATED      3    7
  TIAL1 WILD-TYPE   83  155
     clus
vv    TIAL1 MUTATED TIAL1 WILD-TYPE
  NO              3              83
  YES             7             155
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TIAL1 MUTATED     7   1   0   0
  TIAL1 WILD-TYPE 164  10   7  18
D74V5, multiclass
    clus
vv   TIAL1 MUTATED TIAL1 WILD-TYPE
  R0             7             164
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TIAL1 MUTATED                                  1     1
  TIAL1 WILD-TYPE                                2    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  TIAL1 MUTATED                           0
  TIAL1 WILD-TYPE                        25
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TIAL1 MUTATED                                           0     8
  TIAL1 WILD-TYPE                                         7   185
D74V6, multiclass
                                           clus
vv                                          TIAL1 MUTATED TIAL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      1               2
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             0              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                 8             185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                 cls
clus                0   1
  TIAL1 MUTATED     0   6
  TIAL1 WILD-TYPE   4 161
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIAL1 MUTATED      0    6
  TIAL1 WILD-TYPE    4  161
                        clus
vv                       TIAL1 MUTATED TIAL1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             161
[1] 2 2
[1] FALSE

Clustering(75) Variable = PSMC4 MUTATION ANALYSIS
D75V1, survival
                 sevent
clus2               0   1
  PSMC4 MUTATED    11   0
  PSMC4 WILD-TYPE 213  24
  PSMC4 MUTATED PSMC4 WILD-TYPE 
             11             237 
  PSMC4 MUTATED PSMC4 WILD-TYPE 
              0              24 
$`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         8.22        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        15.95 
TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A 
        1.18        83.67        21.99         5.95        23.31        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        45.53        36.89         7.86        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        31.73        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        41.95        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       28.54        37.78        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       40.67        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        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-A0V6 
       67.20        88.34        82.39        81.57        72.72        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-A168 
        1.91         3.68        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-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-A17H TCGA-D1-A17K 
        1.58         7.00         0.99        30.44        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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  PSMC4 MUTATED PSMC4 WILD-TYPE 
           1.28            0.56 
  PSMC4 MUTATED PSMC4 WILD-TYPE 
          86.93          185.79 
  PSMC4 MUTATED PSMC4 WILD-TYPE 
          42.35           28.67 
[1] "1.3 - 86.9 (42.4)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.7e+07"
D75V2, continuous
                 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
D75V3, 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"
D75V4, binary
                 cls
clus                0   1
  PSMC4 MUTATED     5   6
  PSMC4 WILD-TYPE  81 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMC4 MUTATED      5    6
  PSMC4 WILD-TYPE   81  156
     clus
vv    PSMC4 MUTATED PSMC4 WILD-TYPE
  NO              5              81
  YES             6             156
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PSMC4 MUTATED    11   0   0   0
  PSMC4 WILD-TYPE 160  11   7  18
D75V5, multiclass
    clus
vv   PSMC4 MUTATED PSMC4 WILD-TYPE
  R0            11             160
  R1             0              11
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PSMC4 MUTATED                                  0     2
  PSMC4 WILD-TYPE                                3    11
                 vv
clus              BLACK OR AFRICAN AMERICAN
  PSMC4 MUTATED                           1
  PSMC4 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PSMC4 MUTATED                                           1     7
  PSMC4 WILD-TYPE                                         6   186
D75V6, multiclass
                                           clus
vv                                          PSMC4 MUTATED PSMC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 2              11
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                 7             186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                 cls
clus                0   1
  PSMC4 MUTATED     0   9
  PSMC4 WILD-TYPE   4 158
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMC4 MUTATED      0    9
  PSMC4 WILD-TYPE    4  158
                        clus
vv                       PSMC4 MUTATED PSMC4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             158
[1] 2 2
[1] FALSE

Clustering(76) Variable = MFAP5 MUTATION ANALYSIS
D76V1, survival
                 sevent
clus2               0   1
  MFAP5 MUTATED     9   0
  MFAP5 WILD-TYPE 215  24
  MFAP5 MUTATED MFAP5 WILD-TYPE 
              9             239 
  MFAP5 MUTATED MFAP5 WILD-TYPE 
              0              24 
$`MFAP5 MUTATED`
TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11Y 
        8.22        27.12        46.45        40.11        32.55        18.41 
TCGA-BG-A0M4 TCGA-BS-A0UF TCGA-D1-A15X 
       34.98        85.84        29.88 

$`MFAP5 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        40.67        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z 
       27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       20.94        35.21         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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-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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  MFAP5 MUTATED MFAP5 WILD-TYPE 
           8.22            0.56 
  MFAP5 MUTATED MFAP5 WILD-TYPE 
          85.84          185.79 
  MFAP5 MUTATED MFAP5 WILD-TYPE 
          32.55           28.67 
[1] "8.2 - 85.8 (32.5)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.6e+07"
D76V2, continuous
                 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
D76V3, 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"
D76V4, binary
                 cls
clus                0   1
  MFAP5 MUTATED     3   6
  MFAP5 WILD-TYPE  83 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFAP5 MUTATED      3    6
  MFAP5 WILD-TYPE   83  156
     clus
vv    MFAP5 MUTATED MFAP5 WILD-TYPE
  NO              3              83
  YES             6             156
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MFAP5 MUTATED     6   1   0   0
  MFAP5 WILD-TYPE 165  10   7  18
D76V5, multiclass
    clus
vv   MFAP5 MUTATED MFAP5 WILD-TYPE
  R0             6             165
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MFAP5 MUTATED                                  0     1
  MFAP5 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  MFAP5 MUTATED                           1
  MFAP5 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MFAP5 MUTATED                                           0     6
  MFAP5 WILD-TYPE                                         7   187
D76V6, multiclass
                                           clus
vv                                          MFAP5 MUTATED MFAP5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                 6             187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                 cls
clus                0   1
  MFAP5 MUTATED     1   5
  MFAP5 WILD-TYPE   3 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFAP5 MUTATED      1    5
  MFAP5 WILD-TYPE    3  162
                        clus
vv                       MFAP5 MUTATED MFAP5 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             5             162
[1] 2 2
[1] FALSE

Clustering(77) Variable = RAB3GAP1 MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  RAB3GAP1 MUTATED    15   1
  RAB3GAP1 WILD-TYPE 209  23
  RAB3GAP1 MUTATED RAB3GAP1 WILD-TYPE 
                16                232 
  RAB3GAP1 MUTATED RAB3GAP1 WILD-TYPE 
                 1                 23 
$`RAB3GAP1 MUTATED`
TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A05W TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A0K9 
       86.07         8.22        68.35        46.45        32.55        11.01 
TCGA-B5-A11E TCGA-B5-A11H TCGA-B5-A11N TCGA-B5-A11U TCGA-B5-A11Y TCGA-BS-A0TA 
        8.71        88.34        43.96        16.73        18.41        23.47 
TCGA-BS-A0TE TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A17Q 
        4.80        73.25        21.99         1.78 

$`RAB3GAP1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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-A05Y TCGA-AX-A060 
       41.95        13.58        19.82        29.69        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       35.01        28.54        37.78        40.11        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        40.67        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O 
      185.79       113.36        75.72        54.44        44.78        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG 
       10.16        24.99        46.95        85.55        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       88.34        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74         4.44        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  RAB3GAP1 MUTATED RAB3GAP1 WILD-TYPE 
              1.78               0.56 
  RAB3GAP1 MUTATED RAB3GAP1 WILD-TYPE 
             88.34             185.79 
  RAB3GAP1 MUTATED RAB3GAP1 WILD-TYPE 
             22.73              29.51 
[1] "1.8 - 88.3 (22.7)"  "0.6 - 185.8 (29.5)"
[1] "hr=" "1.5"
D77V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  RAB3GAP1 MUTATED                                        16
  RAB3GAP1 WILD-TYPE                                     184
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  RAB3GAP1 MUTATED                               0
  RAB3GAP1 WILD-TYPE                             4
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  RAB3GAP1 MUTATED                                   0
  RAB3GAP1 WILD-TYPE                                44
D77V3, multiclass
                                         clus
vv                                        RAB3GAP1 MUTATED RAB3GAP1 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"
D77V4, binary
                    cls
clus                   0   1
  RAB3GAP1 MUTATED     5  11
  RAB3GAP1 WILD-TYPE  81 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAB3GAP1 MUTATED      5   11
  RAB3GAP1 WILD-TYPE   81  151
     clus
vv    RAB3GAP1 MUTATED RAB3GAP1 WILD-TYPE
  NO                 5                 81
  YES               11                151
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  RAB3GAP1 MUTATED     6   1   1   1
  RAB3GAP1 WILD-TYPE 165  10   6  17
D77V5, multiclass
    clus
vv   RAB3GAP1 MUTATED RAB3GAP1 WILD-TYPE
  R0                6                165
  R1                1                 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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAB3GAP1 MUTATED                                  0     1
  RAB3GAP1 WILD-TYPE                                3    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  RAB3GAP1 MUTATED                           1
  RAB3GAP1 WILD-TYPE                        24
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RAB3GAP1 MUTATED                                           2    11
  RAB3GAP1 WILD-TYPE                                         5   182
D77V6, multiclass
                                           clus
vv                                          RAB3GAP1 MUTATED RAB3GAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    1                 12
  BLACK OR AFRICAN AMERICAN                                1                 24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  5
  WHITE                                                   11                182
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                    cls
clus                   0   1
  RAB3GAP1 MUTATED     2   6
  RAB3GAP1 WILD-TYPE   2 161
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAB3GAP1 MUTATED      2    6
  RAB3GAP1 WILD-TYPE    2  161
                        clus
vv                       RAB3GAP1 MUTATED RAB3GAP1 WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO                6                161
[1] 2 2
[1] FALSE

Clustering(78) Variable = MSH6 MUTATION ANALYSIS
D78V1, survival
                sevent
clus2              0   1
  MSH6 MUTATED    16   1
  MSH6 WILD-TYPE 208  23
  MSH6 MUTATED MSH6 WILD-TYPE 
            17            231 
  MSH6 MUTATED MSH6 WILD-TYPE 
             1             23 
$`MSH6 MUTATED`
TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LE TCGA-AP-A0LM 
       42.35        83.67        86.07         8.22       110.37        27.12 
TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11R TCGA-BG-A0M4 
       46.45        40.11        32.55         8.71        33.50        34.98 
TCGA-BG-A0M6 TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A17Q 
        7.92        85.84        73.25        21.99         1.78 

$`MSH6 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A 
       15.95         1.18        21.99         5.95        23.31        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        45.53        36.89         7.86        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        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        41.95        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       68.35        72.03        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       65.88        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       80.38        56.91        46.75        43.13        40.67        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        17.85        11.01       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        43.96        40.50        32.09 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M8 TCGA-BG-A0M9 
       19.33        20.94        35.21        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       88.34        82.39        81.57        86.93        72.72        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  MSH6 MUTATED MSH6 WILD-TYPE 
          1.78           0.56 
  MSH6 MUTATED MSH6 WILD-TYPE 
        110.37         185.79 
  MSH6 MUTATED MSH6 WILD-TYPE 
         34.98          28.64 
[1] "1.8 - 110.4 (35.0)" "0.6 - 185.8 (28.6)"
[1] "hr=" "1.9"
D78V2, continuous
                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
D78V3, 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"
D78V4, binary
                cls
clus               0   1
  MSH6 MUTATED     8   9
  MSH6 WILD-TYPE  78 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH6 MUTATED      8    9
  MSH6 WILD-TYPE   78  153
     clus
vv    MSH6 MUTATED MSH6 WILD-TYPE
  NO             8             78
  YES            9            153
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MSH6 MUTATED    13   1   0   0
  MSH6 WILD-TYPE 158  10   7  18
D78V5, multiclass
    clus
vv   MSH6 MUTATED MSH6 WILD-TYPE
  R0           13            158
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MSH6 MUTATED                                  0     1
  MSH6 WILD-TYPE                                3    12
                vv
clus             BLACK OR AFRICAN AMERICAN
  MSH6 MUTATED                           2
  MSH6 WILD-TYPE                        23
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MSH6 MUTATED                                           1    12
  MSH6 WILD-TYPE                                         6   181
D78V6, multiclass
                                           clus
vv                                          MSH6 MUTATED MSH6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                1             12
  BLACK OR AFRICAN AMERICAN                            2             23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                               12            181
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                cls
clus               0   1
  MSH6 MUTATED     1   9
  MSH6 WILD-TYPE   3 158
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH6 MUTATED      1    9
  MSH6 WILD-TYPE    3  158
                        clus
vv                       MSH6 MUTATED MSH6 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            9            158
[1] 2 2
[1] FALSE

Clustering(79) Variable = BMP2K MUTATION ANALYSIS
D79V1, survival
                 sevent
clus2               0   1
  BMP2K MUTATED    13   0
  BMP2K WILD-TYPE 211  24
  BMP2K MUTATED BMP2K WILD-TYPE 
             13             235 
  BMP2K MUTATED BMP2K WILD-TYPE 
              0              24 
$`BMP2K MUTATED`
TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A059 TCGA-AX-A05Z TCGA-AX-A0J1 TCGA-B5-A0JR 
       42.35        83.67         8.22        46.45        65.88        56.91 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-D1-A103 TCGA-D1-A16X TCGA-D1-A17A TCGA-D1-A17Q 
       32.55         8.71        21.99         3.65         1.58         1.78 
TCGA-D1-A17T 
        2.33 

$`BMP2K WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
       15.95         1.18        21.99         5.95        23.31        86.07 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        40.11        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JT 
       36.39        71.24        19.36        80.38        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       17.88        13.74        17.10        17.85        11.01       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        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        67.20        88.34 
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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74         4.44        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-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-A17U 
       26.37        10.22         1.51        11.15        24.30        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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  BMP2K MUTATED BMP2K WILD-TYPE 
           1.58            0.56 
  BMP2K MUTATED BMP2K WILD-TYPE 
          83.67          185.79 
  BMP2K MUTATED BMP2K WILD-TYPE 
          21.99           29.33 
[1] "1.6 - 83.7 (22.0)"  "0.6 - 185.8 (29.3)"
[1] "hr="     "2.6e+07"
D79V2, continuous
                 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
D79V3, 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"
D79V4, binary
                 cls
clus                0   1
  BMP2K MUTATED     3  10
  BMP2K WILD-TYPE  83 152
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP2K MUTATED      3   10
  BMP2K WILD-TYPE   83  152
     clus
vv    BMP2K MUTATED BMP2K WILD-TYPE
  NO              3              83
  YES            10             152
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BMP2K MUTATED     9   1   0   0
  BMP2K WILD-TYPE 162  10   7  18
D79V5, multiclass
    clus
vv   BMP2K MUTATED BMP2K WILD-TYPE
  R0             9             162
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BMP2K MUTATED                                  0     0
  BMP2K WILD-TYPE                                3    13
                 vv
clus              BLACK OR AFRICAN AMERICAN
  BMP2K MUTATED                           0
  BMP2K WILD-TYPE                        25
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BMP2K MUTATED                                           0    12
  BMP2K WILD-TYPE                                         7   181
D79V6, multiclass
                                           clus
vv                                          BMP2K MUTATED BMP2K WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 0              13
  BLACK OR AFRICAN AMERICAN                             0              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                12             181
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                 cls
clus                0   1
  BMP2K MUTATED     1   8
  BMP2K WILD-TYPE   3 159
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP2K MUTATED      1    8
  BMP2K WILD-TYPE    3  159
                        clus
vv                       BMP2K MUTATED BMP2K WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             8             159
[1] 2 2
[1] FALSE

Clustering(80) Variable = ZNF606 MUTATION ANALYSIS
D80V1, survival
                  sevent
clus2                0   1
  ZNF606 MUTATED    16   0
  ZNF606 WILD-TYPE 208  24
  ZNF606 MUTATED ZNF606 WILD-TYPE 
              16              232 
  ZNF606 MUTATED ZNF606 WILD-TYPE 
               0               24 
$`ZNF606 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A05Z TCGA-AX-A063 TCGA-AX-A0J0 
       83.67        86.07         8.22        46.45        66.58        40.11 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-BG-A0MG TCGA-BS-A0TA TCGA-BS-A0UV 
       32.55         8.71        43.96        48.56        23.47        73.25 
TCGA-D1-A0ZO TCGA-D1-A103 TCGA-D1-A16Y TCGA-D1-A17Q 
       19.79        21.99        17.49         1.78 

$`ZNF606 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       28.54        37.78        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       17.88        13.74        17.10        17.85        11.01       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        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MI 
        7.92        38.37        36.49        28.27        41.52        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TC TCGA-BS-A0TD 
       10.22        10.16        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-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        67.20        88.34        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        62.79        63.58        49.55        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-A102 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  ZNF606 MUTATED ZNF606 WILD-TYPE 
            1.78             0.56 
  ZNF606 MUTATED ZNF606 WILD-TYPE 
           86.07           185.79 
  ZNF606 MUTATED ZNF606 WILD-TYPE 
          36.330           28.865 
[1] "1.8 - 86.1 (36.3)"  "0.6 - 185.8 (28.9)"
[1] "hr="     "2.7e+07"
D80V2, continuous
                  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
D80V3, 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"
D80V4, binary
                  cls
clus                 0   1
  ZNF606 MUTATED     4  12
  ZNF606 WILD-TYPE  82 150
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF606 MUTATED      4   12
  ZNF606 WILD-TYPE   82  150
     clus
vv    ZNF606 MUTATED ZNF606 WILD-TYPE
  NO               4               82
  YES             12              150
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF606 MUTATED    10   1   0   2
  ZNF606 WILD-TYPE 161  10   7  16
D80V5, multiclass
    clus
vv   ZNF606 MUTATED ZNF606 WILD-TYPE
  R0             10              161
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF606 MUTATED                                  0     0
  ZNF606 WILD-TYPE                                3    13
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ZNF606 MUTATED                           0
  ZNF606 WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF606 MUTATED                                           2    13
  ZNF606 WILD-TYPE                                         5   180
D80V6, multiclass
                                           clus
vv                                          ZNF606 MUTATED ZNF606 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  0               13
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              2                5
  WHITE                                                 13              180
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                  cls
clus                 0   1
  ZNF606 MUTATED     2   9
  ZNF606 WILD-TYPE   2 158
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF606 MUTATED      2    9
  ZNF606 WILD-TYPE    2  158
                        clus
vv                       ZNF606 MUTATED ZNF606 WILD-TYPE
  HISPANIC OR LATINO                  2                2
  NOT HISPANIC OR LATINO              9              158
[1] 2 2
[1] FALSE

Clustering(81) Variable = ZNF263 MUTATION ANALYSIS
D81V1, survival
                  sevent
clus2                0   1
  ZNF263 MUTATED     7   0
  ZNF263 WILD-TYPE 217  24
  ZNF263 MUTATED ZNF263 WILD-TYPE 
               7              241 
  ZNF263 MUTATED ZNF263 WILD-TYPE 
               0               24 
$`ZNF263 MUTATED`
TCGA-A5-A0GB TCGA-AP-A0LM TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A11G TCGA-D1-A101 
       32.78        27.12        46.45        32.55       113.36         1.74 
TCGA-D1-A17Q 
        1.78 

$`ZNF263 WILD-TYPE`
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         3.22       105.37 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        37.78        40.11        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01         8.71       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A102 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         4.44        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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  ZNF263 MUTATED ZNF263 WILD-TYPE 
            1.74             0.56 
  ZNF263 MUTATED ZNF263 WILD-TYPE 
          113.36           185.79 
  ZNF263 MUTATED ZNF263 WILD-TYPE 
           32.55            29.06 
[1] "1.7 - 113.4 (32.5)" "0.6 - 185.8 (29.1)"
[1] "hr="     "9300000"
D81V2, continuous
                  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
D81V3, 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"
D81V4, binary
                  cls
clus                 0   1
  ZNF263 MUTATED     2   5
  ZNF263 WILD-TYPE  84 157
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF263 MUTATED      2    5
  ZNF263 WILD-TYPE   84  157
     clus
vv    ZNF263 MUTATED ZNF263 WILD-TYPE
  NO               2               84
  YES              5              157
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF263 MUTATED     3   1   0   1
  ZNF263 WILD-TYPE 168  10   7  17
D81V5, multiclass
    clus
vv   ZNF263 MUTATED ZNF263 WILD-TYPE
  R0              3              168
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF263 MUTATED                                  0     0
  ZNF263 WILD-TYPE                                3    13
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ZNF263 MUTATED                           2
  ZNF263 WILD-TYPE                        23
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF263 MUTATED                                           0     4
  ZNF263 WILD-TYPE                                         7   189
D81V6, multiclass
                                           clus
vv                                          ZNF263 MUTATED ZNF263 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  0               13
  BLACK OR AFRICAN AMERICAN                              2               23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                  4              189
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V7, binary
                  cls
clus                 0   1
  ZNF263 MUTATED     1   2
  ZNF263 WILD-TYPE   3 165
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF263 MUTATED      1    2
  ZNF263 WILD-TYPE    3  165
                        clus
vv                       ZNF263 MUTATED ZNF263 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              2              165
[1] 2 2
[1] FALSE

Clustering(82) Variable = CHEK2 MUTATION ANALYSIS
D82V1, survival
                 sevent
clus2               0   1
  CHEK2 MUTATED    12   1
  CHEK2 WILD-TYPE 212  23
  CHEK2 MUTATED CHEK2 WILD-TYPE 
             13             235 
  CHEK2 MUTATED CHEK2 WILD-TYPE 
              1              23 
$`CHEK2 MUTATED`
TCGA-A5-A0GI TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       57.53        23.31        86.07        27.12        46.45        40.11 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11J TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A17Q 
       32.55         8.71        54.44        85.84        73.25         1.78 
TCGA-D1-A1NX 
       18.25 

$`CHEK2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37        74.10        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A059 
       15.95         1.18        83.67        21.99         5.95         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       28.54        37.78        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       17.88        13.74        17.10        17.85        11.01       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       22.92        13.22        16.31        35.38        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  CHEK2 MUTATED CHEK2 WILD-TYPE 
           1.78            0.56 
  CHEK2 MUTATED CHEK2 WILD-TYPE 
          86.07          185.79 
  CHEK2 MUTATED CHEK2 WILD-TYPE 
          40.11           28.67 
[1] "1.8 - 86.1 (40.1)"  "0.6 - 185.8 (28.7)"
[1] "hr=" "1.6"
D82V2, continuous
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CHEK2 MUTATED                                        12
  CHEK2 WILD-TYPE                                     188
                 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
D82V3, multiclass
                                         clus
vv                                        CHEK2 MUTATED CHEK2 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"
D82V4, binary
                 cls
clus                0   1
  CHEK2 MUTATED     4   9
  CHEK2 WILD-TYPE  82 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHEK2 MUTATED      4    9
  CHEK2 WILD-TYPE   82  153
     clus
vv    CHEK2 MUTATED CHEK2 WILD-TYPE
  NO              4              82
  YES             9             153
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CHEK2 MUTATED     8   2   0   0
  CHEK2 WILD-TYPE 163   9   7  18
D82V5, multiclass
    clus
vv   CHEK2 MUTATED CHEK2 WILD-TYPE
  R0             8             163
  R1             2               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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHEK2 MUTATED                                  0     1
  CHEK2 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  CHEK2 MUTATED                           1
  CHEK2 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CHEK2 MUTATED                                           1     9
  CHEK2 WILD-TYPE                                         6   184
D82V6, multiclass
                                           clus
vv                                          CHEK2 MUTATED CHEK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                 9             184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V7, binary
                 cls
clus                0   1
  CHEK2 MUTATED     1   7
  CHEK2 WILD-TYPE   3 160
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHEK2 MUTATED      1    7
  CHEK2 WILD-TYPE    3  160
                        clus
vv                       CHEK2 MUTATED CHEK2 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             7             160
[1] 2 2
[1] FALSE

Clustering(83) Variable = MGA MUTATION ANALYSIS
D83V1, survival
               sevent
clus2             0   1
  MGA MUTATED    24   2
  MGA WILD-TYPE 200  22
  MGA MUTATED MGA WILD-TYPE 
           26           222 
  MGA MUTATED MGA WILD-TYPE 
            2            22 
$`MGA MUTATED`
TCGA-A5-A0VP TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N 
       42.35         1.18        83.67        86.07         8.22         7.86 
TCGA-AP-A0LD TCGA-AP-A0LF TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JR 
      117.99         3.39        27.12        46.45        40.11        56.91 
TCGA-B5-A0JY TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11N TCGA-B5-A11Y TCGA-BS-A0TC 
       32.55        11.01         8.71        43.96        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VQ TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D 
       15.95        21.99         5.95        23.31        39.42        57.80 
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 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        65.88        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JT 
       36.39        71.24        19.36        80.38        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A11F TCGA-B5-A11G 
       17.88        13.74        17.10        17.85       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        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TG 
       10.16        24.99        46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       88.34        82.39        81.57        86.93        72.72        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        21.99        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
        3.68        29.33         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-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-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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  MGA MUTATED MGA WILD-TYPE 
         0.99          0.56 
  MGA MUTATED MGA WILD-TYPE 
       117.99        185.79 
  MGA MUTATED MGA WILD-TYPE 
       32.565        28.865 
[1] "1.0 - 118.0 (32.6)" "0.6 - 185.8 (28.9)"
[1] "hr=" "1.3"
D83V2, continuous
               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
D83V3, 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"
D83V4, binary
               cls
clus              0   1
  MGA MUTATED    11  15
  MGA WILD-TYPE  75 147
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     11   15
  MGA WILD-TYPE   75  147
     clus
vv    MGA MUTATED MGA WILD-TYPE
  NO           11            75
  YES          15           147
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MGA MUTATED    16   1   2   0
  MGA WILD-TYPE 155  10   5  18
D83V5, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  R0          16           155
  R1           1            10
  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"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MGA MUTATED                                  0     3
  MGA WILD-TYPE                                3    10
               vv
clus            BLACK OR AFRICAN AMERICAN
  MGA MUTATED                           1
  MGA WILD-TYPE                        24
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MGA MUTATED                                           1    20
  MGA WILD-TYPE                                         6   173
D83V6, multiclass
                                           clus
vv                                          MGA MUTATED MGA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                    0             3
  ASIAN                                               3            10
  BLACK OR AFRICAN AMERICAN                           1            24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           1             6
  WHITE                                              20           173
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V7, binary
               cls
clus              0   1
  MGA MUTATED     1  13
  MGA WILD-TYPE   3 154
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED      1   13
  MGA WILD-TYPE    3  154
                        clus
vv                       MGA MUTATED MGA WILD-TYPE
  HISPANIC OR LATINO               1             3
  NOT HISPANIC OR LATINO          13           154
[1] 2 2
[1] FALSE

Clustering(84) Variable = RHBDD3 MUTATION ANALYSIS
D84V1, survival
                  sevent
clus2                0   1
  RHBDD3 MUTATED     4   0
  RHBDD3 WILD-TYPE 220  24
  RHBDD3 MUTATED RHBDD3 WILD-TYPE 
               4              244 
  RHBDD3 MUTATED RHBDD3 WILD-TYPE 
               0               24 
$`RHBDD3 MUTATED`
TCGA-AP-A051 TCGA-D1-A103 TCGA-D1-A167 TCGA-D1-A17H 
       83.67        21.99        15.72        28.01 

$`RHBDD3 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       40.11        65.88        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       17.88        13.74        17.10        17.85        11.01         8.71 
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 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        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-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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  RHBDD3 MUTATED RHBDD3 WILD-TYPE 
           15.72             0.56 
  RHBDD3 MUTATED RHBDD3 WILD-TYPE 
           83.67           185.79 
  RHBDD3 MUTATED RHBDD3 WILD-TYPE 
           25.00            29.51 
[1] "15.7 - 83.7 (25.0)" "0.6 - 185.8 (29.5)"
[1] "hr="     "9100000"
D84V2, continuous
                  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
D84V3, 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"
D84V4, binary
                  cls
clus                 0   1
  RHBDD3 MUTATED     2   2
  RHBDD3 WILD-TYPE  84 160
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RHBDD3 MUTATED      2    2
  RHBDD3 WILD-TYPE   84  160
     clus
vv    RHBDD3 MUTATED RHBDD3 WILD-TYPE
  NO               2               84
  YES              2              160
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RHBDD3 MUTATED     4   0   0   0
  RHBDD3 WILD-TYPE 167  11   7  18
D84V5, multiclass
    clus
vv   RHBDD3 MUTATED RHBDD3 WILD-TYPE
  R0              4              167
  R1              0               11
  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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RHBDD3 MUTATED                                  0     0
  RHBDD3 WILD-TYPE                                3    13
                  vv
clus               BLACK OR AFRICAN AMERICAN
  RHBDD3 MUTATED                           0
  RHBDD3 WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RHBDD3 MUTATED                                           0     4
  RHBDD3 WILD-TYPE                                         7   189
D84V6, multiclass
                                           clus
vv                                          RHBDD3 MUTATED RHBDD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  0               13
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                  4              189
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V7, binary
                  cls
clus                 0   1
  RHBDD3 MUTATED     0   3
  RHBDD3 WILD-TYPE   4 164
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RHBDD3 MUTATED      0    3
  RHBDD3 WILD-TYPE    4  164
                        clus
vv                       RHBDD3 MUTATED RHBDD3 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              164
[1] 2 2
[1] FALSE

Clustering(85) Variable = TAP1 MUTATION ANALYSIS
D85V1, survival
                sevent
clus2              0   1
  TAP1 MUTATED     7   1
  TAP1 WILD-TYPE 217  23
  TAP1 MUTATED TAP1 WILD-TYPE 
             8            240 
  TAP1 MUTATED TAP1 WILD-TYPE 
             1             23 
$`TAP1 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0U7 
       83.67        86.07         8.22        32.55         8.71        30.74 
TCGA-BS-A0UV TCGA-D1-A103 
       73.25        21.99 

$`TAP1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        37.78        40.11        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       67.20        88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  TAP1 MUTATED TAP1 WILD-TYPE 
          8.22           0.56 
  TAP1 MUTATED TAP1 WILD-TYPE 
         86.07         185.79 
  TAP1 MUTATED TAP1 WILD-TYPE 
        31.645         28.865 
[1] "8.2 - 86.1 (31.6)"  "0.6 - 185.8 (28.9)"
[1] "hr=" "1.2"
D85V2, continuous
                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
D85V3, 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"
D85V4, binary
                cls
clus               0   1
  TAP1 MUTATED     3   5
  TAP1 WILD-TYPE  83 157
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAP1 MUTATED      3    5
  TAP1 WILD-TYPE   83  157
     clus
vv    TAP1 MUTATED TAP1 WILD-TYPE
  NO             3             83
  YES            5            157
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TAP1 MUTATED     6   0   0   0
  TAP1 WILD-TYPE 165  11   7  18
D85V5, multiclass
    clus
vv   TAP1 MUTATED TAP1 WILD-TYPE
  R0            6            165
  R1            0             11
  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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAP1 MUTATED                                  0     0
  TAP1 WILD-TYPE                                3    13
                vv
clus             BLACK OR AFRICAN AMERICAN
  TAP1 MUTATED                           0
  TAP1 WILD-TYPE                        25
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TAP1 MUTATED                                           1     7
  TAP1 WILD-TYPE                                         6   186
D85V6, multiclass
                                           clus
vv                                          TAP1 MUTATED TAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                0             13
  BLACK OR AFRICAN AMERICAN                            0             25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                                7            186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V7, binary
                cls
clus               0   1
  TAP1 MUTATED     0   4
  TAP1 WILD-TYPE   4 163
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAP1 MUTATED      0    4
  TAP1 WILD-TYPE    4  163
                        clus
vv                       TAP1 MUTATED TAP1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            4            163
[1] 2 2
[1] FALSE

Clustering(86) Variable = RB1 MUTATION ANALYSIS
D86V1, survival
               sevent
clus2             0   1
  RB1 MUTATED    19   1
  RB1 WILD-TYPE 205  23
  RB1 MUTATED RB1 WILD-TYPE 
           20           228 
  RB1 MUTATED RB1 WILD-TYPE 
            1            23 
$`RB1 MUTATED`
TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05P TCGA-AP-A0LM 
       42.35        83.67        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 
       72.03        40.11        65.88        32.55         8.71        28.54 
TCGA-BS-A0TC TCGA-BS-A0U9 TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A16N 
       85.55        67.20        85.84        73.25        21.99        31.07 
TCGA-D1-A16Y TCGA-D1-A17Q 
       17.49         1.78 

$`RB1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A059 TCGA-AP-A05A 
       15.95         1.18        21.99         5.95         8.22        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A0L8 TCGA-AP-A0L9 
       57.80        45.53        36.89         7.86        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        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        41.95        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       68.35        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       26.66        16.34        34.29        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       24.99        46.95        23.47        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41        88.34 
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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       29.92        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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  RB1 MUTATED RB1 WILD-TYPE 
         1.78          0.56 
  RB1 MUTATED RB1 WILD-TYPE 
        86.07        185.79 
  RB1 MUTATED RB1 WILD-TYPE 
       36.330        28.655 
[1] "1.8 - 86.1 (36.3)"  "0.6 - 185.8 (28.7)"
[1] "hr=" "2.5"
D86V2, continuous
               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
D86V3, 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"
D86V4, binary
               cls
clus              0   1
  RB1 MUTATED     5  15
  RB1 WILD-TYPE  81 147
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      5   15
  RB1 WILD-TYPE   81  147
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO            5            81
  YES          15           147
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  RB1 MUTATED    15   1   0   2
  RB1 WILD-TYPE 156  10   7  16
D86V5, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  R0          15           156
  R1           1            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"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RB1 MUTATED                                  0     3
  RB1 WILD-TYPE                                3    10
               vv
clus            BLACK OR AFRICAN AMERICAN
  RB1 MUTATED                           1
  RB1 WILD-TYPE                        24
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RB1 MUTATED                                           2    14
  RB1 WILD-TYPE                                         5   179
D86V6, multiclass
                                           clus
vv                                          RB1 MUTATED RB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                    0             3
  ASIAN                                               3            10
  BLACK OR AFRICAN AMERICAN                           1            24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           2             5
  WHITE                                              14           179
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V7, binary
               cls
clus              0   1
  RB1 MUTATED     0  15
  RB1 WILD-TYPE   4 152
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0   15
  RB1 WILD-TYPE    4  152
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO          15           152
[1] 2 2
[1] FALSE

Clustering(87) Variable = SLC1A3 MUTATION ANALYSIS
D87V1, survival
                  sevent
clus2                0   1
  SLC1A3 MUTATED    11   1
  SLC1A3 WILD-TYPE 213  23
  SLC1A3 MUTATED SLC1A3 WILD-TYPE 
              12              236 
  SLC1A3 MUTATED SLC1A3 WILD-TYPE 
               1               23 
$`SLC1A3 MUTATED`
TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A0LM TCGA-B5-A0JN TCGA-B5-A0JY TCGA-B5-A11R 
       23.31         8.22        27.12        80.38        32.55        33.50 
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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        37.78        40.11        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JR 
       16.96        13.55        36.39        71.24        19.36        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        40.67        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       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        43.96        40.50        32.09        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       24.99        46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       88.34        82.39        81.57        86.93        72.72        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-A168 
        1.91         3.68        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-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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  SLC1A3 MUTATED SLC1A3 WILD-TYPE 
            1.78             0.56 
  SLC1A3 MUTATED SLC1A3 WILD-TYPE 
           85.84           185.79 
  SLC1A3 MUTATED SLC1A3 WILD-TYPE 
          33.025           28.865 
[1] "1.8 - 85.8 (33.0)"  "0.6 - 185.8 (28.9)"
[1] "hr=" "1.4"
D87V2, continuous
                  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
D87V3, 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"
D87V4, binary
                  cls
clus                 0   1
  SLC1A3 MUTATED     4   8
  SLC1A3 WILD-TYPE  82 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC1A3 MUTATED      4    8
  SLC1A3 WILD-TYPE   82  154
     clus
vv    SLC1A3 MUTATED SLC1A3 WILD-TYPE
  NO               4               82
  YES              8              154
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  SLC1A3 MUTATED     8   1   0   0
  SLC1A3 WILD-TYPE 163  10   7  18
D87V5, multiclass
    clus
vv   SLC1A3 MUTATED SLC1A3 WILD-TYPE
  R0              8              163
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC1A3 MUTATED                                  0     2
  SLC1A3 WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  SLC1A3 MUTATED                           4
  SLC1A3 WILD-TYPE                        21
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC1A3 MUTATED                                           1     5
  SLC1A3 WILD-TYPE                                         6   188
D87V6, multiclass
                                           clus
vv                                          SLC1A3 MUTATED SLC1A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              4               21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  5              188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V7, binary
                  cls
clus                 0   1
  SLC1A3 MUTATED     0   7
  SLC1A3 WILD-TYPE   4 160
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC1A3 MUTATED      0    7
  SLC1A3 WILD-TYPE    4  160
                        clus
vv                       SLC1A3 MUTATED SLC1A3 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              160
[1] 2 2
[1] FALSE

Clustering(88) Variable = ATAD5 MUTATION ANALYSIS
D88V1, survival
                 sevent
clus2               0   1
  ATAD5 MUTATED    17   0
  ATAD5 WILD-TYPE 207  24
  ATAD5 MUTATED ATAD5 WILD-TYPE 
             17             231 
  ATAD5 MUTATED ATAD5 WILD-TYPE 
              0              24 
$`ATAD5 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11E 
       83.67        86.07        27.12        40.11        32.55         8.71 
TCGA-B5-A11N TCGA-B5-A11Y TCGA-BG-A0VW TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UJ 
       43.96        18.41        16.34        85.55        85.84        82.39 
TCGA-BS-A0UV TCGA-D1-A0ZS TCGA-D1-A17Q TCGA-D1-A17U TCGA-E6-A1LZ 
       73.25         4.87         1.78        22.92        48.36 

$`ATAD5 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        40.67        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       11.01       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        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        24.39        26.66        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZU TCGA-D1-A0ZV 
       19.79        29.95         8.55         0.56        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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-A1NU TCGA-D1-A1NX TCGA-DI-A0WH 
       11.15        24.30         2.33        13.22        18.25        16.31 
TCGA-DI-A1NN TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 
       35.38        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  ATAD5 MUTATED ATAD5 WILD-TYPE 
           1.78            0.56 
  ATAD5 MUTATED ATAD5 WILD-TYPE 
          86.07          185.79 
  ATAD5 MUTATED ATAD5 WILD-TYPE 
          40.11           28.67 
[1] "1.8 - 86.1 (40.1)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "7.5e+07"
D88V2, continuous
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ATAD5 MUTATED                                        16
  ATAD5 WILD-TYPE                                     184
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  ATAD5 MUTATED                               0
  ATAD5 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  ATAD5 MUTATED                                   1
  ATAD5 WILD-TYPE                                43
D88V3, multiclass
                                         clus
vv                                        ATAD5 MUTATED ATAD5 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"
D88V4, binary
                 cls
clus                0   1
  ATAD5 MUTATED     6  11
  ATAD5 WILD-TYPE  80 151
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD5 MUTATED      6   11
  ATAD5 WILD-TYPE   80  151
     clus
vv    ATAD5 MUTATED ATAD5 WILD-TYPE
  NO              6              80
  YES            11             151
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ATAD5 MUTATED    13   0   0   0
  ATAD5 WILD-TYPE 158  11   7  18
D88V5, multiclass
    clus
vv   ATAD5 MUTATED ATAD5 WILD-TYPE
  R0            13             158
  R1             0              11
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATAD5 MUTATED                                  0     3
  ATAD5 WILD-TYPE                                3    10
                 vv
clus              BLACK OR AFRICAN AMERICAN
  ATAD5 MUTATED                           2
  ATAD5 WILD-TYPE                        23
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATAD5 MUTATED                                           1    11
  ATAD5 WILD-TYPE                                         6   182
D88V6, multiclass
                                           clus
vv                                          ATAD5 MUTATED ATAD5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 3              10
  BLACK OR AFRICAN AMERICAN                             2              23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                11             182
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V7, binary
                 cls
clus                0   1
  ATAD5 MUTATED     0  10
  ATAD5 WILD-TYPE   4 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD5 MUTATED      0   10
  ATAD5 WILD-TYPE    4  157
                        clus
vv                       ATAD5 MUTATED ATAD5 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             157
[1] 2 2
[1] FALSE

Clustering(89) Variable = ALG8 MUTATION ANALYSIS
D89V1, survival
                sevent
clus2              0   1
  ALG8 MUTATED    10   0
  ALG8 WILD-TYPE 214  24
  ALG8 MUTATED ALG8 WILD-TYPE 
            10            238 
  ALG8 MUTATED ALG8 WILD-TYPE 
             0             24 
$`ALG8 MUTATED`
TCGA-A5-A0GJ TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A0J1 TCGA-B5-A11E TCGA-BS-A0TA 
       65.75        72.03        46.45        65.88         8.71        23.47 
TCGA-BS-A0UJ TCGA-D1-A103 TCGA-D1-A167 TCGA-D1-A17F 
       82.39        21.99        15.72         1.28 

$`ALG8 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37        74.10        57.53        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        40.11        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       46.75        43.13        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       10.16        24.99        46.95        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 
       67.20        88.34        85.84        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  ALG8 MUTATED ALG8 WILD-TYPE 
          1.28           0.56 
  ALG8 MUTATED ALG8 WILD-TYPE 
         82.39         185.79 
  ALG8 MUTATED ALG8 WILD-TYPE 
        34.960         29.195 
[1] "1.3 - 82.4 (35.0)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "2.6e+07"
D89V2, continuous
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ALG8 MUTATED                                        10
  ALG8 WILD-TYPE                                     190
                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
D89V3, multiclass
                                         clus
vv                                        ALG8 MUTATED ALG8 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"
D89V4, binary
                cls
clus               0   1
  ALG8 MUTATED     2   8
  ALG8 WILD-TYPE  84 154
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG8 MUTATED      2    8
  ALG8 WILD-TYPE   84  154
     clus
vv    ALG8 MUTATED ALG8 WILD-TYPE
  NO             2             84
  YES            8            154
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ALG8 MUTATED     7   1   0   1
  ALG8 WILD-TYPE 164  10   7  17
D89V5, multiclass
    clus
vv   ALG8 MUTATED ALG8 WILD-TYPE
  R0            7            164
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALG8 MUTATED                                  0     1
  ALG8 WILD-TYPE                                3    12
                vv
clus             BLACK OR AFRICAN AMERICAN
  ALG8 MUTATED                           0
  ALG8 WILD-TYPE                        25
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ALG8 MUTATED                                           1     7
  ALG8 WILD-TYPE                                         6   186
D89V6, multiclass
                                           clus
vv                                          ALG8 MUTATED ALG8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                1             12
  BLACK OR AFRICAN AMERICAN                            0             25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                                7            186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V7, binary
                cls
clus               0   1
  ALG8 MUTATED     2   7
  ALG8 WILD-TYPE   2 160
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG8 MUTATED      2    7
  ALG8 WILD-TYPE    2  160
                        clus
vv                       ALG8 MUTATED ALG8 WILD-TYPE
  HISPANIC OR LATINO                2              2
  NOT HISPANIC OR LATINO            7            160
[1] 2 2
[1] FALSE

Clustering(90) Variable = TIGD4 MUTATION ANALYSIS
D90V1, survival
                 sevent
clus2               0   1
  TIGD4 MUTATED    13   0
  TIGD4 WILD-TYPE 211  24
  TIGD4 MUTATED TIGD4 WILD-TYPE 
             13             235 
  TIGD4 MUTATED TIGD4 WILD-TYPE 
              0              24 
$`TIGD4 MUTATED`
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 
       86.07         8.22        27.12        46.45        40.11        65.88 
TCGA-B5-A0JY TCGA-BK-A0C9 TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A16N TCGA-D1-A16X 
       32.55        35.90        85.84        73.25        31.07         3.65 
TCGA-D1-A177 
       18.02 

$`TIGD4 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       35.01        28.54        37.78        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       17.88        13.74        17.10        17.85        11.01         8.71 
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 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        67.20        88.34 
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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       11.51        29.92        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-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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  TIGD4 MUTATED TIGD4 WILD-TYPE 
           3.65            0.56 
  TIGD4 MUTATED TIGD4 WILD-TYPE 
          86.07          185.79 
  TIGD4 MUTATED TIGD4 WILD-TYPE 
          35.90           28.64 
[1] "3.6 - 86.1 (35.9)"  "0.6 - 185.8 (28.6)"
[1] "hr="     "2.7e+07"
D90V2, continuous
                 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
D90V3, 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"
D90V4, binary
                 cls
clus                0   1
  TIGD4 MUTATED     5   8
  TIGD4 WILD-TYPE  81 154
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD4 MUTATED      5    8
  TIGD4 WILD-TYPE   81  154
     clus
vv    TIGD4 MUTATED TIGD4 WILD-TYPE
  NO              5              81
  YES             8             154
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TIGD4 MUTATED    11   1   0   0
  TIGD4 WILD-TYPE 160  10   7  18
D90V5, multiclass
    clus
vv   TIGD4 MUTATED TIGD4 WILD-TYPE
  R0            11             160
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TIGD4 MUTATED                                  0     1
  TIGD4 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  TIGD4 MUTATED                           1
  TIGD4 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TIGD4 MUTATED                                           1     9
  TIGD4 WILD-TYPE                                         6   184
D90V6, multiclass
                                           clus
vv                                          TIGD4 MUTATED TIGD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                 9             184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V7, binary
                 cls
clus                0   1
  TIGD4 MUTATED     1   9
  TIGD4 WILD-TYPE   3 158
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD4 MUTATED      1    9
  TIGD4 WILD-TYPE    3  158
                        clus
vv                       TIGD4 MUTATED TIGD4 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             9             158
[1] 2 2
[1] FALSE

Clustering(91) Variable = PARG MUTATION ANALYSIS
D91V1, survival
                sevent
clus2              0   1
  PARG MUTATED     9   0
  PARG WILD-TYPE 215  24
  PARG MUTATED PARG WILD-TYPE 
             9            239 
  PARG MUTATED PARG WILD-TYPE 
             0             24 
$`PARG MUTATED`
TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JR TCGA-B5-A11E 
        8.22        27.12        40.11        65.88        56.91         8.71 
TCGA-BG-A0W1 TCGA-BS-A0UF TCGA-D1-A167 
       52.83        85.84        15.72 

$`PARG WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       27.39        60.66        35.01        28.54        37.78        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JS 
       13.55        36.39        71.24        19.36        80.38        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       43.13        40.67        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       11.01       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       16.34        34.29        28.54        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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-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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  PARG MUTATED PARG WILD-TYPE 
          8.22           0.56 
  PARG MUTATED PARG WILD-TYPE 
         85.84         185.79 
  PARG MUTATED PARG WILD-TYPE 
         40.11          29.06 
[1] "8.2 - 85.8 (40.1)"  "0.6 - 185.8 (29.1)"
[1] "hr="     "2.6e+07"
D91V2, continuous
                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
D91V3, 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"
D91V4, binary
                cls
clus               0   1
  PARG MUTATED     3   6
  PARG WILD-TYPE  83 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  PARG MUTATED      3    6
  PARG WILD-TYPE   83  156
     clus
vv    PARG MUTATED PARG WILD-TYPE
  NO             3             83
  YES            6            156
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PARG MUTATED     7   0   0   0
  PARG WILD-TYPE 164  11   7  18
D91V5, multiclass
    clus
vv   PARG MUTATED PARG WILD-TYPE
  R0            7            164
  R1            0             11
  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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PARG MUTATED                                  0     1
  PARG WILD-TYPE                                3    12
                vv
clus             BLACK OR AFRICAN AMERICAN
  PARG MUTATED                           1
  PARG WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PARG MUTATED                                           0     7
  PARG WILD-TYPE                                         7   186
D91V6, multiclass
                                           clus
vv                                          PARG MUTATED PARG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                1             12
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              7
  WHITE                                                7            186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V7, binary
                cls
clus               0   1
  PARG MUTATED     0   6
  PARG WILD-TYPE   4 161
[1] "tbl2"
                cls
clus             [,1] [,2]
  PARG MUTATED      0    6
  PARG WILD-TYPE    4  161
                        clus
vv                       PARG MUTATED PARG WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            161
[1] 2 2
[1] FALSE

Clustering(92) Variable = FAT1 MUTATION ANALYSIS
D92V1, survival
                sevent
clus2              0   1
  FAT1 MUTATED    40   0
  FAT1 WILD-TYPE 184  24
  FAT1 MUTATED FAT1 WILD-TYPE 
            40            208 
  FAT1 MUTATED FAT1 WILD-TYPE 
             0             24 
$`FAT1 MUTATED`
TCGA-A5-A0GB TCGA-A5-A0GH TCGA-A5-A0GW TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A056 
       32.78        74.10        23.21        42.35        83.67        86.07 
TCGA-AP-A059 TCGA-AP-A05H TCGA-AP-A0LM TCGA-AP-A0LT TCGA-AX-A05Z TCGA-AX-A060 
        8.22        45.53        27.12        49.22        46.45        35.34 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JT TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A11E 
       40.11        65.88        43.13        32.55        28.64         8.71 
TCGA-B5-A11H TCGA-B5-A11R TCGA-B5-A11Y TCGA-BG-A0MG TCGA-BK-A0CC TCGA-BK-A139 
       88.34        33.50        18.41        48.56        10.22        10.16 
TCGA-BS-A0TC TCGA-BS-A0U8 TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A0ZO 
       85.55        97.41        85.84        82.39        73.25        19.79 
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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GE 
       46.95        37.02        83.51        17.85         3.22       105.37 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       28.27        20.81        68.65        19.96        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        11.97        15.95         1.18        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N 
        5.95        23.31        39.42        57.80        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A062 TCGA-AX-A063 
       19.82        29.69        68.35        72.03        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       34.98        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       37.78        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JV TCGA-B5-A0K0 TCGA-B5-A0K1 
       80.38        56.91        46.75        40.67        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
       11.01       185.79       113.36        75.72        54.44        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       43.96        40.50        32.09        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MI 
        7.92        38.37        36.49        28.27        41.52        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       24.99        46.95        23.47        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        67.20        88.34 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        86.93        72.72        62.79        63.58        49.55 
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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93        22.55         4.44        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A16B 
        1.91        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-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       17.49        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  FAT1 MUTATED FAT1 WILD-TYPE 
          1.74           0.56 
  FAT1 MUTATED FAT1 WILD-TYPE 
         97.41         185.79 
  FAT1 MUTATED FAT1 WILD-TYPE 
         33.14          28.54 
[1] "1.7 - 97.4 (33.1)"  "0.6 - 185.8 (28.5)"
[1] "hr="     "8.9e+07"
D92V2, continuous
                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
D92V3, 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"
D92V4, binary
                cls
clus               0   1
  FAT1 MUTATED    17  23
  FAT1 WILD-TYPE  69 139
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED     17   23
  FAT1 WILD-TYPE   69  139
     clus
vv    FAT1 MUTATED FAT1 WILD-TYPE
  NO            17             69
  YES           23            139
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FAT1 MUTATED    28   2   0   2
  FAT1 WILD-TYPE 143   9   7  16
D92V5, multiclass
    clus
vv   FAT1 MUTATED FAT1 WILD-TYPE
  R0           28            143
  R1            2              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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAT1 MUTATED                                  1     4
  FAT1 WILD-TYPE                                2     9
                vv
clus             BLACK OR AFRICAN AMERICAN
  FAT1 MUTATED                           3
  FAT1 WILD-TYPE                        22
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAT1 MUTATED                                           1    30
  FAT1 WILD-TYPE                                         6   163
D92V6, multiclass
                                           clus
vv                                          FAT1 MUTATED FAT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     1              2
  ASIAN                                                4              9
  BLACK OR AFRICAN AMERICAN                            3             22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                               30            163
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V7, binary
                cls
clus               0   1
  FAT1 MUTATED     2  25
  FAT1 WILD-TYPE   2 142
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED      2   25
  FAT1 WILD-TYPE    2  142
                        clus
vv                       FAT1 MUTATED FAT1 WILD-TYPE
  HISPANIC OR LATINO                2              2
  NOT HISPANIC OR LATINO           25            142
[1] 2 2
[1] FALSE

Clustering(93) Variable = DYM MUTATION ANALYSIS
D93V1, survival
               sevent
clus2             0   1
  DYM MUTATED    10   0
  DYM WILD-TYPE 214  24
  DYM MUTATED DYM WILD-TYPE 
           10           238 
  DYM MUTATED DYM WILD-TYPE 
            0            24 
$`DYM MUTATED`
TCGA-A5-A0GP TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A0K9 
       46.55        86.07         8.22        40.11        32.55        11.01 
TCGA-B5-A11N TCGA-D1-A103 TCGA-D1-A15X TCGA-D1-A17Q 
       43.96        21.99        29.88         1.78 

$`DYM WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        40.67        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       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        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        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-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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  DYM MUTATED DYM WILD-TYPE 
         1.78          0.56 
  DYM MUTATED DYM WILD-TYPE 
        86.07        185.79 
  DYM MUTATED DYM WILD-TYPE 
       31.215        28.865 
[1] "1.8 - 86.1 (31.2)"  "0.6 - 185.8 (28.9)"
[1] "hr="     "2.6e+07"
D93V2, continuous
               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
D93V3, 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"
D93V4, binary
               cls
clus              0   1
  DYM MUTATED     4   6
  DYM WILD-TYPE  82 156
[1] "tbl2"
               cls
clus            [,1] [,2]
  DYM MUTATED      4    6
  DYM WILD-TYPE   82  156
     clus
vv    DYM MUTATED DYM WILD-TYPE
  NO            4            82
  YES           6           156
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  DYM MUTATED     7   0   0   0
  DYM WILD-TYPE 164  11   7  18
D93V5, multiclass
    clus
vv   DYM MUTATED DYM WILD-TYPE
  R0           7           164
  R1           0            11
  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"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DYM MUTATED                                  0     1
  DYM WILD-TYPE                                3    12
               vv
clus            BLACK OR AFRICAN AMERICAN
  DYM MUTATED                           0
  DYM WILD-TYPE                        25
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DYM MUTATED                                           0     9
  DYM WILD-TYPE                                         7   184
D93V6, multiclass
                                           clus
vv                                          DYM MUTATED DYM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                    0             3
  ASIAN                                               1            12
  BLACK OR AFRICAN AMERICAN                           0            25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             7
  WHITE                                               9           184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V7, binary
               cls
clus              0   1
  DYM MUTATED     0   6
  DYM WILD-TYPE   4 161
[1] "tbl2"
               cls
clus            [,1] [,2]
  DYM MUTATED      0    6
  DYM WILD-TYPE    4  161
                        clus
vv                       DYM MUTATED DYM WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           6           161
[1] 2 2
[1] FALSE

Clustering(94) Variable = PSMD3 MUTATION ANALYSIS
D94V1, survival
                 sevent
clus2               0   1
  PSMD3 MUTATED    11   0
  PSMD3 WILD-TYPE 213  24
  PSMD3 MUTATED PSMD3 WILD-TYPE 
             11             237 
  PSMD3 MUTATED PSMD3 WILD-TYPE 
              0              24 
$`PSMD3 MUTATED`
TCGA-A5-A0GH TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A0J1 TCGA-B5-A0K6 
       74.10        83.67         8.22        27.12        65.88        13.74 
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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
       15.95         1.18        21.99         5.95        23.31        86.07 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        40.11        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       43.13        40.67        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       25.91        23.01        17.88        17.10        17.85        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       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        43.96        40.50        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        19.59        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       88.34        85.84        81.57        86.93        72.72        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z 
        1.74         4.44        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-A16G TCGA-D1-A16I 
       37.32        36.36        37.51        36.79        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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  PSMD3 MUTATED PSMD3 WILD-TYPE 
           2.63            0.56 
  PSMD3 MUTATED PSMD3 WILD-TYPE 
          83.67          185.79 
  PSMD3 MUTATED PSMD3 WILD-TYPE 
          29.88           29.06 
[1] "2.6 - 83.7 (29.9)"  "0.6 - 185.8 (29.1)"
[1] "hr="     "2.6e+07"
D94V2, continuous
                 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
D94V3, 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"
D94V4, binary
                 cls
clus                0   1
  PSMD3 MUTATED     4   7
  PSMD3 WILD-TYPE  82 155
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMD3 MUTATED      4    7
  PSMD3 WILD-TYPE   82  155
     clus
vv    PSMD3 MUTATED PSMD3 WILD-TYPE
  NO              4              82
  YES             7             155
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PSMD3 MUTATED     9   0   0   0
  PSMD3 WILD-TYPE 162  11   7  18
D94V5, multiclass
    clus
vv   PSMD3 MUTATED PSMD3 WILD-TYPE
  R0             9             162
  R1             0              11
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PSMD3 MUTATED                                  0     1
  PSMD3 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  PSMD3 MUTATED                           1
  PSMD3 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PSMD3 MUTATED                                           1     8
  PSMD3 WILD-TYPE                                         6   185
D94V6, multiclass
                                           clus
vv                                          PSMD3 MUTATED PSMD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                 8             185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V7, binary
                 cls
clus                0   1
  PSMD3 MUTATED     0   7
  PSMD3 WILD-TYPE   4 160
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMD3 MUTATED      0    7
  PSMD3 WILD-TYPE    4  160
                        clus
vv                       PSMD3 MUTATED PSMD3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             160
[1] 2 2
[1] FALSE

Clustering(95) Variable = PPM1D MUTATION ANALYSIS
D95V1, survival
                 sevent
clus2               0   1
  PPM1D MUTATED    11   0
  PPM1D WILD-TYPE 213  24
  PPM1D MUTATED PPM1D WILD-TYPE 
             11             237 
  PPM1D MUTATED PPM1D WILD-TYPE 
              0              24 
$`PPM1D MUTATED`
TCGA-AP-A056 TCGA-AX-A05Z TCGA-AX-A063 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11H 
       86.07        46.45        66.58        32.55         8.71        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       72.03        35.34        45.99        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        37.78        40.11        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J 
       17.85        11.01       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        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-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       67.20        88.34        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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-A17K 
        1.58         7.00         0.99        30.44         1.28        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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  PPM1D MUTATED PPM1D WILD-TYPE 
           3.65            0.56 
  PPM1D MUTATED PPM1D WILD-TYPE 
          88.34          185.79 
  PPM1D MUTATED PPM1D WILD-TYPE 
          46.45           28.67 
[1] "3.6 - 88.3 (46.5)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.7e+07"
D95V2, continuous
                 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
D95V3, 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"
D95V4, binary
                 cls
clus                0   1
  PPM1D MUTATED     2   9
  PPM1D WILD-TYPE  84 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      2    9
  PPM1D WILD-TYPE   84  153
     clus
vv    PPM1D MUTATED PPM1D WILD-TYPE
  NO              2              84
  YES             9             153
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PPM1D MUTATED     7   1   0   0
  PPM1D WILD-TYPE 164  10   7  18
D95V5, multiclass
    clus
vv   PPM1D MUTATED PPM1D WILD-TYPE
  R0             7             164
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPM1D MUTATED                                  0     2
  PPM1D WILD-TYPE                                3    11
                 vv
clus              BLACK OR AFRICAN AMERICAN
  PPM1D MUTATED                           0
  PPM1D WILD-TYPE                        25
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPM1D MUTATED                                           0     8
  PPM1D WILD-TYPE                                         7   185
D95V6, multiclass
                                           clus
vv                                          PPM1D MUTATED PPM1D WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 2              11
  BLACK OR AFRICAN AMERICAN                             0              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                 8             185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V7, binary
                 cls
clus                0   1
  PPM1D MUTATED     1   6
  PPM1D WILD-TYPE   3 161
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      1    6
  PPM1D WILD-TYPE    3  161
                        clus
vv                       PPM1D MUTATED PPM1D WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             6             161
[1] 2 2
[1] FALSE

Clustering(96) Variable = ZMYM2 MUTATION ANALYSIS
D96V1, survival
                 sevent
clus2               0   1
  ZMYM2 MUTATED    17   0
  ZMYM2 WILD-TYPE 207  24
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
             17             231 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
              0              24 
$`ZMYM2 MUTATED`
TCGA-A5-A0VO TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LF TCGA-AP-A0LM TCGA-AP-A0LT 
       11.97        86.07         8.22         3.39        27.12        49.22 
TCGA-AX-A063 TCGA-AX-A0J0 TCGA-B5-A0JS TCGA-B5-A0JY TCGA-B5-A11E TCGA-BG-A0MO 
       66.58        40.11        46.75        32.55         8.71        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        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        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        31.73        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        41.95        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A064 
       68.35        72.03        46.45        35.34        45.99        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       65.88        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       80.38        56.91        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MQ 
       36.49        28.27        41.52        48.56        23.47        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        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 
       67.20        88.34        82.39        86.93        72.72        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
           1.78            0.56 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
          86.07          185.79 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
          40.11           28.67 
[1] "1.8 - 86.1 (40.1)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "7.5e+07"
D96V2, continuous
                 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
D96V3, 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"
D96V4, binary
                 cls
clus                0   1
  ZMYM2 MUTATED     6  11
  ZMYM2 WILD-TYPE  80 151
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM2 MUTATED      6   11
  ZMYM2 WILD-TYPE   80  151
     clus
vv    ZMYM2 MUTATED ZMYM2 WILD-TYPE
  NO              6              80
  YES            11             151
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZMYM2 MUTATED    12   0   1   1
  ZMYM2 WILD-TYPE 159  11   6  17
D96V5, multiclass
    clus
vv   ZMYM2 MUTATED ZMYM2 WILD-TYPE
  R0            12             159
  R1             0              11
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZMYM2 MUTATED                                  0     1
  ZMYM2 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  ZMYM2 MUTATED                           1
  ZMYM2 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZMYM2 MUTATED                                           2    13
  ZMYM2 WILD-TYPE                                         5   180
D96V6, multiclass
                                           clus
vv                                          ZMYM2 MUTATED ZMYM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             2               5
  WHITE                                                13             180
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V7, binary
                 cls
clus                0   1
  ZMYM2 MUTATED     0  11
  ZMYM2 WILD-TYPE   4 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM2 MUTATED      0   11
  ZMYM2 WILD-TYPE    4  156
                        clus
vv                       ZMYM2 MUTATED ZMYM2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            11             156
[1] 2 2
[1] FALSE

Clustering(97) Variable = INPP4B MUTATION ANALYSIS
D97V1, survival
                  sevent
clus2                0   1
  INPP4B MUTATED    11   1
  INPP4B WILD-TYPE 213  23
  INPP4B MUTATED INPP4B WILD-TYPE 
              12              236 
  INPP4B MUTATED INPP4B WILD-TYPE 
               1               23 
$`INPP4B MUTATED`
TCGA-AP-A054 TCGA-AP-A056 TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JS 
       23.31        86.07        46.45        40.11        65.88        46.75 
TCGA-B5-A0JY TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UM TCGA-BS-A0UV TCGA-D1-A17Q 
       32.55        85.55        85.84        86.93        73.25         1.78 

$`INPP4B WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 
       60.66        35.01        28.54        37.78        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JT 
       36.39        71.24        19.36        80.38        56.91        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       17.88        13.74        17.10        17.85        11.01         8.71 
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 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        23.47        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        67.20        88.34 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       82.39        81.57        72.72        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  INPP4B MUTATED INPP4B WILD-TYPE 
            1.78             0.56 
  INPP4B MUTATED INPP4B WILD-TYPE 
           86.93           185.79 
  INPP4B MUTATED INPP4B WILD-TYPE 
          56.315           28.540 
[1] "1.8 - 86.9 (56.3)"  "0.6 - 185.8 (28.5)"
[1] "hr=" "1.8"
D97V2, continuous
                  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
D97V3, 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"
D97V4, binary
                  cls
clus                 0   1
  INPP4B MUTATED     1  11
  INPP4B WILD-TYPE  85 151
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPP4B MUTATED      1   11
  INPP4B WILD-TYPE   85  151
     clus
vv    INPP4B MUTATED INPP4B WILD-TYPE
  NO               1               85
  YES             11              151
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  INPP4B MUTATED     8   2   0   0
  INPP4B WILD-TYPE 163   9   7  18
D97V5, multiclass
    clus
vv   INPP4B MUTATED INPP4B WILD-TYPE
  R0              8              163
  R1              2                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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  INPP4B MUTATED                                  0     2
  INPP4B WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  INPP4B MUTATED                           0
  INPP4B WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  INPP4B MUTATED                                           1     8
  INPP4B WILD-TYPE                                         6   185
D97V6, multiclass
                                           clus
vv                                          INPP4B MUTATED INPP4B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  8              185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V7, binary
                  cls
clus                 0   1
  INPP4B MUTATED     1   8
  INPP4B WILD-TYPE   3 159
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPP4B MUTATED      1    8
  INPP4B WILD-TYPE    3  159
                        clus
vv                       INPP4B MUTATED INPP4B WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              8              159
[1] 2 2
[1] FALSE

Clustering(98) Variable = USP28 MUTATION ANALYSIS
D98V1, survival
                 sevent
clus2               0   1
  USP28 MUTATED    10   0
  USP28 WILD-TYPE 214  24
  USP28 MUTATED USP28 WILD-TYPE 
             10             238 
  USP28 MUTATED USP28 WILD-TYPE 
              0              24 
$`USP28 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11G TCGA-BS-A0UF 
       83.67         8.22        65.88        32.55       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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        35.01        28.54        37.78        40.11 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01         8.71       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93        22.55         4.44        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  USP28 MUTATED USP28 WILD-TYPE 
           1.74            0.56 
  USP28 MUTATED USP28 WILD-TYPE 
         113.36          185.79 
  USP28 MUTATED USP28 WILD-TYPE 
         49.215          28.865 
[1] "1.7 - 113.4 (49.2)" "0.6 - 185.8 (28.9)"
[1] "hr="     "2.6e+07"
D98V2, continuous
                 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
D98V3, 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"
D98V4, binary
                 cls
clus                0   1
  USP28 MUTATED     2   8
  USP28 WILD-TYPE  84 154
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      2    8
  USP28 WILD-TYPE   84  154
     clus
vv    USP28 MUTATED USP28 WILD-TYPE
  NO              2              84
  YES             8             154
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  USP28 MUTATED     7   0   0   1
  USP28 WILD-TYPE 164  11   7  17
D98V5, multiclass
    clus
vv   USP28 MUTATED USP28 WILD-TYPE
  R0             7             164
  R1             0              11
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP28 MUTATED                                  0     1
  USP28 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  USP28 MUTATED                           1
  USP28 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  USP28 MUTATED                                           1     7
  USP28 WILD-TYPE                                         6   186
D98V6, multiclass
                                           clus
vv                                          USP28 MUTATED USP28 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                 7             186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V7, binary
                 cls
clus                0   1
  USP28 MUTATED     0   7
  USP28 WILD-TYPE   4 160
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      0    7
  USP28 WILD-TYPE    4  160
                        clus
vv                       USP28 MUTATED USP28 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             160
[1] 2 2
[1] FALSE

Clustering(99) Variable = EMR1 MUTATION ANALYSIS
D99V1, survival
                sevent
clus2              0   1
  EMR1 MUTATED    13   0
  EMR1 WILD-TYPE 211  24
  EMR1 MUTATED EMR1 WILD-TYPE 
            13            235 
  EMR1 MUTATED EMR1 WILD-TYPE 
             0             24 
$`EMR1 MUTATED`
TCGA-A5-A0GP TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A063 
       46.55        86.07         8.22        27.12        46.45        66.58 
TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A0K2 TCGA-B5-A11N TCGA-BS-A0UF TCGA-D1-A103 
       40.11        32.55        25.91        43.96        85.84        21.99 
TCGA-D1-A17Q 
        1.78 

$`EMR1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       34.98        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       37.78        65.88        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.64        28.34        30.51        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         8.71       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        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  EMR1 MUTATED EMR1 WILD-TYPE 
          1.78           0.56 
  EMR1 MUTATED EMR1 WILD-TYPE 
         86.07         185.79 
  EMR1 MUTATED EMR1 WILD-TYPE 
         40.11          28.67 
[1] "1.8 - 86.1 (40.1)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.7e+07"
D99V2, continuous
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  EMR1 MUTATED                                        13
  EMR1 WILD-TYPE                                     187
                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
D99V3, multiclass
                                         clus
vv                                        EMR1 MUTATED EMR1 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"
D99V4, binary
                cls
clus               0   1
  EMR1 MUTATED     3  10
  EMR1 WILD-TYPE  83 152
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMR1 MUTATED      3   10
  EMR1 WILD-TYPE   83  152
     clus
vv    EMR1 MUTATED EMR1 WILD-TYPE
  NO             3             83
  YES           10            152
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EMR1 MUTATED     9   1   0   0
  EMR1 WILD-TYPE 162  10   7  18
D99V5, multiclass
    clus
vv   EMR1 MUTATED EMR1 WILD-TYPE
  R0            9            162
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EMR1 MUTATED                                  0     2
  EMR1 WILD-TYPE                                3    11
                vv
clus             BLACK OR AFRICAN AMERICAN
  EMR1 MUTATED                           1
  EMR1 WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EMR1 MUTATED                                           0     9
  EMR1 WILD-TYPE                                         7   184
D99V6, multiclass
                                           clus
vv                                          EMR1 MUTATED EMR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                2             11
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              7
  WHITE                                                9            184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V7, binary
                cls
clus               0   1
  EMR1 MUTATED     1   7
  EMR1 WILD-TYPE   3 160
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMR1 MUTATED      1    7
  EMR1 WILD-TYPE    3  160
                        clus
vv                       EMR1 MUTATED EMR1 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            7            160
[1] 2 2
[1] FALSE

Clustering(100) Variable = ZNF385B MUTATION ANALYSIS
D100V1, survival
                   sevent
clus2                 0   1
  ZNF385B MUTATED     7   0
  ZNF385B WILD-TYPE 217  24
  ZNF385B MUTATED ZNF385B WILD-TYPE 
                7               241 
  ZNF385B MUTATED ZNF385B WILD-TYPE 
                0                24 
$`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         8.71        85.84        21.99 
TCGA-D1-A16X 
        3.65 

$`ZNF385B WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        35.01        28.54        37.78        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        46.75        43.13        40.67        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        17.85        11.01       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  ZNF385B MUTATED ZNF385B WILD-TYPE 
             3.65              0.56 
  ZNF385B MUTATED ZNF385B WILD-TYPE 
            86.07            185.79 
  ZNF385B MUTATED ZNF385B WILD-TYPE 
            27.12             29.33 
[1] "3.6 - 86.1 (27.1)"  "0.6 - 185.8 (29.3)"
[1] "hr="     "2.5e+07"
D100V2, continuous
                   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
D100V3, 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"
D100V4, binary
                   cls
clus                  0   1
  ZNF385B MUTATED     2   5
  ZNF385B WILD-TYPE  84 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF385B MUTATED      2    5
  ZNF385B WILD-TYPE   84  157
     clus
vv    ZNF385B MUTATED ZNF385B WILD-TYPE
  NO                2                84
  YES               5               157
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZNF385B MUTATED     6   0   0   0
  ZNF385B WILD-TYPE 165  11   7  18
D100V5, multiclass
    clus
vv   ZNF385B MUTATED ZNF385B WILD-TYPE
  R0               6               165
  R1               0                11
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF385B MUTATED                                  0     1
  ZNF385B WILD-TYPE                                3    12
                   vv
clus                BLACK OR AFRICAN AMERICAN
  ZNF385B MUTATED                           1
  ZNF385B WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF385B MUTATED                                           0     5
  ZNF385B WILD-TYPE                                         7   188
D100V6, multiclass
                                           clus
vv                                          ZNF385B MUTATED ZNF385B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                12
  BLACK OR AFRICAN AMERICAN                               1                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 7
  WHITE                                                   5               188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V7, binary
                   cls
clus                  0   1
  ZNF385B MUTATED     0   4
  ZNF385B WILD-TYPE   4 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF385B MUTATED      0    4
  ZNF385B WILD-TYPE    4  163
                        clus
vv                       ZNF385B MUTATED ZNF385B WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               4               163
[1] 2 2
[1] FALSE

Clustering(101) Variable = RAE1 MUTATION ANALYSIS
D101V1, survival
                sevent
clus2              0   1
  RAE1 MUTATED    11   0
  RAE1 WILD-TYPE 213  24
  RAE1 MUTATED RAE1 WILD-TYPE 
            11            237 
  RAE1 MUTATED RAE1 WILD-TYPE 
             0             24 
$`RAE1 MUTATED`
TCGA-A5-A0GH TCGA-AP-A056 TCGA-AX-A064 TCGA-AX-A0J1 TCGA-B5-A11E TCGA-B5-A11J 
       74.10        86.07        34.98        65.88         8.71        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A06B TCGA-AX-A06H 
       46.45        35.34        45.99        66.58        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        40.11        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       46.75        43.13        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        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 
       67.20        88.34        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74         4.44        21.99        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-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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  RAE1 MUTATED RAE1 WILD-TYPE 
          1.78           0.56 
  RAE1 MUTATED RAE1 WILD-TYPE 
         86.07         185.79 
  RAE1 MUTATED RAE1 WILD-TYPE 
         54.44          28.64 
[1] "1.8 - 86.1 (54.4)"  "0.6 - 185.8 (28.6)"
[1] "hr="     "2.7e+07"
D101V2, continuous
                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
D101V3, 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"
D101V4, binary
                cls
clus               0   1
  RAE1 MUTATED     2   9
  RAE1 WILD-TYPE  84 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAE1 MUTATED      2    9
  RAE1 WILD-TYPE   84  153
     clus
vv    RAE1 MUTATED RAE1 WILD-TYPE
  NO             2             84
  YES            9            153
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RAE1 MUTATED     8   0   0   0
  RAE1 WILD-TYPE 163  11   7  18
D101V5, multiclass
    clus
vv   RAE1 MUTATED RAE1 WILD-TYPE
  R0            8            163
  R1            0             11
  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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAE1 MUTATED                                  0     1
  RAE1 WILD-TYPE                                3    12
                vv
clus             BLACK OR AFRICAN AMERICAN
  RAE1 MUTATED                           0
  RAE1 WILD-TYPE                        25
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RAE1 MUTATED                                           1     9
  RAE1 WILD-TYPE                                         6   184
D101V6, multiclass
                                           clus
vv                                          RAE1 MUTATED RAE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                1             12
  BLACK OR AFRICAN AMERICAN                            0             25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                                9            184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V7, binary
                cls
clus               0   1
  RAE1 MUTATED     0   7
  RAE1 WILD-TYPE   4 160
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAE1 MUTATED      0    7
  RAE1 WILD-TYPE    4  160
                        clus
vv                       RAE1 MUTATED RAE1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            160
[1] 2 2
[1] FALSE

Clustering(102) Variable = TRIM59 MUTATION ANALYSIS
D102V1, survival
                  sevent
clus2                0   1
  TRIM59 MUTATED     9   0
  TRIM59 WILD-TYPE 215  24
  TRIM59 MUTATED TRIM59 WILD-TYPE 
               9              239 
  TRIM59 MUTATED TRIM59 WILD-TYPE 
               0               24 
$`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        43.96        52.83        85.55 
TCGA-BS-A0UF TCGA-D1-A17Q TCGA-DI-A0WH 
       85.84         1.78        16.31 

$`TRIM59 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        37.78        40.11        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        46.75        43.13        40.67        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         8.71       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        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 
       24.39        26.66        16.34        34.29        28.54        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE 
       10.16        24.99        46.95        23.47        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 
       67.20        88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        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-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       18.25        35.38        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  TRIM59 MUTATED TRIM59 WILD-TYPE 
            1.78             0.56 
  TRIM59 MUTATED TRIM59 WILD-TYPE 
           86.07           185.79 
  TRIM59 MUTATED TRIM59 WILD-TYPE 
           46.55            28.67 
[1] "1.8 - 86.1 (46.5)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.6e+07"
D102V2, continuous
                  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
D102V3, 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"
D102V4, binary
                  cls
clus                 0   1
  TRIM59 MUTATED     3   6
  TRIM59 WILD-TYPE  83 156
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM59 MUTATED      3    6
  TRIM59 WILD-TYPE   83  156
     clus
vv    TRIM59 MUTATED TRIM59 WILD-TYPE
  NO               3               83
  YES              6              156
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TRIM59 MUTATED     8   0   0   0
  TRIM59 WILD-TYPE 163  11   7  18
D102V5, multiclass
    clus
vv   TRIM59 MUTATED TRIM59 WILD-TYPE
  R0              8              163
  R1              0               11
  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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM59 MUTATED                                  0     3
  TRIM59 WILD-TYPE                                3    10
                  vv
clus               BLACK OR AFRICAN AMERICAN
  TRIM59 MUTATED                           1
  TRIM59 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRIM59 MUTATED                                           0     5
  TRIM59 WILD-TYPE                                         7   188
D102V6, multiclass
                                           clus
vv                                          TRIM59 MUTATED TRIM59 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  3               10
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                  5              188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V7, binary
                  cls
clus                 0   1
  TRIM59 MUTATED     0   6
  TRIM59 WILD-TYPE   4 161
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM59 MUTATED      0    6
  TRIM59 WILD-TYPE    4  161
                        clus
vv                       TRIM59 MUTATED TRIM59 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              161
[1] 2 2
[1] FALSE

Clustering(103) Variable = ZNF721 MUTATION ANALYSIS
D103V1, survival
                  sevent
clus2                0   1
  ZNF721 MUTATED    13   0
  ZNF721 WILD-TYPE 211  24
  ZNF721 MUTATED ZNF721 WILD-TYPE 
              13              235 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
               0               24 
$`ZNF721 MUTATED`
TCGA-A5-A0GP TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       46.55        86.07         8.22        27.12        46.45        40.11 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-BG-A187 TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 
       32.55         8.71        14.73        85.84        73.25        21.99 
TCGA-D1-A16X 
        3.65 

$`ZNF721 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       28.54        37.78        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       17.88        13.74        17.10        17.85        11.01       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        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  ZNF721 MUTATED ZNF721 WILD-TYPE 
            3.65             0.56 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
           86.07           185.79 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
           32.55            29.06 
[1] "3.6 - 86.1 (32.5)"  "0.6 - 185.8 (29.1)"
[1] "hr="     "2.6e+07"
D103V2, continuous
                  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
D103V3, 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"
D103V4, binary
                  cls
clus                 0   1
  ZNF721 MUTATED     3  10
  ZNF721 WILD-TYPE  83 152
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF721 MUTATED      3   10
  ZNF721 WILD-TYPE   83  152
     clus
vv    ZNF721 MUTATED ZNF721 WILD-TYPE
  NO               3               83
  YES             10              152
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF721 MUTATED    10   1   0   0
  ZNF721 WILD-TYPE 161  10   7  18
D103V5, multiclass
    clus
vv   ZNF721 MUTATED ZNF721 WILD-TYPE
  R0             10              161
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF721 MUTATED                                  0     2
  ZNF721 WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ZNF721 MUTATED                           1
  ZNF721 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF721 MUTATED                                           1     8
  ZNF721 WILD-TYPE                                         6   185
D103V6, multiclass
                                           clus
vv                                          ZNF721 MUTATED ZNF721 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  8              185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V7, binary
                  cls
clus                 0   1
  ZNF721 MUTATED     1   8
  ZNF721 WILD-TYPE   3 159
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF721 MUTATED      1    8
  ZNF721 WILD-TYPE    3  159
                        clus
vv                       ZNF721 MUTATED ZNF721 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              8              159
[1] 2 2
[1] FALSE

Clustering(104) Variable = MCTP1 MUTATION ANALYSIS
D104V1, survival
                 sevent
clus2               0   1
  MCTP1 MUTATED    13   0
  MCTP1 WILD-TYPE 211  24
  MCTP1 MUTATED MCTP1 WILD-TYPE 
             13             235 
  MCTP1 MUTATED MCTP1 WILD-TYPE 
              0              24 
$`MCTP1 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       83.67         8.22        36.89        27.12        46.45        40.11 
TCGA-B5-A0JY TCGA-BS-A0TC TCGA-BS-A0U8 TCGA-BS-A0UV TCGA-D1-A0ZR TCGA-D1-A0ZS 
       32.55        85.55        97.41        73.25         0.56         4.87 
TCGA-D1-A17Q 
        1.78 

$`MCTP1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05P 
       86.07        39.42        57.80        45.53         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       28.54        37.78        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       17.88        13.74        17.10        17.85        11.01         8.71 
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 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        23.47        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        67.20        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  MCTP1 MUTATED MCTP1 WILD-TYPE 
           0.56            0.66 
  MCTP1 MUTATED MCTP1 WILD-TYPE 
          97.41          185.79 
  MCTP1 MUTATED MCTP1 WILD-TYPE 
          36.89           28.67 
[1] "0.6 - 97.4 (36.9)"  "0.7 - 185.8 (28.7)"
[1] "hr="     "2.7e+07"
D104V2, continuous
                 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
D104V3, 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"
D104V4, binary
                 cls
clus                0   1
  MCTP1 MUTATED     6   7
  MCTP1 WILD-TYPE  80 155
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCTP1 MUTATED      6    7
  MCTP1 WILD-TYPE   80  155
     clus
vv    MCTP1 MUTATED MCTP1 WILD-TYPE
  NO              6              80
  YES             7             155
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MCTP1 MUTATED    10   1   0   0
  MCTP1 WILD-TYPE 161  10   7  18
D104V5, multiclass
    clus
vv   MCTP1 MUTATED MCTP1 WILD-TYPE
  R0            10             161
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MCTP1 MUTATED                                  0     1
  MCTP1 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  MCTP1 MUTATED                           1
  MCTP1 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MCTP1 MUTATED                                           1     9
  MCTP1 WILD-TYPE                                         6   184
D104V6, multiclass
                                           clus
vv                                          MCTP1 MUTATED MCTP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                 9             184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V7, binary
                 cls
clus                0   1
  MCTP1 MUTATED     1   8
  MCTP1 WILD-TYPE   3 159
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCTP1 MUTATED      1    8
  MCTP1 WILD-TYPE    3  159
                        clus
vv                       MCTP1 MUTATED MCTP1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             8             159
[1] 2 2
[1] FALSE

Clustering(105) Variable = ZNF774 MUTATION ANALYSIS
D105V1, survival
                  sevent
clus2                0   1
  ZNF774 MUTATED    10   0
  ZNF774 WILD-TYPE 214  24
  ZNF774 MUTATED ZNF774 WILD-TYPE 
              10              238 
  ZNF774 MUTATED ZNF774 WILD-TYPE 
               0               24 
$`ZNF774 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A0K8 
       83.67         8.22        27.12        46.45        32.55        17.85 
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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       35.01        28.54        37.78        40.11        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        40.67        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       25.91        23.01        17.88        13.74        17.10        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        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 
       67.20        88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       30.08        29.88         1.91        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-A177 
       10.65         0.69        18.67        17.49        19.53        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  ZNF774 MUTATED ZNF774 WILD-TYPE 
            3.65             0.56 
  ZNF774 MUTATED ZNF774 WILD-TYPE 
           85.84           185.79 
  ZNF774 MUTATED ZNF774 WILD-TYPE 
          28.635           29.195 
[1] "3.6 - 85.8 (28.6)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "2.6e+07"
D105V2, continuous
                  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
D105V3, 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"
D105V4, binary
                  cls
clus                 0   1
  ZNF774 MUTATED     3   7
  ZNF774 WILD-TYPE  83 155
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF774 MUTATED      3    7
  ZNF774 WILD-TYPE   83  155
     clus
vv    ZNF774 MUTATED ZNF774 WILD-TYPE
  NO               3               83
  YES              7              155
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF774 MUTATED     7   1   0   0
  ZNF774 WILD-TYPE 164  10   7  18
D105V5, multiclass
    clus
vv   ZNF774 MUTATED ZNF774 WILD-TYPE
  R0              7              164
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF774 MUTATED                                  0     1
  ZNF774 WILD-TYPE                                3    12
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ZNF774 MUTATED                           1
  ZNF774 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF774 MUTATED                                           0     7
  ZNF774 WILD-TYPE                                         7   186
D105V6, multiclass
                                           clus
vv                                          ZNF774 MUTATED ZNF774 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  1               12
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                  7              186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V7, binary
                  cls
clus                 0   1
  ZNF774 MUTATED     1   5
  ZNF774 WILD-TYPE   3 162
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF774 MUTATED      1    5
  ZNF774 WILD-TYPE    3  162
                        clus
vv                       ZNF774 MUTATED ZNF774 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              5              162
[1] 2 2
[1] FALSE

Clustering(106) Variable = FAM9A MUTATION ANALYSIS
D106V1, survival
                 sevent
clus2               0   1
  FAM9A MUTATED    14   0
  FAM9A WILD-TYPE 210  24
  FAM9A MUTATED FAM9A WILD-TYPE 
             14             234 
  FAM9A MUTATED FAM9A WILD-TYPE 
              0              24 
$`FAM9A MUTATED`
TCGA-A5-A0VP TCGA-AP-A059 TCGA-AX-A0J0 TCGA-AX-A2HF TCGA-B5-A0JY TCGA-B5-A0K1 
       42.35         8.22        40.11        19.36        32.55        30.51 
TCGA-B5-A11E TCGA-B5-A11N TCGA-BG-A0MO TCGA-BG-A0YV TCGA-D1-A103 TCGA-D1-A15X 
        8.71        43.96        43.04        12.56        21.99        29.88 
TCGA-D1-A177 TCGA-FI-A2EX 
       18.02         9.07 

$`FAM9A WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        35.01        28.54        37.78        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-B5-A0JN TCGA-B5-A0JR 
       16.96        13.55        36.39        71.24        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K2 
       46.75        43.13        40.67        28.64        28.34        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
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 
       40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
        4.44        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-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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2F8 
       10.78        15.09         3.62        36.00        59.01        25.02 

  FAM9A MUTATED FAM9A WILD-TYPE 
           8.22            0.56 
  FAM9A MUTATED FAM9A WILD-TYPE 
          43.96          185.79 
  FAM9A MUTATED FAM9A WILD-TYPE 
         25.935          29.195 
[1] "8.2 - 44.0 (25.9)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "2.6e+07"
D106V2, continuous
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  FAM9A MUTATED                                        10
  FAM9A WILD-TYPE                                     190
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  FAM9A MUTATED                               0
  FAM9A WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  FAM9A MUTATED                                   4
  FAM9A WILD-TYPE                                40
D106V3, multiclass
                                         clus
vv                                        FAM9A MUTATED FAM9A WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            10             190
  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"
D106V4, binary
                 cls
clus                0   1
  FAM9A MUTATED     6   8
  FAM9A WILD-TYPE  80 154
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED      6    8
  FAM9A WILD-TYPE   80  154
     clus
vv    FAM9A MUTATED FAM9A WILD-TYPE
  NO              6              80
  YES             8             154
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FAM9A MUTATED    10   0   0   0
  FAM9A WILD-TYPE 161  11   7  18
D106V5, multiclass
    clus
vv   FAM9A MUTATED FAM9A WILD-TYPE
  R0            10             161
  R1             0              11
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM9A MUTATED                                  0     0
  FAM9A WILD-TYPE                                3    13
                 vv
clus              BLACK OR AFRICAN AMERICAN
  FAM9A MUTATED                           0
  FAM9A WILD-TYPE                        25
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM9A MUTATED                                           0    14
  FAM9A WILD-TYPE                                         7   179
D106V6, multiclass
                                           clus
vv                                          FAM9A MUTATED FAM9A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 0              13
  BLACK OR AFRICAN AMERICAN                             0              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                14             179
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V7, binary
                 cls
clus                0   1
  FAM9A MUTATED     0  10
  FAM9A WILD-TYPE   4 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED      0   10
  FAM9A WILD-TYPE    4  157
                        clus
vv                       FAM9A MUTATED FAM9A WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             157
[1] 2 2
[1] FALSE

Clustering(107) Variable = CFP MUTATION ANALYSIS
D107V1, survival
               sevent
clus2             0   1
  CFP MUTATED     6   2
  CFP WILD-TYPE 218  22
  CFP MUTATED CFP WILD-TYPE 
            8           240 
  CFP MUTATED CFP WILD-TYPE 
            2            22 
$`CFP MUTATED`
TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05S TCGA-B5-A0K6 TCGA-BS-A0UV TCGA-D1-A0ZO 
        8.22        27.12        13.58        13.74        73.25        19.79 
TCGA-D1-A15Z TCGA-D1-A16Y 
        1.91        17.49 

$`CFP WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       41.95        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        37.78        40.11        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        46.75        43.13        40.67        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K7 
       28.34        30.51        25.91        23.01        17.88        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         8.71       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55 
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-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       39.48        30.08        29.88         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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  CFP MUTATED CFP WILD-TYPE 
         1.91          0.56 
  CFP MUTATED CFP WILD-TYPE 
        73.25        185.79 
  CFP MUTATED CFP WILD-TYPE 
       15.615        29.900 
[1] "1.9 - 73.2 (15.6)"  "0.6 - 185.8 (29.9)"
[1] "hr=" "4.5"
D107V2, continuous
               vv
clus            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CFP MUTATED                                         8
  CFP WILD-TYPE                                     192
               vv
clus            MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
  CFP MUTATED                               0                                 0
  CFP WILD-TYPE                             4                                44
D107V3, multiclass
                                         clus
vv                                        CFP MUTATED CFP 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"
D107V4, binary
               cls
clus              0   1
  CFP MUTATED     3   5
  CFP WILD-TYPE  83 157
[1] "tbl2"
               cls
clus            [,1] [,2]
  CFP MUTATED      3    5
  CFP WILD-TYPE   83  157
     clus
vv    CFP MUTATED CFP WILD-TYPE
  NO            3            83
  YES           5           157
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  CFP MUTATED     5   0   1   1
  CFP WILD-TYPE 166  11   6  17
D107V5, multiclass
    clus
vv   CFP MUTATED CFP WILD-TYPE
  R0           5           166
  R1           0            11
  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"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CFP MUTATED                                  0     0
  CFP WILD-TYPE                                3    13
               vv
clus            BLACK OR AFRICAN AMERICAN
  CFP MUTATED                           1
  CFP WILD-TYPE                        24
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CFP MUTATED                                           1     6
  CFP WILD-TYPE                                         6   187
D107V6, multiclass
                                           clus
vv                                          CFP MUTATED CFP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                    0             3
  ASIAN                                               0            13
  BLACK OR AFRICAN AMERICAN                           1            24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           1             6
  WHITE                                               6           187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V7, binary
               cls
clus              0   1
  CFP MUTATED     0   6
  CFP WILD-TYPE   4 161
[1] "tbl2"
               cls
clus            [,1] [,2]
  CFP MUTATED      0    6
  CFP WILD-TYPE    4  161
                        clus
vv                       CFP MUTATED CFP WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           6           161
[1] 2 2
[1] FALSE

Clustering(108) Variable = PER3 MUTATION ANALYSIS
D108V1, survival
                sevent
clus2              0   1
  PER3 MUTATED    12   0
  PER3 WILD-TYPE 212  24
  PER3 MUTATED PER3 WILD-TYPE 
            12            236 
  PER3 MUTATED PER3 WILD-TYPE 
             0             24 
$`PER3 MUTATED`
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY 
       86.07         8.22        27.12        40.11        65.88        32.55 
TCGA-B5-A0K2 TCGA-B5-A11E TCGA-B5-A11N TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A167 
       25.91         8.71        43.96        73.25        21.99        15.72 

$`PER3 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 
       60.66        35.01        28.54        37.78        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K3 
       43.13        40.67        28.64        28.34        30.51        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       17.88        13.74        17.10        17.85        11.01       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        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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-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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  PER3 MUTATED PER3 WILD-TYPE 
          8.22           0.56 
  PER3 MUTATED PER3 WILD-TYPE 
         86.07         185.79 
  PER3 MUTATED PER3 WILD-TYPE 
        29.835         29.195 
[1] "8.2 - 86.1 (29.8)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "2.6e+07"
D108V2, continuous
                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
D108V3, 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"
D108V4, binary
                cls
clus               0   1
  PER3 MUTATED     4   8
  PER3 WILD-TYPE  82 154
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED      4    8
  PER3 WILD-TYPE   82  154
     clus
vv    PER3 MUTATED PER3 WILD-TYPE
  NO             4             82
  YES            8            154
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PER3 MUTATED     8   0   0   0
  PER3 WILD-TYPE 163  11   7  18
D108V5, multiclass
    clus
vv   PER3 MUTATED PER3 WILD-TYPE
  R0            8            163
  R1            0             11
  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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PER3 MUTATED                                  0     0
  PER3 WILD-TYPE                                3    13
                vv
clus             BLACK OR AFRICAN AMERICAN
  PER3 MUTATED                           1
  PER3 WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PER3 MUTATED                                           1    10
  PER3 WILD-TYPE                                         6   183
D108V6, multiclass
                                           clus
vv                                          PER3 MUTATED PER3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                0             13
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                               10            183
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V7, binary
                cls
clus               0   1
  PER3 MUTATED     0   6
  PER3 WILD-TYPE   4 161
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED      0    6
  PER3 WILD-TYPE    4  161
                        clus
vv                       PER3 MUTATED PER3 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            161
[1] 2 2
[1] FALSE

Clustering(109) Variable = ZRANB3 MUTATION ANALYSIS
D109V1, survival
                  sevent
clus2                0   1
  ZRANB3 MUTATED     8   0
  ZRANB3 WILD-TYPE 216  24
  ZRANB3 MUTATED ZRANB3 WILD-TYPE 
               8              240 
  ZRANB3 MUTATED ZRANB3 WILD-TYPE 
               0               24 
$`ZRANB3 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-BS-A0UF TCGA-BS-A0UV 
       83.67        86.07        65.88        32.55        85.84        73.25 
TCGA-D1-A15X TCGA-D1-A177 
       29.88        18.02 

$`ZRANB3 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        35.01        28.54        37.78        40.11 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         8.71       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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-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-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  ZRANB3 MUTATED ZRANB3 WILD-TYPE 
           18.02             0.56 
  ZRANB3 MUTATED ZRANB3 WILD-TYPE 
           86.07           185.79 
  ZRANB3 MUTATED ZRANB3 WILD-TYPE 
          69.565           28.590 
[1] "18.0 - 86.1 (69.6)" "0.6 - 185.8 (28.6)"
[1] "hr="     "2.6e+07"
D109V2, continuous
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZRANB3 MUTATED                                         7
  ZRANB3 WILD-TYPE                                     193
                  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
D109V3, multiclass
                                         clus
vv                                        ZRANB3 MUTATED ZRANB3 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"
D109V4, binary
                  cls
clus                 0   1
  ZRANB3 MUTATED     4   4
  ZRANB3 WILD-TYPE  82 158
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZRANB3 MUTATED      4    4
  ZRANB3 WILD-TYPE   82  158
     clus
vv    ZRANB3 MUTATED ZRANB3 WILD-TYPE
  NO               4               82
  YES              4              158
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZRANB3 MUTATED     7   0   0   0
  ZRANB3 WILD-TYPE 164  11   7  18
D109V5, multiclass
    clus
vv   ZRANB3 MUTATED ZRANB3 WILD-TYPE
  R0              7              164
  R1              0               11
  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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZRANB3 MUTATED                                  0     1
  ZRANB3 WILD-TYPE                                3    12
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ZRANB3 MUTATED                           0
  ZRANB3 WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZRANB3 MUTATED                                           1     6
  ZRANB3 WILD-TYPE                                         6   187
D109V6, multiclass
                                           clus
vv                                          ZRANB3 MUTATED ZRANB3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  1               12
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  6              187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V7, binary
                  cls
clus                 0   1
  ZRANB3 MUTATED     0   5
  ZRANB3 WILD-TYPE   4 162
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZRANB3 MUTATED      0    5
  ZRANB3 WILD-TYPE    4  162
                        clus
vv                       ZRANB3 MUTATED ZRANB3 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              162
[1] 2 2
[1] FALSE

Clustering(110) Variable = OMA1 MUTATION ANALYSIS
D110V1, survival
                sevent
clus2              0   1
  OMA1 MUTATED    10   0
  OMA1 WILD-TYPE 214  24
  OMA1 MUTATED OMA1 WILD-TYPE 
            10            238 
  OMA1 MUTATED OMA1 WILD-TYPE 
             0             24 
$`OMA1 MUTATED`
TCGA-AP-A0LM TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-BS-A0TC 
       27.12        46.45        32.55         8.71        43.96        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89         7.86        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       72.03        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        35.01        28.54        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       65.88        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       80.38        56.91        46.75        43.13        40.67        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        17.85        11.01       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        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE 
       10.16        24.99        46.95        23.47        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 
       67.20        88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        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-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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  OMA1 MUTATED OMA1 WILD-TYPE 
          2.63           0.56 
  OMA1 MUTATED OMA1 WILD-TYPE 
         85.55         185.79 
  OMA1 MUTATED OMA1 WILD-TYPE 
        29.835         29.195 
[1] "2.6 - 85.5 (29.8)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "2.6e+07"
D110V2, continuous
                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
D110V3, 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"
D110V4, binary
                cls
clus               0   1
  OMA1 MUTATED     1   9
  OMA1 WILD-TYPE  85 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  OMA1 MUTATED      1    9
  OMA1 WILD-TYPE   85  153
     clus
vv    OMA1 MUTATED OMA1 WILD-TYPE
  NO             1             85
  YES            9            153
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  OMA1 MUTATED     6   1   0   0
  OMA1 WILD-TYPE 165  10   7  18
D110V5, multiclass
    clus
vv   OMA1 MUTATED OMA1 WILD-TYPE
  R0            6            165
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OMA1 MUTATED                                  0     1
  OMA1 WILD-TYPE                                3    12
                vv
clus             BLACK OR AFRICAN AMERICAN
  OMA1 MUTATED                           1
  OMA1 WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OMA1 MUTATED                                           1     6
  OMA1 WILD-TYPE                                         6   187
D110V6, multiclass
                                           clus
vv                                          OMA1 MUTATED OMA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                1             12
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                                6            187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V7, binary
                cls
clus               0   1
  OMA1 MUTATED     1   5
  OMA1 WILD-TYPE   3 162
[1] "tbl2"
                cls
clus             [,1] [,2]
  OMA1 MUTATED      1    5
  OMA1 WILD-TYPE    3  162
                        clus
vv                       OMA1 MUTATED OMA1 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            5            162
[1] 2 2
[1] FALSE

Clustering(111) Variable = CLDN15 MUTATION ANALYSIS
D111V1, survival
                  sevent
clus2                0   1
  CLDN15 MUTATED     5   0
  CLDN15 WILD-TYPE 219  24
  CLDN15 MUTATED CLDN15 WILD-TYPE 
               5              243 
  CLDN15 MUTATED CLDN15 WILD-TYPE 
               0               24 
$`CLDN15 MUTATED`
TCGA-AX-A05Z TCGA-BS-A0UL TCGA-D1-A160 TCGA-D1-A177 TCGA-D1-A17Q 
       46.45        81.57         3.68        18.02         1.78 

$`CLDN15 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89         7.86        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
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        41.95        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       68.35        72.03        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       40.11        65.88        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       17.88        13.74        17.10        17.85        11.01         8.71 
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 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        21.99        39.48        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-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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  CLDN15 MUTATED CLDN15 WILD-TYPE 
            1.78             0.56 
  CLDN15 MUTATED CLDN15 WILD-TYPE 
           81.57           185.79 
  CLDN15 MUTATED CLDN15 WILD-TYPE 
           18.02            29.33 
[1] "1.8 - 81.6 (18.0)"  "0.6 - 185.8 (29.3)"
[1] "hr="     "9100000"
D111V2, continuous
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CLDN15 MUTATED                                         5
  CLDN15 WILD-TYPE                                     195
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  CLDN15 MUTATED                               0
  CLDN15 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  CLDN15 MUTATED                                   0
  CLDN15 WILD-TYPE                                44
D111V3, multiclass
                                         clus
vv                                        CLDN15 MUTATED CLDN15 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"
D111V4, binary
                  cls
clus                 0   1
  CLDN15 MUTATED     1   4
  CLDN15 WILD-TYPE  85 158
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN15 MUTATED      1    4
  CLDN15 WILD-TYPE   85  158
     clus
vv    CLDN15 MUTATED CLDN15 WILD-TYPE
  NO               1               85
  YES              4              158
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CLDN15 MUTATED     4   1   0   0
  CLDN15 WILD-TYPE 167  10   7  18
D111V5, multiclass
    clus
vv   CLDN15 MUTATED CLDN15 WILD-TYPE
  R0              4              167
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLDN15 MUTATED                                  0     0
  CLDN15 WILD-TYPE                                3    13
                  vv
clus               BLACK OR AFRICAN AMERICAN
  CLDN15 MUTATED                           0
  CLDN15 WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CLDN15 MUTATED                                           1     3
  CLDN15 WILD-TYPE                                         6   190
D111V6, multiclass
                                           clus
vv                                          CLDN15 MUTATED CLDN15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  0               13
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  3              190
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V7, binary
                  cls
clus                 0   1
  CLDN15 MUTATED     1   4
  CLDN15 WILD-TYPE   3 163
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN15 MUTATED      1    4
  CLDN15 WILD-TYPE    3  163
                        clus
vv                       CLDN15 MUTATED CLDN15 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              4              163
[1] 2 2
[1] FALSE

Clustering(112) Variable = TTC39C MUTATION ANALYSIS
D112V1, survival
                  sevent
clus2                0   1
  TTC39C MUTATED     7   0
  TTC39C WILD-TYPE 217  24
  TTC39C MUTATED TTC39C WILD-TYPE 
               7              241 
  TTC39C MUTATED TTC39C WILD-TYPE 
               0               24 
$`TTC39C MUTATED`
TCGA-AP-A056 TCGA-AP-A0LT TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0UF 
       86.07        49.22        65.88        32.55         8.71        85.84 
TCGA-D1-A16X 
        3.65 

$`TTC39C WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        35.01        28.54        37.78        40.11 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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-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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  TTC39C MUTATED TTC39C WILD-TYPE 
            3.65             0.56 
  TTC39C MUTATED TTC39C WILD-TYPE 
           86.07           185.79 
  TTC39C MUTATED TTC39C WILD-TYPE 
           49.22            28.67 
[1] "3.6 - 86.1 (49.2)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.6e+07"
D112V2, continuous
                  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
D112V3, 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"
D112V4, binary
                  cls
clus                 0   1
  TTC39C MUTATED     2   5
  TTC39C WILD-TYPE  84 157
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TTC39C MUTATED      2    5
  TTC39C WILD-TYPE   84  157
     clus
vv    TTC39C MUTATED TTC39C WILD-TYPE
  NO               2               84
  YES              5              157
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TTC39C MUTATED     5   0   0   0
  TTC39C WILD-TYPE 166  11   7  18
D112V5, multiclass
    clus
vv   TTC39C MUTATED TTC39C WILD-TYPE
  R0              5              166
  R1              0               11
  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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TTC39C MUTATED                                  0     1
  TTC39C WILD-TYPE                                3    12
                  vv
clus               BLACK OR AFRICAN AMERICAN
  TTC39C MUTATED                           0
  TTC39C WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TTC39C MUTATED                                           0     6
  TTC39C WILD-TYPE                                         7   187
D112V6, multiclass
                                           clus
vv                                          TTC39C MUTATED TTC39C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  1               12
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                  6              187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V7, binary
                  cls
clus                 0   1
  TTC39C MUTATED     0   3
  TTC39C WILD-TYPE   4 164
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TTC39C MUTATED      0    3
  TTC39C WILD-TYPE    4  164
                        clus
vv                       TTC39C MUTATED TTC39C WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              164
[1] 2 2
[1] FALSE

Clustering(113) Variable = TXNRD1 MUTATION ANALYSIS
D113V1, survival
                  sevent
clus2                0   1
  TXNRD1 MUTATED     8   0
  TXNRD1 WILD-TYPE 216  24
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
               8              240 
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
               0               24 
$`TXNRD1 MUTATED`
TCGA-AP-A051 TCGA-AP-A0LD TCGA-AP-A0LF TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY 
       83.67       117.99         3.39        40.11        65.88        32.55 
TCGA-B5-A11E TCGA-D1-A17Q 
        8.71         1.78 

$`TXNRD1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LE TCGA-AP-A0LG 
        7.86        20.91        48.79       125.42       110.37        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 
       60.66        35.01        28.54        37.78        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        40.67        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
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 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
            1.78             0.56 
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
          117.99           185.79 
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
          36.330           28.865 
[1] "1.8 - 118.0 (36.3)" "0.6 - 185.8 (28.9)"
[1] "hr="     "2.6e+07"
D113V2, continuous
                  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
D113V3, 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"
D113V4, binary
                  cls
clus                 0   1
  TXNRD1 MUTATED     2   6
  TXNRD1 WILD-TYPE  84 156
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNRD1 MUTATED      2    6
  TXNRD1 WILD-TYPE   84  156
     clus
vv    TXNRD1 MUTATED TXNRD1 WILD-TYPE
  NO               2               84
  YES              6              156
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TXNRD1 MUTATED     5   0   1   0
  TXNRD1 WILD-TYPE 166  11   6  18
D113V5, multiclass
    clus
vv   TXNRD1 MUTATED TXNRD1 WILD-TYPE
  R0              5              166
  R1              0               11
  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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TXNRD1 MUTATED                                  0     0
  TXNRD1 WILD-TYPE                                3    13
                  vv
clus               BLACK OR AFRICAN AMERICAN
  TXNRD1 MUTATED                           0
  TXNRD1 WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TXNRD1 MUTATED                                           0     8
  TXNRD1 WILD-TYPE                                         7   185
D113V6, multiclass
                                           clus
vv                                          TXNRD1 MUTATED TXNRD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  0               13
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                  8              185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V7, binary
                  cls
clus                 0   1
  TXNRD1 MUTATED     0   4
  TXNRD1 WILD-TYPE   4 163
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNRD1 MUTATED      0    4
  TXNRD1 WILD-TYPE    4  163
                        clus
vv                       TXNRD1 MUTATED TXNRD1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              163
[1] 2 2
[1] FALSE

Clustering(114) Variable = MECOM MUTATION ANALYSIS
D114V1, survival
                 sevent
clus2               0   1
  MECOM MUTATED    12   0
  MECOM WILD-TYPE 212  24
  MECOM MUTATED MECOM WILD-TYPE 
             12             236 
  MECOM MUTATED MECOM WILD-TYPE 
              0              24 
$`MECOM MUTATED`
TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A0J1 TCGA-B5-A0JR 
       42.35        83.67        86.07         8.22        65.88        56.91 
TCGA-B5-A11G TCGA-B5-A11V TCGA-BG-A0VV TCGA-D1-A103 TCGA-D1-A161 TCGA-D1-A165 
      113.36        19.56        26.66        21.99        29.33         0.66 

$`MECOM WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A 
       15.95         1.18        21.99         5.95        23.31        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        45.53        36.89         7.86        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        40.11        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JT 
       36.39        71.24        19.36        80.38        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       40.67        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
        8.71       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-A11U 
       43.96        40.50        32.09        33.50        27.35        16.73 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        24.39        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
        3.68        32.58        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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  MECOM MUTATED MECOM WILD-TYPE 
           0.66            0.56 
  MECOM MUTATED MECOM WILD-TYPE 
         113.36          185.79 
  MECOM MUTATED MECOM WILD-TYPE 
         35.840          28.865 
[1] "0.7 - 113.4 (35.8)" "0.6 - 185.8 (28.9)"
[1] "hr="     "2.7e+07"
D114V2, continuous
                 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
D114V3, 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"
D114V4, binary
                 cls
clus                0   1
  MECOM MUTATED     4   8
  MECOM WILD-TYPE  82 154
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MECOM MUTATED      4    8
  MECOM WILD-TYPE   82  154
     clus
vv    MECOM MUTATED MECOM WILD-TYPE
  NO              4              82
  YES             8             154
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MECOM MUTATED     9   0   0   0
  MECOM WILD-TYPE 162  11   7  18
D114V5, multiclass
    clus
vv   MECOM MUTATED MECOM WILD-TYPE
  R0             9             162
  R1             0              11
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MECOM MUTATED                                  0     0
  MECOM WILD-TYPE                                3    13
                 vv
clus              BLACK OR AFRICAN AMERICAN
  MECOM MUTATED                           2
  MECOM WILD-TYPE                        23
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MECOM MUTATED                                           0    10
  MECOM WILD-TYPE                                         7   183
D114V6, multiclass
                                           clus
vv                                          MECOM MUTATED MECOM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 0              13
  BLACK OR AFRICAN AMERICAN                             2              23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                10             183
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V7, binary
                 cls
clus                0   1
  MECOM MUTATED     0   7
  MECOM WILD-TYPE   4 160
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MECOM MUTATED      0    7
  MECOM WILD-TYPE    4  160
                        clus
vv                       MECOM MUTATED MECOM WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             160
[1] 2 2
[1] FALSE

Clustering(115) Variable = CCDC147 MUTATION ANALYSIS
D115V1, survival
                   sevent
clus2                 0   1
  CCDC147 MUTATED    15   0
  CCDC147 WILD-TYPE 209  24
  CCDC147 MUTATED CCDC147 WILD-TYPE 
               15               233 
  CCDC147 MUTATED CCDC147 WILD-TYPE 
                0                24 
$`CCDC147 MUTATED`
TCGA-A5-A0GP TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AP-A0LT TCGA-AX-A05Z 
       46.55        86.07         8.22        27.12        49.22        46.45 
TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11N TCGA-B5-A11Y TCGA-BS-A0UF TCGA-BS-A0UV 
       40.11        32.55        43.96        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        68.35        72.03        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       34.98        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       37.78        65.88        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        17.85        11.01         8.71       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        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74         4.44        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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  CCDC147 MUTATED CCDC147 WILD-TYPE 
             1.78              0.56 
  CCDC147 MUTATED CCDC147 WILD-TYPE 
            86.07            185.79 
  CCDC147 MUTATED CCDC147 WILD-TYPE 
            40.11             28.64 
[1] "1.8 - 86.1 (40.1)"  "0.6 - 185.8 (28.6)"
[1] "hr="     "2.7e+07"
D115V2, continuous
                   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
D115V3, 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"
D115V4, binary
                   cls
clus                  0   1
  CCDC147 MUTATED     5  10
  CCDC147 WILD-TYPE  81 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC147 MUTATED      5   10
  CCDC147 WILD-TYPE   81  152
     clus
vv    CCDC147 MUTATED CCDC147 WILD-TYPE
  NO                5                81
  YES              10               152
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC147 MUTATED    11   1   0   0
  CCDC147 WILD-TYPE 160  10   7  18
D115V5, multiclass
    clus
vv   CCDC147 MUTATED CCDC147 WILD-TYPE
  R0              11               160
  R1               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC147 MUTATED                                  0     2
  CCDC147 WILD-TYPE                                3    11
                   vv
clus                BLACK OR AFRICAN AMERICAN
  CCDC147 MUTATED                           1
  CCDC147 WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC147 MUTATED                                           1    10
  CCDC147 WILD-TYPE                                         6   183
D115V6, multiclass
                                           clus
vv                                          CCDC147 MUTATED CCDC147 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   2                11
  BLACK OR AFRICAN AMERICAN                               1                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 6
  WHITE                                                  10               183
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V7, binary
                   cls
clus                  0   1
  CCDC147 MUTATED     1   8
  CCDC147 WILD-TYPE   3 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC147 MUTATED      1    8
  CCDC147 WILD-TYPE    3  159
                        clus
vv                       CCDC147 MUTATED CCDC147 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               8               159
[1] 2 2
[1] FALSE

Clustering(116) Variable = SACS MUTATION ANALYSIS
D116V1, survival
                sevent
clus2              0   1
  SACS MUTATED    26   0
  SACS WILD-TYPE 198  24
  SACS MUTATED SACS WILD-TYPE 
            26            222 
  SACS MUTATED SACS WILD-TYPE 
             0             24 
$`SACS MUTATED`
TCGA-A5-A0GB TCGA-A5-A0GP TCGA-A5-A0VQ TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 
       32.78        46.55        15.95        83.67        86.07         8.22 
TCGA-AP-A05J TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A0J0 
       36.89        27.12        46.45        35.34        66.58        40.11 
TCGA-AX-A0J1 TCGA-B5-A0JR TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-BG-A0M4 
       65.88        56.91        32.55         8.71        43.96        34.98 
TCGA-BG-A0VX TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A0ZO 
       34.29        23.47        85.55        85.84        73.25        19.79 
TCGA-D1-A103 TCGA-D1-A16X 
       21.99         3.65 

$`SACS WILD-TYPE`
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         3.22       105.37 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GQ 
       74.10        57.53        65.75        60.53        60.53        38.37 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-AJ-A23M 
       19.59        24.62        29.06        11.97        42.35         1.18 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       21.99         5.95        23.31        39.42        57.80        45.53 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       28.54        37.78        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       19.36        80.38        46.75        43.13        40.67        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        17.85        11.01       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        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       19.33        20.94        35.21         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       16.34        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        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-A0UA TCGA-BS-A0UJ 
       96.49        30.74        97.41        67.20        88.34        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        62.79        63.58        49.55 
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-A102 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74         4.44        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-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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  SACS MUTATED SACS WILD-TYPE 
          3.65           0.56 
  SACS MUTATED SACS WILD-TYPE 
         86.07         185.79 
  SACS MUTATED SACS WILD-TYPE 
        36.115         28.440 
[1] "3.6 - 86.1 (36.1)"  "0.6 - 185.8 (28.4)"
[1] "hr="     "8.2e+07"
D116V2, continuous
                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
D116V3, 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"
D116V4, binary
                cls
clus               0   1
  SACS MUTATED     9  17
  SACS WILD-TYPE  77 145
[1] "tbl2"
                cls
clus             [,1] [,2]
  SACS MUTATED      9   17
  SACS WILD-TYPE   77  145
     clus
vv    SACS MUTATED SACS WILD-TYPE
  NO             9             77
  YES           17            145
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SACS MUTATED    18   2   0   2
  SACS WILD-TYPE 153   9   7  16
D116V5, multiclass
    clus
vv   SACS MUTATED SACS WILD-TYPE
  R0           18            153
  R1            2              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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SACS MUTATED                                  1     3
  SACS WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN
  SACS MUTATED                           1
  SACS WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SACS MUTATED                                           2    17
  SACS WILD-TYPE                                         5   176
D116V6, multiclass
                                           clus
vv                                          SACS MUTATED SACS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     1              2
  ASIAN                                                3             10
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            2              5
  WHITE                                               17            176
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V7, binary
                cls
clus               0   1
  SACS MUTATED     3  14
  SACS WILD-TYPE   1 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  SACS MUTATED      3   14
  SACS WILD-TYPE    1  153
                        clus
vv                       SACS MUTATED SACS WILD-TYPE
  HISPANIC OR LATINO                3              1
  NOT HISPANIC OR LATINO           14            153
[1] 2 2
[1] FALSE

Clustering(117) Variable = MUTED MUTATION ANALYSIS
D117V1, survival
                 sevent
clus2               0   1
  MUTED MUTATED     7   0
  MUTED WILD-TYPE 217  24
  MUTED MUTATED MUTED WILD-TYPE 
              7             241 
  MUTED MUTATED MUTED WILD-TYPE 
              0              24 
$`MUTED MUTATED`
TCGA-AP-A056 TCGA-B5-A0JY TCGA-B5-A11R TCGA-BS-A0TC TCGA-BS-A0UF TCGA-D1-A103 
       86.07        32.55        33.50        85.55        85.84        21.99 
TCGA-D1-A17Q 
        1.78 

$`MUTED WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       40.11        65.88        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        17.85        11.01         8.71       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        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       40.50        32.09        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  MUTED MUTATED MUTED WILD-TYPE 
           1.78            0.56 
  MUTED MUTATED MUTED WILD-TYPE 
          86.07          185.79 
  MUTED MUTATED MUTED WILD-TYPE 
          33.50           28.67 
[1] "1.8 - 86.1 (33.5)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.6e+07"
D117V2, continuous
                 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
D117V3, 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"
D117V4, binary
                 cls
clus                0   1
  MUTED MUTATED     2   5
  MUTED WILD-TYPE  84 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUTED MUTATED      2    5
  MUTED WILD-TYPE   84  157
     clus
vv    MUTED MUTATED MUTED WILD-TYPE
  NO              2              84
  YES             5             157
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MUTED MUTATED     5   0   0   0
  MUTED WILD-TYPE 166  11   7  18
D117V5, multiclass
    clus
vv   MUTED MUTATED MUTED WILD-TYPE
  R0             5             166
  R1             0              11
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MUTED MUTATED                                  0     2
  MUTED WILD-TYPE                                3    11
                 vv
clus              BLACK OR AFRICAN AMERICAN
  MUTED MUTATED                           1
  MUTED WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MUTED MUTATED                                           0     4
  MUTED WILD-TYPE                                         7   189
D117V6, multiclass
                                           clus
vv                                          MUTED MUTATED MUTED WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 2              11
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                 4             189
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V7, binary
                 cls
clus                0   1
  MUTED MUTATED     0   4
  MUTED WILD-TYPE   4 163
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUTED MUTATED      0    4
  MUTED WILD-TYPE    4  163
                        clus
vv                       MUTED MUTATED MUTED WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             163
[1] 2 2
[1] FALSE

Clustering(118) Variable = SLC44A3 MUTATION ANALYSIS
D118V1, survival
                   sevent
clus2                 0   1
  SLC44A3 MUTATED     6   0
  SLC44A3 WILD-TYPE 218  24
  SLC44A3 MUTATED SLC44A3 WILD-TYPE 
                6               242 
  SLC44A3 MUTATED SLC44A3 WILD-TYPE 
                0                24 
$`SLC44A3 MUTATED`
TCGA-AP-A051 TCGA-AP-A0LM TCGA-B5-A11E TCGA-BG-A0YU TCGA-BS-A0UF TCGA-D1-A16X 
       83.67        27.12         8.71        14.83        85.84         3.65 

$`SLC44A3 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        35.01        28.54        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       65.88        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       80.38        56.91        46.75        43.13        40.67        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        17.85        11.01       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  SLC44A3 MUTATED SLC44A3 WILD-TYPE 
             3.65              0.56 
  SLC44A3 MUTATED SLC44A3 WILD-TYPE 
            85.84            185.79 
  SLC44A3 MUTATED SLC44A3 WILD-TYPE 
           20.975            29.510 
[1] "3.6 - 85.8 (21.0)"  "0.6 - 185.8 (29.5)"
[1] "hr="     "9200000"
D118V2, continuous
                   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
D118V3, 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"
D118V4, binary
                   cls
clus                  0   1
  SLC44A3 MUTATED     2   4
  SLC44A3 WILD-TYPE  84 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A3 MUTATED      2    4
  SLC44A3 WILD-TYPE   84  158
     clus
vv    SLC44A3 MUTATED SLC44A3 WILD-TYPE
  NO                2                84
  YES               4               158
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC44A3 MUTATED     4   0   0   1
  SLC44A3 WILD-TYPE 167  11   7  17
D118V5, multiclass
    clus
vv   SLC44A3 MUTATED SLC44A3 WILD-TYPE
  R0               4               167
  R1               0                11
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC44A3 MUTATED                                  0     1
  SLC44A3 WILD-TYPE                                3    12
                   vv
clus                BLACK OR AFRICAN AMERICAN
  SLC44A3 MUTATED                           1
  SLC44A3 WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC44A3 MUTATED                                           0     4
  SLC44A3 WILD-TYPE                                         7   189
D118V6, multiclass
                                           clus
vv                                          SLC44A3 MUTATED SLC44A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                12
  BLACK OR AFRICAN AMERICAN                               1                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 7
  WHITE                                                   4               189
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V7, binary
                   cls
clus                  0   1
  SLC44A3 MUTATED     0   3
  SLC44A3 WILD-TYPE   4 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A3 MUTATED      0    3
  SLC44A3 WILD-TYPE    4  164
                        clus
vv                       SLC44A3 MUTATED SLC44A3 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               3               164
[1] 2 2
[1] FALSE

Clustering(119) Variable = ZNF674 MUTATION ANALYSIS
D119V1, survival
                  sevent
clus2                0   1
  ZNF674 MUTATED    14   0
  ZNF674 WILD-TYPE 210  24
  ZNF674 MUTATED ZNF674 WILD-TYPE 
              14              234 
  ZNF674 MUTATED ZNF674 WILD-TYPE 
               0               24 
$`ZNF674 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LE TCGA-AP-A0LI TCGA-AP-A0LM 
       83.67        86.07         8.22       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        32.55         8.71        34.29        85.55        85.84 
TCGA-BS-A0UV TCGA-D1-A17Q 
       73.25         1.78 

$`ZNF674 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99         3.39        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        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        41.95        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       34.98        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       37.78        65.88        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        17.85        11.01       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        24.39        26.66        16.34        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  ZNF674 MUTATED ZNF674 WILD-TYPE 
            1.78             0.56 
  ZNF674 MUTATED ZNF674 WILD-TYPE 
          110.37           185.79 
  ZNF674 MUTATED ZNF674 WILD-TYPE 
           56.68            28.59 
[1] "1.8 - 110.4 (56.7)" "0.6 - 185.8 (28.6)"
[1] "hr="     "7.5e+07"
D119V2, continuous
                  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
D119V3, 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"
D119V4, binary
                  cls
clus                 0   1
  ZNF674 MUTATED     6   8
  ZNF674 WILD-TYPE  80 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF674 MUTATED      6    8
  ZNF674 WILD-TYPE   80  154
     clus
vv    ZNF674 MUTATED ZNF674 WILD-TYPE
  NO               6               80
  YES              8              154
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF674 MUTATED    10   0   1   1
  ZNF674 WILD-TYPE 161  11   6  17
D119V5, multiclass
    clus
vv   ZNF674 MUTATED ZNF674 WILD-TYPE
  R0             10              161
  R1              0               11
  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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF674 MUTATED                                  0     2
  ZNF674 WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ZNF674 MUTATED                           2
  ZNF674 WILD-TYPE                        23
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF674 MUTATED                                           1     9
  ZNF674 WILD-TYPE                                         6   184
D119V6, multiclass
                                           clus
vv                                          ZNF674 MUTATED ZNF674 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              2               23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  9              184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V7, binary
                  cls
clus                 0   1
  ZNF674 MUTATED     0   7
  ZNF674 WILD-TYPE   4 160
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF674 MUTATED      0    7
  ZNF674 WILD-TYPE    4  160
                        clus
vv                       ZNF674 MUTATED ZNF674 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              160
[1] 2 2
[1] FALSE

Clustering(120) Variable = CCDC144A MUTATION ANALYSIS
D120V1, survival
                    sevent
clus2                  0   1
  CCDC144A MUTATED    17   1
  CCDC144A WILD-TYPE 207  23
  CCDC144A MUTATED CCDC144A WILD-TYPE 
                18                230 
  CCDC144A MUTATED CCDC144A WILD-TYPE 
                 1                 23 
$`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        46.45        35.34        40.11 
TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-B5-A11W TCGA-BS-A0UF 
       65.88        32.55         8.71        43.96        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         9.07 

$`CCDC144A WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A062 
       13.58        19.82        29.69        68.35        72.03        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       28.54        37.78        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        17.85        11.01       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        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11X TCGA-B5-A11Y 
       33.50        27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        81.57        86.93        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
        2.63        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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2F8 
       59.01        25.02 

  CCDC144A MUTATED CCDC144A WILD-TYPE 
              1.78               0.56 
  CCDC144A MUTATED CCDC144A WILD-TYPE 
             86.07             185.79 
  CCDC144A MUTATED CCDC144A WILD-TYPE 
            37.725             28.655 
[1] "1.8 - 86.1 (37.7)"  "0.6 - 185.8 (28.7)"
[1] "hr=" "2.1"
D120V2, continuous
                    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
D120V3, 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"
D120V4, binary
                    cls
clus                   0   1
  CCDC144A MUTATED     5  13
  CCDC144A WILD-TYPE  81 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CCDC144A MUTATED      5   13
  CCDC144A WILD-TYPE   81  149
     clus
vv    CCDC144A MUTATED CCDC144A WILD-TYPE
  NO                 5                 81
  YES               13                149
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  CCDC144A MUTATED    11   2   0   1
  CCDC144A WILD-TYPE 160   9   7  17
D120V5, multiclass
    clus
vv   CCDC144A MUTATED CCDC144A WILD-TYPE
  R0               11                160
  R1                2                  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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC144A MUTATED                                  1     3
  CCDC144A WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  CCDC144A MUTATED                           1
  CCDC144A WILD-TYPE                        24
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC144A MUTATED                                           1    11
  CCDC144A WILD-TYPE                                         6   182
D120V6, multiclass
                                           clus
vv                                          CCDC144A MUTATED CCDC144A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  2
  ASIAN                                                    3                 10
  BLACK OR AFRICAN AMERICAN                                1                 24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  6
  WHITE                                                   11                182
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V7, binary
                    cls
clus                   0   1
  CCDC144A MUTATED     1  11
  CCDC144A WILD-TYPE   3 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CCDC144A MUTATED      1   11
  CCDC144A WILD-TYPE    3  156
                        clus
vv                       CCDC144A MUTATED CCDC144A WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               11                156
[1] 2 2
[1] FALSE

Clustering(121) Variable = OR8B8 MUTATION ANALYSIS
D121V1, survival
                 sevent
clus2               0   1
  OR8B8 MUTATED     7   0
  OR8B8 WILD-TYPE 217  24
  OR8B8 MUTATED OR8B8 WILD-TYPE 
              7             241 
  OR8B8 MUTATED OR8B8 WILD-TYPE 
              0              24 
$`OR8B8 MUTATED`
TCGA-A5-A0GH TCGA-AP-A059 TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0UV 
       74.10         8.22        46.45        32.55         8.71        73.25 
TCGA-D1-A17Q 
        1.78 

$`OR8B8 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        37.78        40.11        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  OR8B8 MUTATED OR8B8 WILD-TYPE 
           1.78            0.56 
  OR8B8 MUTATED OR8B8 WILD-TYPE 
          74.10          185.79 
  OR8B8 MUTATED OR8B8 WILD-TYPE 
          32.55           29.06 
[1] "1.8 - 74.1 (32.5)"  "0.6 - 185.8 (29.1)"
[1] "hr="     "2.5e+07"
D121V2, continuous
                 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
D121V3, 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"
D121V4, binary
                 cls
clus                0   1
  OR8B8 MUTATED     1   6
  OR8B8 WILD-TYPE  85 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8B8 MUTATED      1    6
  OR8B8 WILD-TYPE   85  156
     clus
vv    OR8B8 MUTATED OR8B8 WILD-TYPE
  NO              1              85
  YES             6             156
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  OR8B8 MUTATED     4   1   0   0
  OR8B8 WILD-TYPE 167  10   7  18
D121V5, multiclass
    clus
vv   OR8B8 MUTATED OR8B8 WILD-TYPE
  R0             4             167
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR8B8 MUTATED                                  0     0
  OR8B8 WILD-TYPE                                3    13
                 vv
clus              BLACK OR AFRICAN AMERICAN
  OR8B8 MUTATED                           0
  OR8B8 WILD-TYPE                        25
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OR8B8 MUTATED                                           1     5
  OR8B8 WILD-TYPE                                         6   188
D121V6, multiclass
                                           clus
vv                                          OR8B8 MUTATED OR8B8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 0              13
  BLACK OR AFRICAN AMERICAN                             0              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                 5             188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V7, binary
                 cls
clus                0   1
  OR8B8 MUTATED     1   4
  OR8B8 WILD-TYPE   3 163
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8B8 MUTATED      1    4
  OR8B8 WILD-TYPE    3  163
                        clus
vv                       OR8B8 MUTATED OR8B8 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             4             163
[1] 2 2
[1] FALSE

Clustering(122) Variable = LNX2 MUTATION ANALYSIS
D122V1, survival
                sevent
clus2              0   1
  LNX2 MUTATED    14   0
  LNX2 WILD-TYPE 210  24
  LNX2 MUTATED LNX2 WILD-TYPE 
            14            234 
  LNX2 MUTATED LNX2 WILD-TYPE 
             0             24 
$`LNX2 MUTATED`
TCGA-AP-A051 TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E 
       83.67        46.45        40.11        65.88        32.55         8.71 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A0ZO TCGA-D1-A101 TCGA-D1-A103 
       85.84        82.39        73.25        19.79         1.74        21.99 
TCGA-D1-A160 TCGA-D1-A167 
        3.68        15.72 

$`LNX2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       72.03        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       27.39        60.66        35.01        28.54        37.78        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        40.67        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       11.01       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        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-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       67.20        88.34        81.57        86.93        72.72        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        49.55        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-A102 
        0.56         4.87        28.67        23.93        22.55         4.44 
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-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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  LNX2 MUTATED LNX2 WILD-TYPE 
          1.74           0.56 
  LNX2 MUTATED LNX2 WILD-TYPE 
         85.84         185.79 
  LNX2 MUTATED LNX2 WILD-TYPE 
        36.330         28.865 
[1] "1.7 - 85.8 (36.3)"  "0.6 - 185.8 (28.9)"
[1] "hr="     "2.7e+07"
D122V2, continuous
                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
D122V3, 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"
D122V4, binary
                cls
clus               0   1
  LNX2 MUTATED     2  12
  LNX2 WILD-TYPE  84 150
[1] "tbl2"
                cls
clus             [,1] [,2]
  LNX2 MUTATED      2   12
  LNX2 WILD-TYPE   84  150
     clus
vv    LNX2 MUTATED LNX2 WILD-TYPE
  NO             2             84
  YES           12            150
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LNX2 MUTATED    10   1   0   1
  LNX2 WILD-TYPE 161  10   7  17
D122V5, multiclass
    clus
vv   LNX2 MUTATED LNX2 WILD-TYPE
  R0           10            161
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LNX2 MUTATED                                  0     2
  LNX2 WILD-TYPE                                3    11
                vv
clus             BLACK OR AFRICAN AMERICAN
  LNX2 MUTATED                           0
  LNX2 WILD-TYPE                        25
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LNX2 MUTATED                                           1    10
  LNX2 WILD-TYPE                                         6   183
D122V6, multiclass
                                           clus
vv                                          LNX2 MUTATED LNX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                2             11
  BLACK OR AFRICAN AMERICAN                            0             25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                               10            183
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V7, binary
                cls
clus               0   1
  LNX2 MUTATED     1  10
  LNX2 WILD-TYPE   3 157
[1] "tbl2"
                cls
clus             [,1] [,2]
  LNX2 MUTATED      1   10
  LNX2 WILD-TYPE    3  157
                        clus
vv                       LNX2 MUTATED LNX2 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           10            157
[1] 2 2
[1] FALSE

Clustering(123) Variable = TMEM62 MUTATION ANALYSIS
D123V1, survival
                  sevent
clus2                0   1
  TMEM62 MUTATED     9   0
  TMEM62 WILD-TYPE 215  24
  TMEM62 MUTATED TMEM62 WILD-TYPE 
               9              239 
  TMEM62 MUTATED TMEM62 WILD-TYPE 
               0               24 
$`TMEM62 MUTATED`
TCGA-A5-A0VP TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A063 TCGA-B5-A0JY TCGA-BG-A0VW 
       42.35        27.12        46.45        66.58        32.55        16.34 
TCGA-BK-A0CB TCGA-BS-A0UV TCGA-D1-A103 
        6.21        73.25        21.99 

$`TMEM62 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       35.34        45.99        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       35.01        28.54        37.78        40.11        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        40.67        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       26.66        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       88.34        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74         4.44        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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  TMEM62 MUTATED TMEM62 WILD-TYPE 
            6.21             0.56 
  TMEM62 MUTATED TMEM62 WILD-TYPE 
           73.25           185.79 
  TMEM62 MUTATED TMEM62 WILD-TYPE 
           32.55            29.06 
[1] "6.2 - 73.2 (32.5)"  "0.6 - 185.8 (29.1)"
[1] "hr="     "2.6e+07"
D123V2, continuous
                  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
D123V3, 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"
D123V4, binary
                  cls
clus                 0   1
  TMEM62 MUTATED     2   7
  TMEM62 WILD-TYPE  84 155
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM62 MUTATED      2    7
  TMEM62 WILD-TYPE   84  155
     clus
vv    TMEM62 MUTATED TMEM62 WILD-TYPE
  NO               2               84
  YES              7              155
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TMEM62 MUTATED     7   1   0   0
  TMEM62 WILD-TYPE 164  10   7  18
D123V5, multiclass
    clus
vv   TMEM62 MUTATED TMEM62 WILD-TYPE
  R0              7              164
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM62 MUTATED                                  0     0
  TMEM62 WILD-TYPE                                3    13
                  vv
clus               BLACK OR AFRICAN AMERICAN
  TMEM62 MUTATED                           1
  TMEM62 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM62 MUTATED                                           1     6
  TMEM62 WILD-TYPE                                         6   187
D123V6, multiclass
                                           clus
vv                                          TMEM62 MUTATED TMEM62 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  0               13
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  6              187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V7, binary
                  cls
clus                 0   1
  TMEM62 MUTATED     1   6
  TMEM62 WILD-TYPE   3 161
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM62 MUTATED      1    6
  TMEM62 WILD-TYPE    3  161
                        clus
vv                       TMEM62 MUTATED TMEM62 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              6              161
[1] 2 2
[1] FALSE

Clustering(124) Variable = ATF7IP MUTATION ANALYSIS
D124V1, survival
                  sevent
clus2                0   1
  ATF7IP MUTATED    17   0
  ATF7IP WILD-TYPE 207  24
  ATF7IP MUTATED ATF7IP WILD-TYPE 
              17              231 
  ATF7IP MUTATED ATF7IP WILD-TYPE 
               0               24 
$`ATF7IP MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AX-A05W TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY 
       83.67         8.22        68.35        46.45        40.11        32.55 
TCGA-B5-A11E TCGA-B5-A11G TCGA-B5-A11H TCGA-BG-A0VZ TCGA-BS-A0UM TCGA-BS-A0UV 
        8.71       113.36        88.34        28.54        86.93        73.25 
TCGA-D1-A0ZS TCGA-D1-A103 TCGA-D1-A167 TCGA-D1-A16Y TCGA-D1-A17Q 
        4.87        21.99        15.72        17.49         1.78 

$`ATF7IP WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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-A05Y TCGA-AX-A060 
       41.95        13.58        19.82        29.69        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        65.88        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        40.67        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11F TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
      185.79        75.72        54.44        44.78        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0W1 
       15.42        24.39        26.66        16.34        34.29        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       81.57        72.72        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZU 
       16.83        19.79        29.95         8.55         0.56        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        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-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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  ATF7IP MUTATED ATF7IP WILD-TYPE 
            1.78             0.56 
  ATF7IP MUTATED ATF7IP WILD-TYPE 
          113.36           185.79 
  ATF7IP MUTATED ATF7IP WILD-TYPE 
           32.55            29.06 
[1] "1.8 - 113.4 (32.5)" "0.6 - 185.8 (29.1)"
[1] "hr="     "7.5e+07"
D124V2, continuous
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ATF7IP MUTATED                                        17
  ATF7IP WILD-TYPE                                     183
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ATF7IP MUTATED                               0
  ATF7IP WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ATF7IP MUTATED                                   0
  ATF7IP WILD-TYPE                                44
D124V3, multiclass
                                         clus
vv                                        ATF7IP MUTATED ATF7IP 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"
D124V4, binary
                  cls
clus                 0   1
  ATF7IP MUTATED     4  13
  ATF7IP WILD-TYPE  82 149
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATF7IP MUTATED      4   13
  ATF7IP WILD-TYPE   82  149
     clus
vv    ATF7IP MUTATED ATF7IP WILD-TYPE
  NO               4               82
  YES             13              149
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ATF7IP MUTATED    11   1   0   1
  ATF7IP WILD-TYPE 160  10   7  17
D124V5, multiclass
    clus
vv   ATF7IP MUTATED ATF7IP WILD-TYPE
  R0             11              160
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATF7IP MUTATED                                  0     0
  ATF7IP WILD-TYPE                                3    13
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ATF7IP MUTATED                           1
  ATF7IP WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATF7IP MUTATED                                           1    14
  ATF7IP WILD-TYPE                                         6   179
D124V6, multiclass
                                           clus
vv                                          ATF7IP MUTATED ATF7IP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  0               13
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                 14              179
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V7, binary
                  cls
clus                 0   1
  ATF7IP MUTATED     1  11
  ATF7IP WILD-TYPE   3 156
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATF7IP MUTATED      1   11
  ATF7IP WILD-TYPE    3  156
                        clus
vv                       ATF7IP MUTATED ATF7IP WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             11              156
[1] 2 2
[1] FALSE

Clustering(125) Variable = IL20 MUTATION ANALYSIS
D125V1, survival
                sevent
clus2              0   1
  IL20 MUTATED     7   0
  IL20 WILD-TYPE 217  24
  IL20 MUTATED IL20 WILD-TYPE 
             7            241 
  IL20 MUTATED IL20 WILD-TYPE 
             0             24 
$`IL20 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A060 TCGA-BS-A0UV 
       83.67        86.07        27.12        46.45        35.34        73.25 
TCGA-D1-A17N 
        1.51 

$`IL20 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A062 
       13.58        19.82        29.69        68.35        72.03        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       28.54        37.78        40.11        65.88        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       43.13        40.67        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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-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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  IL20 MUTATED IL20 WILD-TYPE 
          1.51           0.56 
  IL20 MUTATED IL20 WILD-TYPE 
         86.07         185.79 
  IL20 MUTATED IL20 WILD-TYPE 
         46.45          28.67 
[1] "1.5 - 86.1 (46.5)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.6e+07"
D125V2, continuous
                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
D125V3, 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"
D125V4, binary
                cls
clus               0   1
  IL20 MUTATED     4   3
  IL20 WILD-TYPE  82 159
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL20 MUTATED      4    3
  IL20 WILD-TYPE   82  159
     clus
vv    IL20 MUTATED IL20 WILD-TYPE
  NO             4             82
  YES            3            159
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IL20 MUTATED     5   2   0   0
  IL20 WILD-TYPE 166   9   7  18
D125V5, multiclass
    clus
vv   IL20 MUTATED IL20 WILD-TYPE
  R0            5            166
  R1            2              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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL20 MUTATED                                  1     0
  IL20 WILD-TYPE                                2    13
                vv
clus             BLACK OR AFRICAN AMERICAN
  IL20 MUTATED                           1
  IL20 WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IL20 MUTATED                                           1     2
  IL20 WILD-TYPE                                         6   191
D125V6, multiclass
                                           clus
vv                                          IL20 MUTATED IL20 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     1              2
  ASIAN                                                0             13
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                                2            191
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V7, binary
                cls
clus               0   1
  IL20 MUTATED     1   3
  IL20 WILD-TYPE   3 164
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL20 MUTATED      1    3
  IL20 WILD-TYPE    3  164
                        clus
vv                       IL20 MUTATED IL20 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            3            164
[1] 2 2
[1] FALSE

Clustering(126) Variable = C3AR1 MUTATION ANALYSIS
D126V1, survival
                 sevent
clus2               0   1
  C3AR1 MUTATED     8   0
  C3AR1 WILD-TYPE 216  24
  C3AR1 MUTATED C3AR1 WILD-TYPE 
              8             240 
  C3AR1 MUTATED C3AR1 WILD-TYPE 
              0              24 
$`C3AR1 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AX-A05Z TCGA-BG-A0M7 TCGA-BS-A0TC TCGA-BS-A0UA 
       83.67        86.07        46.45        38.37        85.55        88.34 
TCGA-BS-A0UF TCGA-D1-A17Q 
       85.84         1.78 

$`C3AR1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        37.78        40.11        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        46.75        43.13        40.67        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         8.71       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
        7.92        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD 
       10.22        10.16        24.99        46.95        23.47        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-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       97.41        67.20        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  C3AR1 MUTATED C3AR1 WILD-TYPE 
           1.78            0.56 
  C3AR1 MUTATED C3AR1 WILD-TYPE 
          88.34          185.79 
  C3AR1 MUTATED C3AR1 WILD-TYPE 
          84.61           28.59 
[1] "1.8 - 88.3 (84.6)"  "0.6 - 185.8 (28.6)"
[1] "hr="     "2.7e+07"
D126V2, continuous
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  C3AR1 MUTATED                                         8
  C3AR1 WILD-TYPE                                     192
                 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
D126V3, multiclass
                                         clus
vv                                        C3AR1 MUTATED C3AR1 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"
D126V4, binary
                 cls
clus                0   1
  C3AR1 MUTATED     3   5
  C3AR1 WILD-TYPE  83 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C3AR1 MUTATED      3    5
  C3AR1 WILD-TYPE   83  157
     clus
vv    C3AR1 MUTATED C3AR1 WILD-TYPE
  NO              3              83
  YES             5             157
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  C3AR1 MUTATED     7   1   0   0
  C3AR1 WILD-TYPE 164  10   7  18
D126V5, multiclass
    clus
vv   C3AR1 MUTATED C3AR1 WILD-TYPE
  R0             7             164
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C3AR1 MUTATED                                  0     2
  C3AR1 WILD-TYPE                                3    11
                 vv
clus              BLACK OR AFRICAN AMERICAN
  C3AR1 MUTATED                           0
  C3AR1 WILD-TYPE                        25
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C3AR1 MUTATED                                           0     5
  C3AR1 WILD-TYPE                                         7   188
D126V6, multiclass
                                           clus
vv                                          C3AR1 MUTATED C3AR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 2              11
  BLACK OR AFRICAN AMERICAN                             0              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                 5             188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V7, binary
                 cls
clus                0   1
  C3AR1 MUTATED     1   5
  C3AR1 WILD-TYPE   3 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C3AR1 MUTATED      1    5
  C3AR1 WILD-TYPE    3  162
                        clus
vv                       C3AR1 MUTATED C3AR1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             5             162
[1] 2 2
[1] FALSE

Clustering(127) Variable = PKD2 MUTATION ANALYSIS
D127V1, survival
                sevent
clus2              0   1
  PKD2 MUTATED     8   0
  PKD2 WILD-TYPE 216  24
  PKD2 MUTATED PKD2 WILD-TYPE 
             8            240 
  PKD2 MUTATED PKD2 WILD-TYPE 
             0             24 
$`PKD2 MUTATED`
TCGA-A5-A0GV TCGA-AP-A056 TCGA-AX-A05Z TCGA-B5-A0JY TCGA-BK-A0C9 TCGA-BS-A0UV 
       20.81        86.07        46.45        32.55        35.90        73.25 
TCGA-D1-A0ZO TCGA-D1-A17Q 
       19.79         1.78 

$`PKD2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       46.55        38.37        28.27        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        37.78        40.11        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         8.71       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        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-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  PKD2 MUTATED PKD2 WILD-TYPE 
          1.78           0.56 
  PKD2 MUTATED PKD2 WILD-TYPE 
         86.07         185.79 
  PKD2 MUTATED PKD2 WILD-TYPE 
        34.225         28.865 
[1] "1.8 - 86.1 (34.2)"  "0.6 - 185.8 (28.9)"
[1] "hr="     "2.6e+07"
D127V2, continuous
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PKD2 MUTATED                                         8
  PKD2 WILD-TYPE                                     192
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  PKD2 MUTATED                               0
  PKD2 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  PKD2 MUTATED                                   0
  PKD2 WILD-TYPE                                44
D127V3, multiclass
                                         clus
vv                                        PKD2 MUTATED PKD2 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"
D127V4, binary
                cls
clus               0   1
  PKD2 MUTATED     1   7
  PKD2 WILD-TYPE  85 155
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKD2 MUTATED      1    7
  PKD2 WILD-TYPE   85  155
     clus
vv    PKD2 MUTATED PKD2 WILD-TYPE
  NO             1             85
  YES            7            155
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PKD2 MUTATED     6   1   0   0
  PKD2 WILD-TYPE 165  10   7  18
D127V5, multiclass
    clus
vv   PKD2 MUTATED PKD2 WILD-TYPE
  R0            6            165
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PKD2 MUTATED                                  0     0
  PKD2 WILD-TYPE                                3    13
                vv
clus             BLACK OR AFRICAN AMERICAN
  PKD2 MUTATED                           0
  PKD2 WILD-TYPE                        25
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PKD2 MUTATED                                           1     6
  PKD2 WILD-TYPE                                         6   187
D127V6, multiclass
                                           clus
vv                                          PKD2 MUTATED PKD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                0             13
  BLACK OR AFRICAN AMERICAN                            0             25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                                6            187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V7, binary
                cls
clus               0   1
  PKD2 MUTATED     1   5
  PKD2 WILD-TYPE   3 162
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKD2 MUTATED      1    5
  PKD2 WILD-TYPE    3  162
                        clus
vv                       PKD2 MUTATED PKD2 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            5            162
[1] 2 2
[1] FALSE

Clustering(128) Variable = BMP5 MUTATION ANALYSIS
D128V1, survival
                sevent
clus2              0   1
  BMP5 MUTATED    13   0
  BMP5 WILD-TYPE 211  24
  BMP5 MUTATED BMP5 WILD-TYPE 
            13            235 
  BMP5 MUTATED BMP5 WILD-TYPE 
             0             24 
$`BMP5 MUTATED`
TCGA-A5-A0GP TCGA-AP-A051 TCGA-AP-A056 TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 
       46.55        83.67        86.07        46.45        40.11        65.88 
TCGA-B5-A11R TCGA-BG-A2AE TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A17Q 
       33.50        23.70        85.55        85.84        73.25         1.78 
TCGA-FI-A2EX 
        9.07 

$`BMP5 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A059 
       15.95         1.18        21.99         5.95        23.31         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       35.01        28.54        37.78        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       40.67        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       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        43.96        40.50        32.09        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BK-A0C9 
       13.78        14.73        14.01        15.45        15.45        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
       34.98         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       23.47        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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2F8 
       25.02 

  BMP5 MUTATED BMP5 WILD-TYPE 
          1.78           0.56 
  BMP5 MUTATED BMP5 WILD-TYPE 
         86.07         185.79 
  BMP5 MUTATED BMP5 WILD-TYPE 
         46.55          28.54 
[1] "1.8 - 86.1 (46.5)"  "0.6 - 185.8 (28.5)"
[1] "hr="     "7.5e+07"
D128V2, continuous
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  BMP5 MUTATED                                        12
  BMP5 WILD-TYPE                                     188
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  BMP5 MUTATED                               0
  BMP5 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  BMP5 MUTATED                                   1
  BMP5 WILD-TYPE                                43
D128V3, multiclass
                                         clus
vv                                        BMP5 MUTATED BMP5 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"
D128V4, binary
                cls
clus               0   1
  BMP5 MUTATED     3  10
  BMP5 WILD-TYPE  83 152
[1] "tbl2"
                cls
clus             [,1] [,2]
  BMP5 MUTATED      3   10
  BMP5 WILD-TYPE   83  152
     clus
vv    BMP5 MUTATED BMP5 WILD-TYPE
  NO             3             83
  YES           10            152
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BMP5 MUTATED    10   1   0   0
  BMP5 WILD-TYPE 161  10   7  18
D128V5, multiclass
    clus
vv   BMP5 MUTATED BMP5 WILD-TYPE
  R0           10            161
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BMP5 MUTATED                                  0     3
  BMP5 WILD-TYPE                                3    10
                vv
clus             BLACK OR AFRICAN AMERICAN
  BMP5 MUTATED                           1
  BMP5 WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BMP5 MUTATED                                           1     7
  BMP5 WILD-TYPE                                         6   186
D128V6, multiclass
                                           clus
vv                                          BMP5 MUTATED BMP5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                3             10
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                                7            186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V7, binary
                cls
clus               0   1
  BMP5 MUTATED     1   9
  BMP5 WILD-TYPE   3 158
[1] "tbl2"
                cls
clus             [,1] [,2]
  BMP5 MUTATED      1    9
  BMP5 WILD-TYPE    3  158
                        clus
vv                       BMP5 MUTATED BMP5 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            9            158
[1] 2 2
[1] FALSE

Clustering(129) Variable = OR52I2 MUTATION ANALYSIS
D129V1, survival
                  sevent
clus2                0   1
  OR52I2 MUTATED     7   1
  OR52I2 WILD-TYPE 217  23
  OR52I2 MUTATED OR52I2 WILD-TYPE 
               8              240 
  OR52I2 MUTATED OR52I2 WILD-TYPE 
               1               23 
$`OR52I2 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A0L8 TCGA-AX-A0J0 TCGA-BK-A0CA TCGA-BS-A0UV 
       83.67        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       20.91       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       46.75        43.13        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         8.71       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        15.45        23.70        35.90         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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-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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  OR52I2 MUTATED OR52I2 WILD-TYPE 
            1.78             0.56 
  OR52I2 MUTATED OR52I2 WILD-TYPE 
           86.07           185.79 
  OR52I2 MUTATED OR52I2 WILD-TYPE 
          44.450           28.655 
[1] "1.8 - 86.1 (44.5)"  "0.6 - 185.8 (28.7)"
[1] "hr=" "1"  
D129V2, continuous
                  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
D129V3, 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"
D129V4, binary
                  cls
clus                 0   1
  OR52I2 MUTATED     4   4
  OR52I2 WILD-TYPE  82 158
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52I2 MUTATED      4    4
  OR52I2 WILD-TYPE   82  158
     clus
vv    OR52I2 MUTATED OR52I2 WILD-TYPE
  NO               4               82
  YES              4              158
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  OR52I2 MUTATED     7   0   0   1
  OR52I2 WILD-TYPE 164  11   7  17
D129V5, multiclass
    clus
vv   OR52I2 MUTATED OR52I2 WILD-TYPE
  R0              7              164
  R1              0               11
  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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR52I2 MUTATED                                  0     0
  OR52I2 WILD-TYPE                                3    13
                  vv
clus               BLACK OR AFRICAN AMERICAN
  OR52I2 MUTATED                           1
  OR52I2 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OR52I2 MUTATED                                           1     6
  OR52I2 WILD-TYPE                                         6   187
D129V6, multiclass
                                           clus
vv                                          OR52I2 MUTATED OR52I2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  0               13
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  6              187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V7, binary
                  cls
clus                 0   1
  OR52I2 MUTATED     0   5
  OR52I2 WILD-TYPE   4 162
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52I2 MUTATED      0    5
  OR52I2 WILD-TYPE    4  162
                        clus
vv                       OR52I2 MUTATED OR52I2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              162
[1] 2 2
[1] FALSE

Clustering(130) Variable = C1ORF100 MUTATION ANALYSIS
D130V1, survival
                    sevent
clus2                  0   1
  C1ORF100 MUTATED     9   0
  C1ORF100 WILD-TYPE 215  24
  C1ORF100 MUTATED C1ORF100 WILD-TYPE 
                 9                239 
  C1ORF100 MUTATED C1ORF100 WILD-TYPE 
                 0                 24 
$`C1ORF100 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LE TCGA-AX-A05Z TCGA-AX-A0J1 TCGA-B5-A0JY 
       83.67         8.22       110.37        46.45        65.88        32.55 
TCGA-B5-A11E TCGA-B5-A11R TCGA-BS-A0UV 
        8.71        33.50        73.25 

$`C1ORF100 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LF TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        40.11        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        40.67        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
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 
       43.96        40.50        32.09        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        67.20        88.34 
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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  C1ORF100 MUTATED C1ORF100 WILD-TYPE 
              8.22               0.56 
  C1ORF100 MUTATED C1ORF100 WILD-TYPE 
            110.37             185.79 
  C1ORF100 MUTATED C1ORF100 WILD-TYPE 
             46.45              28.64 
[1] "8.2 - 110.4 (46.5)" "0.6 - 185.8 (28.6)"
[1] "hr="     "2.6e+07"
D130V2, continuous
                    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
D130V3, 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"
D130V4, binary
                    cls
clus                   0   1
  C1ORF100 MUTATED     4   5
  C1ORF100 WILD-TYPE  82 157
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF100 MUTATED      4    5
  C1ORF100 WILD-TYPE   82  157
     clus
vv    C1ORF100 MUTATED C1ORF100 WILD-TYPE
  NO                 4                 82
  YES                5                157
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C1ORF100 MUTATED     5   1   0   0
  C1ORF100 WILD-TYPE 166  10   7  18
D130V5, multiclass
    clus
vv   C1ORF100 MUTATED C1ORF100 WILD-TYPE
  R0                5                166
  R1                1                 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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF100 MUTATED                                  0     0
  C1ORF100 WILD-TYPE                                3    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  C1ORF100 MUTATED                           1
  C1ORF100 WILD-TYPE                        24
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C1ORF100 MUTATED                                           1     6
  C1ORF100 WILD-TYPE                                         6   187
D130V6, multiclass
                                           clus
vv                                          C1ORF100 MUTATED C1ORF100 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    0                 13
  BLACK OR AFRICAN AMERICAN                                1                 24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  6
  WHITE                                                    6                187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V7, binary
                    cls
clus                   0   1
  C1ORF100 MUTATED     1   3
  C1ORF100 WILD-TYPE   3 164
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF100 MUTATED      1    3
  C1ORF100 WILD-TYPE    3  164
                        clus
vv                       C1ORF100 MUTATED C1ORF100 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO                3                164
[1] 2 2
[1] FALSE

Clustering(131) Variable = CCDC160 MUTATION ANALYSIS
D131V1, survival
                   sevent
clus2                 0   1
  CCDC160 MUTATED    11   0
  CCDC160 WILD-TYPE 213  24
  CCDC160 MUTATED CCDC160 WILD-TYPE 
               11               237 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
                0                24 
$`CCDC160 MUTATED`
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A0LM TCGA-B5-A0JY 
       74.10        57.53        83.67        86.07        27.12        32.55 
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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      105.37        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.59        24.62        29.06        11.97        42.35        15.95 
TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A 
        1.18        21.99         5.95        23.31         8.22        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        45.53        36.89         7.86        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        31.73        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        41.95        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       28.54        37.78        40.11        65.88        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        40.67        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        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 
       67.20        88.34        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74         4.44        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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  CCDC160 MUTATED CCDC160 WILD-TYPE 
             1.78              0.56 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
            86.07            185.79 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
            57.53             28.67 
[1] "1.8 - 86.1 (57.5)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.7e+07"
D131V2, continuous
                   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
D131V3, 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"
D131V4, binary
                   cls
clus                  0   1
  CCDC160 MUTATED     4   7
  CCDC160 WILD-TYPE  82 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC160 MUTATED      4    7
  CCDC160 WILD-TYPE   82  155
     clus
vv    CCDC160 MUTATED CCDC160 WILD-TYPE
  NO                4                82
  YES               7               155
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC160 MUTATED    10   0   0   0
  CCDC160 WILD-TYPE 161  11   7  18
D131V5, multiclass
    clus
vv   CCDC160 MUTATED CCDC160 WILD-TYPE
  R0              10               161
  R1               0                11
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC160 MUTATED                                  0     1
  CCDC160 WILD-TYPE                                3    12
                   vv
clus                BLACK OR AFRICAN AMERICAN
  CCDC160 MUTATED                           1
  CCDC160 WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC160 MUTATED                                           1     8
  CCDC160 WILD-TYPE                                         6   185
D131V6, multiclass
                                           clus
vv                                          CCDC160 MUTATED CCDC160 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                12
  BLACK OR AFRICAN AMERICAN                               1                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 6
  WHITE                                                   8               185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V7, binary
                   cls
clus                  0   1
  CCDC160 MUTATED     0   7
  CCDC160 WILD-TYPE   4 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC160 MUTATED      0    7
  CCDC160 WILD-TYPE    4  160
                        clus
vv                       CCDC160 MUTATED CCDC160 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               160
[1] 2 2
[1] FALSE

Clustering(132) Variable = NAA15 MUTATION ANALYSIS
D132V1, survival
                 sevent
clus2               0   1
  NAA15 MUTATED    13   1
  NAA15 WILD-TYPE 211  23
  NAA15 MUTATED NAA15 WILD-TYPE 
             14             234 
  NAA15 MUTATED NAA15 WILD-TYPE 
              1              23 
$`NAA15 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J1 
       83.67        86.07         8.22        27.12        46.45        65.88 
TCGA-B5-A11E TCGA-B5-A121 TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A16G 
        8.71        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       28.54        37.78        40.11        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       40.67        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
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 
       43.96        40.50        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A1MU 
       19.56        19.50        19.59        18.41        17.36        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       23.47        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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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-A16I TCGA-D1-A16N 
       36.36        37.51        36.79         2.63        11.51        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-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 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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  NAA15 MUTATED NAA15 WILD-TYPE 
           8.22            0.56 
  NAA15 MUTATED NAA15 WILD-TYPE 
          86.07          185.79 
  NAA15 MUTATED NAA15 WILD-TYPE 
         38.185          28.865 
[1] "8.2 - 86.1 (38.2)"  "0.6 - 185.8 (28.9)"
[1] "hr=" "1.8"
D132V2, continuous
                 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
D132V3, 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"
D132V4, binary
                 cls
clus                0   1
  NAA15 MUTATED     7   7
  NAA15 WILD-TYPE  79 155
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA15 MUTATED      7    7
  NAA15 WILD-TYPE   79  155
     clus
vv    NAA15 MUTATED NAA15 WILD-TYPE
  NO              7              79
  YES             7             155
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NAA15 MUTATED    10   1   0   1
  NAA15 WILD-TYPE 161  10   7  17
D132V5, multiclass
    clus
vv   NAA15 MUTATED NAA15 WILD-TYPE
  R0            10             161
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NAA15 MUTATED                                  0     2
  NAA15 WILD-TYPE                                3    11
                 vv
clus              BLACK OR AFRICAN AMERICAN
  NAA15 MUTATED                           1
  NAA15 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NAA15 MUTATED                                           1     9
  NAA15 WILD-TYPE                                         6   184
D132V6, multiclass
                                           clus
vv                                          NAA15 MUTATED NAA15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 2              11
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                 9             184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V7, binary
                 cls
clus                0   1
  NAA15 MUTATED     1   8
  NAA15 WILD-TYPE   3 159
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA15 MUTATED      1    8
  NAA15 WILD-TYPE    3  159
                        clus
vv                       NAA15 MUTATED NAA15 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             8             159
[1] 2 2
[1] FALSE

Clustering(133) Variable = RNF31 MUTATION ANALYSIS
D133V1, survival
                 sevent
clus2               0   1
  RNF31 MUTATED    17   0
  RNF31 WILD-TYPE 207  24
  RNF31 MUTATED RNF31 WILD-TYPE 
             17             231 
  RNF31 MUTATED RNF31 WILD-TYPE 
              0              24 
$`RNF31 MUTATED`
TCGA-A5-A0GP TCGA-A5-A0GV TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM 
       46.55        20.81        83.67        86.07         8.22        27.12 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-B5-A0JY TCGA-B5-A0K4 TCGA-B5-A11E TCGA-BS-A0UV 
       46.45        35.34        32.55        17.88         8.71        73.25 
TCGA-D1-A0ZO TCGA-D1-A167 TCGA-D1-A17C TCGA-FI-A2EW TCGA-FI-A2EX 
       19.79        15.72         0.99        59.01         9.07 

$`RNF31 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       38.37        28.27        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.59        24.62        29.06        11.97        42.35        15.95 
TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D 
        1.18        21.99         5.95        23.31        39.42        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89         7.86        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        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        41.95        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       68.35        72.03        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        35.01        28.54        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       65.88        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       80.38        56.91        46.75        43.13        40.67        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 
       28.34        30.51        25.91        23.01        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        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-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        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-A17D TCGA-D1-A17F 
       30.15        18.02         1.58         7.00        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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2F8 
        3.62        36.00        25.02 

  RNF31 MUTATED RNF31 WILD-TYPE 
           0.99            0.56 
  RNF31 MUTATED RNF31 WILD-TYPE 
          86.07          185.79 
  RNF31 MUTATED RNF31 WILD-TYPE 
          27.12           29.33 
[1] "1.0 - 86.1 (27.1)"  "0.6 - 185.8 (29.3)"
[1] "hr="     "2.7e+07"
D133V2, continuous
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  RNF31 MUTATED                                        15
  RNF31 WILD-TYPE                                     185
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  RNF31 MUTATED                               0
  RNF31 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  RNF31 MUTATED                                   2
  RNF31 WILD-TYPE                                42
D133V3, multiclass
                                         clus
vv                                        RNF31 MUTATED RNF31 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"
D133V4, binary
                 cls
clus                0   1
  RNF31 MUTATED     7  10
  RNF31 WILD-TYPE  79 152
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF31 MUTATED      7   10
  RNF31 WILD-TYPE   79  152
     clus
vv    RNF31 MUTATED RNF31 WILD-TYPE
  NO              7              79
  YES            10             152
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RNF31 MUTATED    12   2   0   0
  RNF31 WILD-TYPE 159   9   7  18
D133V5, multiclass
    clus
vv   RNF31 MUTATED RNF31 WILD-TYPE
  R0            12             159
  R1             2               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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF31 MUTATED                                  1     1
  RNF31 WILD-TYPE                                2    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  RNF31 MUTATED                           2
  RNF31 WILD-TYPE                        23
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RNF31 MUTATED                                           1    10
  RNF31 WILD-TYPE                                         6   183
D133V6, multiclass
                                           clus
vv                                          RNF31 MUTATED RNF31 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      1               2
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             2              23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                10             183
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V7, binary
                 cls
clus                0   1
  RNF31 MUTATED     1   9
  RNF31 WILD-TYPE   3 158
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF31 MUTATED      1    9
  RNF31 WILD-TYPE    3  158
                        clus
vv                       RNF31 MUTATED RNF31 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             9             158
[1] 2 2
[1] FALSE

Clustering(134) Variable = NFE2L3 MUTATION ANALYSIS
D134V1, survival
                  sevent
clus2                0   1
  NFE2L3 MUTATED    12   0
  NFE2L3 WILD-TYPE 212  24
  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
              12              236 
  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
               0               24 
$`NFE2L3 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-B5-A11I TCGA-BS-A0UV 
       83.67        86.07         8.22        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        15.09        36.00 

$`NFE2L3 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       35.01        28.54        37.78        40.11        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       46.75        43.13        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         8.71       185.79       113.36        88.34 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        44.78        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74         4.44        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-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-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-A212 TCGA-FI-A2EW 
       35.38        48.36        10.92        10.78         3.62        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
            1.78             0.56 
  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
           86.07           185.79 
  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
          30.160           28.865 
[1] "1.8 - 86.1 (30.2)"  "0.6 - 185.8 (28.9)"
[1] "hr="     "2.6e+07"
D134V2, continuous
                  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
D134V3, 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"
D134V4, binary
                  cls
clus                 0   1
  NFE2L3 MUTATED     7   5
  NFE2L3 WILD-TYPE  79 157
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L3 MUTATED      7    5
  NFE2L3 WILD-TYPE   79  157
     clus
vv    NFE2L3 MUTATED NFE2L3 WILD-TYPE
  NO               7               79
  YES              5              157
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NFE2L3 MUTATED    10   0   1   0
  NFE2L3 WILD-TYPE 161  11   6  18
D134V5, multiclass
    clus
vv   NFE2L3 MUTATED NFE2L3 WILD-TYPE
  R0             10              161
  R1              0               11
  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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFE2L3 MUTATED                                  0     0
  NFE2L3 WILD-TYPE                                3    13
                  vv
clus               BLACK OR AFRICAN AMERICAN
  NFE2L3 MUTATED                           3
  NFE2L3 WILD-TYPE                        22
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NFE2L3 MUTATED                                           1     8
  NFE2L3 WILD-TYPE                                         6   185
D134V6, multiclass
                                           clus
vv                                          NFE2L3 MUTATED NFE2L3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  0               13
  BLACK OR AFRICAN AMERICAN                              3               22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  8              185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V7, binary
                  cls
clus                 0   1
  NFE2L3 MUTATED     0   8
  NFE2L3 WILD-TYPE   4 159
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L3 MUTATED      0    8
  NFE2L3 WILD-TYPE    4  159
                        clus
vv                       NFE2L3 MUTATED NFE2L3 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              159
[1] 2 2
[1] FALSE

Clustering(135) Variable = ZKSCAN1 MUTATION ANALYSIS
D135V1, survival
                   sevent
clus2                 0   1
  ZKSCAN1 MUTATED     7   0
  ZKSCAN1 WILD-TYPE 217  24
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                7               241 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                0                24 
$`ZKSCAN1 MUTATED`
TCGA-AP-A059 TCGA-AX-A0J1 TCGA-BG-A18B TCGA-BS-A0UF TCGA-D1-A103 TCGA-D1-A15X 
        8.22        65.88        15.45        85.84        21.99        29.88 
TCGA-D1-A163 
       32.58 

$`ZKSCAN1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       40.11        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       80.38        56.91        46.75        43.13        40.67        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        17.85        11.01         8.71       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        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
        4.44        39.48        30.08         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-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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
             8.22              0.56 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
            85.84            185.79 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
            29.88             29.06 
[1] "8.2 - 85.8 (29.9)"  "0.6 - 185.8 (29.1)"
[1] "hr="     "2.5e+07"
D135V2, continuous
                   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
D135V3, 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"
D135V4, binary
                   cls
clus                  0   1
  ZKSCAN1 MUTATED     3   4
  ZKSCAN1 WILD-TYPE  83 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN1 MUTATED      3    4
  ZKSCAN1 WILD-TYPE   83  158
     clus
vv    ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  NO                3                83
  YES               4               158
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZKSCAN1 MUTATED     6   0   0   1
  ZKSCAN1 WILD-TYPE 165  11   7  17
D135V5, multiclass
    clus
vv   ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  R0               6               165
  R1               0                11
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZKSCAN1 MUTATED                                  0     1
  ZKSCAN1 WILD-TYPE                                3    12
                   vv
clus                BLACK OR AFRICAN AMERICAN
  ZKSCAN1 MUTATED                           0
  ZKSCAN1 WILD-TYPE                        25
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZKSCAN1 MUTATED                                           0     6
  ZKSCAN1 WILD-TYPE                                         7   187
D135V6, multiclass
                                           clus
vv                                          ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                12
  BLACK OR AFRICAN AMERICAN                               0                25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 7
  WHITE                                                   6               187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V7, binary
                   cls
clus                  0   1
  ZKSCAN1 MUTATED     0   7
  ZKSCAN1 WILD-TYPE   4 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN1 MUTATED      0    7
  ZKSCAN1 WILD-TYPE    4  160
                        clus
vv                       ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               160
[1] 2 2
[1] FALSE

Clustering(136) Variable = CDKL1 MUTATION ANALYSIS
D136V1, survival
                 sevent
clus2               0   1
  CDKL1 MUTATED     7   0
  CDKL1 WILD-TYPE 217  24
  CDKL1 MUTATED CDKL1 WILD-TYPE 
              7             241 
  CDKL1 MUTATED CDKL1 WILD-TYPE 
              0              24 
$`CDKL1 MUTATED`
TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-BG-A186 TCGA-BS-A0UV TCGA-D1-A16X 
       86.07        27.12        46.45        13.78        73.25         3.65 
TCGA-D1-A17Q 
        1.78 

$`CDKL1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        37.78        40.11        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        46.75        43.13        40.67        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         8.71       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  CDKL1 MUTATED CDKL1 WILD-TYPE 
           1.78            0.56 
  CDKL1 MUTATED CDKL1 WILD-TYPE 
          86.07          185.79 
  CDKL1 MUTATED CDKL1 WILD-TYPE 
          27.12           29.33 
[1] "1.8 - 86.1 (27.1)"  "0.6 - 185.8 (29.3)"
[1] "hr="     "2.5e+07"
D136V2, continuous
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CDKL1 MUTATED                                         7
  CDKL1 WILD-TYPE                                     193
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  CDKL1 MUTATED                               0
  CDKL1 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  CDKL1 MUTATED                                   0
  CDKL1 WILD-TYPE                                44
D136V3, multiclass
                                         clus
vv                                        CDKL1 MUTATED CDKL1 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"
D136V4, binary
                 cls
clus                0   1
  CDKL1 MUTATED     2   5
  CDKL1 WILD-TYPE  84 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL1 MUTATED      2    5
  CDKL1 WILD-TYPE   84  157
     clus
vv    CDKL1 MUTATED CDKL1 WILD-TYPE
  NO              2              84
  YES             5             157
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDKL1 MUTATED     5   1   0   1
  CDKL1 WILD-TYPE 166  10   7  17
D136V5, multiclass
    clus
vv   CDKL1 MUTATED CDKL1 WILD-TYPE
  R0             5             166
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDKL1 MUTATED                                  0     0
  CDKL1 WILD-TYPE                                3    13
                 vv
clus              BLACK OR AFRICAN AMERICAN
  CDKL1 MUTATED                           2
  CDKL1 WILD-TYPE                        23
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDKL1 MUTATED                                           1     3
  CDKL1 WILD-TYPE                                         6   190
D136V6, multiclass
                                           clus
vv                                          CDKL1 MUTATED CDKL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 0              13
  BLACK OR AFRICAN AMERICAN                             2              23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                 3             190
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V7, binary
                 cls
clus                0   1
  CDKL1 MUTATED     1   4
  CDKL1 WILD-TYPE   3 163
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL1 MUTATED      1    4
  CDKL1 WILD-TYPE    3  163
                        clus
vv                       CDKL1 MUTATED CDKL1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             4             163
[1] 2 2
[1] FALSE

Clustering(137) Variable = ERBB3 MUTATION ANALYSIS
D137V1, survival
                 sevent
clus2               0   1
  ERBB3 MUTATED    17   0
  ERBB3 WILD-TYPE 207  24
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             17             231 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
              0              24 
$`ERBB3 MUTATED`
TCGA-A5-A0VP TCGA-AP-A051 TCGA-AX-A060 TCGA-AX-A0J0 TCGA-B5-A11R TCGA-B5-A11V 
       42.35        83.67        35.34        40.11        33.50        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
       15.95         1.18        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       46.45        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       46.75        43.13        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         8.71       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        43.96        40.50        32.09 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YV 
       16.34        34.29        28.54        52.83        56.58        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       13.78        14.73        14.01        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        67.20        88.34 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        86.93        72.72        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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-A16N 
       37.51        36.79         2.63        27.42        11.51        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A176 
       33.63        10.65         0.69        18.67         3.65        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-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
       24.30         2.33        22.92        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  ERBB3 MUTATED ERBB3 WILD-TYPE 
          13.22            0.56 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
          85.84          185.79 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
          29.92           29.06 
[1] "13.2 - 85.8 (29.9)" "0.6 - 185.8 (29.1)"
[1] "hr="     "7.4e+07"
D137V2, continuous
                 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
D137V3, 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"
D137V4, binary
                 cls
clus                0   1
  ERBB3 MUTATED     7  10
  ERBB3 WILD-TYPE  79 152
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      7   10
  ERBB3 WILD-TYPE   79  152
     clus
vv    ERBB3 MUTATED ERBB3 WILD-TYPE
  NO              7              79
  YES            10             152
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ERBB3 MUTATED    11   1   0   3
  ERBB3 WILD-TYPE 160  10   7  15
D137V5, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  R0            11             160
  R1             1              10
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERBB3 MUTATED                                  1     2
  ERBB3 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN
  ERBB3 MUTATED                           2
  ERBB3 WILD-TYPE                        23
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ERBB3 MUTATED                                           1    11
  ERBB3 WILD-TYPE                                         6   182
D137V6, multiclass
                                           clus
vv                                          ERBB3 MUTATED ERBB3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      1               2
  ASIAN                                                 2              11
  BLACK OR AFRICAN AMERICAN                             2              23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                11             182
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V7, binary
                 cls
clus                0   1
  ERBB3 MUTATED     0  14
  ERBB3 WILD-TYPE   4 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      0   14
  ERBB3 WILD-TYPE    4  153
                        clus
vv                       ERBB3 MUTATED ERBB3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            14             153
[1] 2 2
[1] FALSE

Clustering(138) Variable = SELP MUTATION ANALYSIS
D138V1, survival
                sevent
clus2              0   1
  SELP MUTATED     8   1
  SELP WILD-TYPE 216  23
  SELP MUTATED SELP WILD-TYPE 
             9            239 
  SELP MUTATED SELP WILD-TYPE 
             1             23 
$`SELP MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A05Z TCGA-B5-A0JY TCGA-BS-A0TE 
       83.67        86.07         8.22        46.45        32.55         4.80 
TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A16X 
       85.84        73.25         3.65 

$`SELP WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       35.01        28.54        37.78        40.11        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        40.67        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        85.55        78.21 
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 
       67.20        88.34        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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-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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  SELP MUTATED SELP WILD-TYPE 
          3.65           0.56 
  SELP MUTATED SELP WILD-TYPE 
         86.07         185.79 
  SELP MUTATED SELP WILD-TYPE 
         46.45          28.67 
[1] "3.6 - 86.1 (46.5)"  "0.6 - 185.8 (28.7)"
[1] "hr=" "1"  
D138V2, continuous
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SELP MUTATED                                         9
  SELP WILD-TYPE                                     191
                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
D138V3, multiclass
                                         clus
vv                                        SELP MUTATED SELP 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"
D138V4, binary
                cls
clus               0   1
  SELP MUTATED     3   6
  SELP WILD-TYPE  83 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELP MUTATED      3    6
  SELP WILD-TYPE   83  156
     clus
vv    SELP MUTATED SELP WILD-TYPE
  NO             3             83
  YES            6            156
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SELP MUTATED     6   1   1   0
  SELP WILD-TYPE 165  10   6  18
D138V5, multiclass
    clus
vv   SELP MUTATED SELP WILD-TYPE
  R0            6            165
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SELP MUTATED                                  0     2
  SELP WILD-TYPE                                3    11
                vv
clus             BLACK OR AFRICAN AMERICAN
  SELP MUTATED                           0
  SELP WILD-TYPE                        25
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SELP MUTATED                                           1     5
  SELP WILD-TYPE                                         6   188
D138V6, multiclass
                                           clus
vv                                          SELP MUTATED SELP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                2             11
  BLACK OR AFRICAN AMERICAN                            0             25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                                5            188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V7, binary
                cls
clus               0   1
  SELP MUTATED     1   5
  SELP WILD-TYPE   3 162
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELP MUTATED      1    5
  SELP WILD-TYPE    3  162
                        clus
vv                       SELP MUTATED SELP WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            5            162
[1] 2 2
[1] FALSE

Clustering(139) Variable = PPIG MUTATION ANALYSIS
D139V1, survival
                sevent
clus2              0   1
  PPIG MUTATED    16   0
  PPIG WILD-TYPE 208  24
  PPIG MUTATED PPIG WILD-TYPE 
            16            232 
  PPIG MUTATED PPIG WILD-TYPE 
             0             24 
$`PPIG MUTATED`
TCGA-A5-A0GB TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z 
       32.78        83.67        86.07         8.22        27.12        46.45 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-BG-A0LX TCGA-D1-A0ZS TCGA-D1-A103 
       40.11        65.88        32.55        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GE 
       46.95        37.02        83.51        17.85         3.22       105.37 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A 
       15.95         1.18        21.99         5.95        23.31        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        45.53        36.89         7.86        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        31.73        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        41.95        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        68.35        72.03        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       34.98        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       37.78        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       80.38        56.91        46.75        43.13        40.67        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         8.71       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       18.61        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        0.56        28.67        23.93        22.55         1.74         4.44 
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-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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  PPIG MUTATED PPIG WILD-TYPE 
          1.78           0.56 
  PPIG MUTATED PPIG WILD-TYPE 
         86.07         185.79 
  PPIG MUTATED PPIG WILD-TYPE 
        24.555         29.510 
[1] "1.8 - 86.1 (24.6)"  "0.6 - 185.8 (29.5)"
[1] "hr="     "2.6e+07"
D139V2, continuous
                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
D139V3, 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"
D139V4, binary
                cls
clus               0   1
  PPIG MUTATED     8   8
  PPIG WILD-TYPE  78 154
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      8    8
  PPIG WILD-TYPE   78  154
     clus
vv    PPIG MUTATED PPIG WILD-TYPE
  NO             8             78
  YES            8            154
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PPIG MUTATED    13   1   0   1
  PPIG WILD-TYPE 158  10   7  17
D139V5, multiclass
    clus
vv   PPIG MUTATED PPIG WILD-TYPE
  R0           13            158
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPIG MUTATED                                  0     0
  PPIG WILD-TYPE                                3    13
                vv
clus             BLACK OR AFRICAN AMERICAN
  PPIG MUTATED                           1
  PPIG WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPIG MUTATED                                           0    14
  PPIG WILD-TYPE                                         7   179
D139V6, multiclass
                                           clus
vv                                          PPIG MUTATED PPIG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                0             13
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              7
  WHITE                                               14            179
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V7, binary
                cls
clus               0   1
  PPIG MUTATED     1  10
  PPIG WILD-TYPE   3 157
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      1   10
  PPIG WILD-TYPE    3  157
                        clus
vv                       PPIG MUTATED PPIG WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           10            157
[1] 2 2
[1] FALSE

Clustering(140) Variable = GPRASP1 MUTATION ANALYSIS
D140V1, survival
                   sevent
clus2                 0   1
  GPRASP1 MUTATED    21   0
  GPRASP1 WILD-TYPE 203  24
  GPRASP1 MUTATED GPRASP1 WILD-TYPE 
               21               227 
  GPRASP1 MUTATED GPRASP1 WILD-TYPE 
                0                24 
$`GPRASP1 MUTATED`
TCGA-A5-A0GP TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM 
       46.55         1.18        83.67        86.07         8.22        27.12 
TCGA-AP-A0LQ TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A11E 
       80.78        46.45        40.11        32.55        28.64         8.71 
TCGA-BG-A0M3 TCGA-BG-A0MG TCGA-BG-A0VZ TCGA-BS-A0UF TCGA-D1-A103 TCGA-D1-A16X 
       35.21        48.56        28.54        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D 
       15.95        21.99         5.95        23.31        39.42        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89         7.86        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LT 
       31.73        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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       72.03        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        35.01        28.54        37.78        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0K0 TCGA-B5-A0K1 
       56.91        46.75        43.13        40.67        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       11.01       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        43.96        40.50        32.09        33.50        27.35 
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-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       20.94        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       41.52        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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-A17C 
       17.49        19.53        30.15        18.02         1.58         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-EY-A1GS 
       16.31        35.38        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  GPRASP1 MUTATED GPRASP1 WILD-TYPE 
             1.18              0.56 
  GPRASP1 MUTATED GPRASP1 WILD-TYPE 
            86.07            185.79 
  GPRASP1 MUTATED GPRASP1 WILD-TYPE 
            30.44             29.06 
[1] "1.2 - 86.1 (30.4)"  "0.6 - 185.8 (29.1)"
[1] "hr="     "7.5e+07"
D140V2, continuous
                   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
D140V3, 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"
D140V4, binary
                   cls
clus                  0   1
  GPRASP1 MUTATED     8  13
  GPRASP1 WILD-TYPE  78 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPRASP1 MUTATED      8   13
  GPRASP1 WILD-TYPE   78  149
     clus
vv    GPRASP1 MUTATED GPRASP1 WILD-TYPE
  NO                8                78
  YES              13               149
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  GPRASP1 MUTATED    16   1   0   0
  GPRASP1 WILD-TYPE 155  10   7  18
D140V5, multiclass
    clus
vv   GPRASP1 MUTATED GPRASP1 WILD-TYPE
  R0              16               155
  R1               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPRASP1 MUTATED                                  0     2
  GPRASP1 WILD-TYPE                                3    11
                   vv
clus                BLACK OR AFRICAN AMERICAN
  GPRASP1 MUTATED                           1
  GPRASP1 WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPRASP1 MUTATED                                           0    17
  GPRASP1 WILD-TYPE                                         7   176
D140V6, multiclass
                                           clus
vv                                          GPRASP1 MUTATED GPRASP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   2                11
  BLACK OR AFRICAN AMERICAN                               1                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 7
  WHITE                                                  17               176
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V7, binary
                   cls
clus                  0   1
  GPRASP1 MUTATED     1  12
  GPRASP1 WILD-TYPE   3 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPRASP1 MUTATED      1   12
  GPRASP1 WILD-TYPE    3  155
                        clus
vv                       GPRASP1 MUTATED GPRASP1 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              12               155
[1] 2 2
[1] FALSE

Clustering(141) Variable = REV3L MUTATION ANALYSIS
D141V1, survival
                 sevent
clus2               0   1
  REV3L MUTATED    20   0
  REV3L WILD-TYPE 204  24
  REV3L MUTATED REV3L WILD-TYPE 
             20             228 
  REV3L MUTATED REV3L WILD-TYPE 
              0              24 
$`REV3L MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       83.67        86.07         8.22        27.12        46.45        40.11 
TCGA-B5-A0JY TCGA-B5-A11H TCGA-B5-A11N TCGA-B5-A11U TCGA-BG-A0VX TCGA-BS-A0TC 
       32.55        88.34        43.96        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       28.54        37.78        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       17.88        13.74        17.10        17.85        11.01         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11O 
      185.79       113.36        75.72        54.44        44.78        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       32.09        33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       24.39        26.66        16.34        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE 
       10.16        24.99        46.95        23.47        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 
       67.20        88.34        82.39        86.93        72.72        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        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-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-A1Y5 TCGA-EO-A1Y8 
       18.25        16.31        35.38        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  REV3L MUTATED REV3L WILD-TYPE 
           1.78            0.56 
  REV3L MUTATED REV3L WILD-TYPE 
          88.34          185.79 
  REV3L MUTATED REV3L WILD-TYPE 
          37.20           28.59 
[1] "1.8 - 88.3 (37.2)"  "0.6 - 185.8 (28.6)"
[1] "hr="     "7.7e+07"
D141V2, continuous
                 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
D141V3, 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"
D141V4, binary
                 cls
clus                0   1
  REV3L MUTATED     5  15
  REV3L WILD-TYPE  81 147
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REV3L MUTATED      5   15
  REV3L WILD-TYPE   81  147
     clus
vv    REV3L MUTATED REV3L WILD-TYPE
  NO              5              81
  YES            15             147
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  REV3L MUTATED    14   1   0   1
  REV3L WILD-TYPE 157  10   7  17
D141V5, multiclass
    clus
vv   REV3L MUTATED REV3L WILD-TYPE
  R0            14             157
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  REV3L MUTATED                                  0     2
  REV3L WILD-TYPE                                3    11
                 vv
clus              BLACK OR AFRICAN AMERICAN
  REV3L MUTATED                           2
  REV3L WILD-TYPE                        23
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  REV3L MUTATED                                           2    13
  REV3L WILD-TYPE                                         5   180
D141V6, multiclass
                                           clus
vv                                          REV3L MUTATED REV3L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 2              11
  BLACK OR AFRICAN AMERICAN                             2              23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             2               5
  WHITE                                                13             180
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V7, binary
                 cls
clus                0   1
  REV3L MUTATED     1  12
  REV3L WILD-TYPE   3 155
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REV3L MUTATED      1   12
  REV3L WILD-TYPE    3  155
                        clus
vv                       REV3L MUTATED REV3L WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            12             155
[1] 2 2
[1] FALSE

Clustering(142) Variable = CTNNA1 MUTATION ANALYSIS
D142V1, survival
                  sevent
clus2                0   1
  CTNNA1 MUTATED    13   0
  CTNNA1 WILD-TYPE 211  24
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
              13              235 
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
               0               24 
$`CTNNA1 MUTATED`
TCGA-A5-A0VP TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A0J1 TCGA-BS-A0TC 
       42.35        86.07         8.22        27.12        65.88        85.55 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A16X TCGA-D1-A174 
       85.84        82.39        73.25        21.99         3.65        19.53 
TCGA-EY-A1GS 
       15.09 

$`CTNNA1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        40.11        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       43.13        40.67        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE 
       10.16        24.99        46.95        23.47        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-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       67.20        88.34        81.57        86.93        72.72        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        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-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       18.67        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-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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        10.78         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
            3.65             0.56 
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
           86.07           185.79 
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
           42.35            29.06 
[1] "3.6 - 86.1 (42.4)"  "0.6 - 185.8 (29.1)"
[1] "hr="     "2.7e+07"
D142V2, continuous
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CTNNA1 MUTATED                                        12
  CTNNA1 WILD-TYPE                                     188
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  CTNNA1 MUTATED                               0
  CTNNA1 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  CTNNA1 MUTATED                                   1
  CTNNA1 WILD-TYPE                                43
D142V3, multiclass
                                         clus
vv                                        CTNNA1 MUTATED CTNNA1 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"
D142V4, binary
                  cls
clus                 0   1
  CTNNA1 MUTATED     5   8
  CTNNA1 WILD-TYPE  81 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA1 MUTATED      5    8
  CTNNA1 WILD-TYPE   81  154
     clus
vv    CTNNA1 MUTATED CTNNA1 WILD-TYPE
  NO               5               81
  YES              8              154
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CTNNA1 MUTATED    12   0   1   0
  CTNNA1 WILD-TYPE 159  11   6  18
D142V5, multiclass
    clus
vv   CTNNA1 MUTATED CTNNA1 WILD-TYPE
  R0             12              159
  R1              0               11
  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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTNNA1 MUTATED                                  0     3
  CTNNA1 WILD-TYPE                                3    10
                  vv
clus               BLACK OR AFRICAN AMERICAN
  CTNNA1 MUTATED                           2
  CTNNA1 WILD-TYPE                        23
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTNNA1 MUTATED                                           1     7
  CTNNA1 WILD-TYPE                                         6   186
D142V6, multiclass
                                           clus
vv                                          CTNNA1 MUTATED CTNNA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  3               10
  BLACK OR AFRICAN AMERICAN                              2               23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  7              186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V7, binary
                  cls
clus                 0   1
  CTNNA1 MUTATED     0  11
  CTNNA1 WILD-TYPE   4 156
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA1 MUTATED      0   11
  CTNNA1 WILD-TYPE    4  156
                        clus
vv                       CTNNA1 MUTATED CTNNA1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              156
[1] 2 2
[1] FALSE

Clustering(143) Variable = MRPL47 MUTATION ANALYSIS
D143V1, survival
                  sevent
clus2                0   1
  MRPL47 MUTATED     6   0
  MRPL47 WILD-TYPE 218  24
  MRPL47 MUTATED MRPL47 WILD-TYPE 
               6              242 
  MRPL47 MUTATED MRPL47 WILD-TYPE 
               0               24 
$`MRPL47 MUTATED`
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J TCGA-AX-A05Z TCGA-D1-A103 TCGA-D1-A17Q 
       86.07         8.22        36.89        46.45        21.99         1.78 

$`MRPL47 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05P 
       23.31        39.42        57.80        45.53         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       35.01        28.54        37.78        40.11        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       46.75        43.13        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         8.71       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  MRPL47 MUTATED MRPL47 WILD-TYPE 
            1.78             0.56 
  MRPL47 MUTATED MRPL47 WILD-TYPE 
           86.07           185.79 
  MRPL47 MUTATED MRPL47 WILD-TYPE 
          29.440           29.195 
[1] "1.8 - 86.1 (29.4)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "9200000"
D143V2, continuous
                  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
D143V3, 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"
D143V4, binary
                  cls
clus                 0   1
  MRPL47 MUTATED     3   3
  MRPL47 WILD-TYPE  83 159
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL47 MUTATED      3    3
  MRPL47 WILD-TYPE   83  159
     clus
vv    MRPL47 MUTATED MRPL47 WILD-TYPE
  NO               3               83
  YES              3              159
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MRPL47 MUTATED     5   1   0   0
  MRPL47 WILD-TYPE 166  10   7  18
D143V5, multiclass
    clus
vv   MRPL47 MUTATED MRPL47 WILD-TYPE
  R0              5              166
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MRPL47 MUTATED                                  0     0
  MRPL47 WILD-TYPE                                3    13
                  vv
clus               BLACK OR AFRICAN AMERICAN
  MRPL47 MUTATED                           0
  MRPL47 WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MRPL47 MUTATED                                           0     5
  MRPL47 WILD-TYPE                                         7   188
D143V6, multiclass
                                           clus
vv                                          MRPL47 MUTATED MRPL47 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  0               13
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                  5              188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V7, binary
                  cls
clus                 0   1
  MRPL47 MUTATED     1   3
  MRPL47 WILD-TYPE   3 164
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL47 MUTATED      1    3
  MRPL47 WILD-TYPE    3  164
                        clus
vv                       MRPL47 MUTATED MRPL47 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              3              164
[1] 2 2
[1] FALSE

Clustering(144) Variable = DEPDC1B MUTATION ANALYSIS
D144V1, survival
                   sevent
clus2                 0   1
  DEPDC1B MUTATED    10   1
  DEPDC1B WILD-TYPE 214  23
  DEPDC1B MUTATED DEPDC1B WILD-TYPE 
               11               237 
  DEPDC1B MUTATED DEPDC1B WILD-TYPE 
                1                23 
$`DEPDC1B MUTATED`
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A060 TCGA-BS-A0TC 
       23.31        86.07         8.22        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A062 
       19.82        29.69        68.35        72.03        46.45        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       28.54        37.78        40.11        65.88        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       43.13        40.67        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE 
       10.16        24.99        46.95        23.47        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 
       67.20        88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        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-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-A17H TCGA-D1-A17K 
        1.58         7.00         0.99        30.44        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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  DEPDC1B MUTATED DEPDC1B WILD-TYPE 
             1.28              0.56 
  DEPDC1B MUTATED DEPDC1B WILD-TYPE 
            86.07            185.79 
  DEPDC1B MUTATED DEPDC1B WILD-TYPE 
            27.12             29.33 
[1] "1.3 - 86.1 (27.1)"  "0.6 - 185.8 (29.3)"
[1] "hr=" "1"  
D144V2, continuous
                   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
D144V3, 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"
D144V4, binary
                   cls
clus                  0   1
  DEPDC1B MUTATED     5   6
  DEPDC1B WILD-TYPE  81 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DEPDC1B MUTATED      5    6
  DEPDC1B WILD-TYPE   81  156
     clus
vv    DEPDC1B MUTATED DEPDC1B WILD-TYPE
  NO                5                81
  YES               6               156
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  DEPDC1B MUTATED     8   2   0   1
  DEPDC1B WILD-TYPE 163   9   7  17
D144V5, multiclass
    clus
vv   DEPDC1B MUTATED DEPDC1B WILD-TYPE
  R0               8               163
  R1               2                 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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEPDC1B MUTATED                                  1     2
  DEPDC1B WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN
  DEPDC1B MUTATED                           1
  DEPDC1B WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEPDC1B MUTATED                                           0     7
  DEPDC1B WILD-TYPE                                         7   186
D144V6, multiclass
                                           clus
vv                                          DEPDC1B MUTATED DEPDC1B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   2                11
  BLACK OR AFRICAN AMERICAN                               1                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 7
  WHITE                                                   7               186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V7, binary
                   cls
clus                  0   1
  DEPDC1B MUTATED     0   9
  DEPDC1B WILD-TYPE   4 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DEPDC1B MUTATED      0    9
  DEPDC1B WILD-TYPE    4  158
                        clus
vv                       DEPDC1B MUTATED DEPDC1B WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               9               158
[1] 2 2
[1] FALSE

Clustering(145) Variable = CASP8 MUTATION ANALYSIS
D145V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED    16   1
  CASP8 WILD-TYPE 208  23
  CASP8 MUTATED CASP8 WILD-TYPE 
             17             231 
  CASP8 MUTATED CASP8 WILD-TYPE 
              1              23 
$`CASP8 MUTATED`
TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A05S TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A11E 
       86.07         8.22        13.58        46.45        40.11         8.71 
TCGA-B5-A11N TCGA-BS-A0TA TCGA-BS-A0TJ TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UV 
       43.96        23.47        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        65.88        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       43.13        40.67        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       11.01       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        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        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        67.20        88.34        81.57 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       86.93        72.72        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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-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-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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00         9.07        25.02 

  CASP8 MUTATED CASP8 WILD-TYPE 
           1.78            0.56 
  CASP8 MUTATED CASP8 WILD-TYPE 
          86.07          185.79 
  CASP8 MUTATED CASP8 WILD-TYPE 
          40.11           28.67 
[1] "1.8 - 86.1 (40.1)"  "0.6 - 185.8 (28.7)"
[1] "hr=" "1.9"
D145V2, continuous
                 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
D145V3, 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"
D145V4, binary
                 cls
clus                0   1
  CASP8 MUTATED     6  11
  CASP8 WILD-TYPE  80 151
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      6   11
  CASP8 WILD-TYPE   80  151
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO              6              80
  YES            11             151
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CASP8 MUTATED    12   1   1   1
  CASP8 WILD-TYPE 159  10   6  17
D145V5, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  R0            12             159
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASP8 MUTATED                                  0     3
  CASP8 WILD-TYPE                                3    10
                 vv
clus              BLACK OR AFRICAN AMERICAN
  CASP8 MUTATED                           1
  CASP8 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CASP8 MUTATED                                           2    10
  CASP8 WILD-TYPE                                         5   183
D145V6, multiclass
                                           clus
vv                                          CASP8 MUTATED CASP8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 3              10
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             2               5
  WHITE                                                10             183
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V7, binary
                 cls
clus                0   1
  CASP8 MUTATED     2  11
  CASP8 WILD-TYPE   2 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      2   11
  CASP8 WILD-TYPE    2  156
                        clus
vv                       CASP8 MUTATED CASP8 WILD-TYPE
  HISPANIC OR LATINO                 2               2
  NOT HISPANIC OR LATINO            11             156
[1] 2 2
[1] FALSE

Clustering(146) Variable = CACNB4 MUTATION ANALYSIS
D146V1, survival
                  sevent
clus2                0   1
  CACNB4 MUTATED    10   0
  CACNB4 WILD-TYPE 214  24
  CACNB4 MUTATED CACNB4 WILD-TYPE 
              10              238 
  CACNB4 MUTATED CACNB4 WILD-TYPE 
               0               24 
$`CACNB4 MUTATED`
TCGA-AP-A0LM TCGA-AX-A060 TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11E TCGA-BG-A0W1 
       27.12        35.34        40.11        32.55         8.71        52.83 
TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A16Y TCGA-D1-A17Q 
       73.25        21.99        17.49         1.78 

$`CACNB4 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89         7.86        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       72.03        46.45        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        35.01        28.54        37.78        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU 
       26.66        16.34        34.29        28.54        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        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 
       67.20        88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  CACNB4 MUTATED CACNB4 WILD-TYPE 
            1.78             0.56 
  CACNB4 MUTATED CACNB4 WILD-TYPE 
           73.25           185.79 
  CACNB4 MUTATED CACNB4 WILD-TYPE 
          29.835           29.195 
[1] "1.8 - 73.2 (29.8)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "2.6e+07"
D146V2, continuous
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CACNB4 MUTATED                                        10
  CACNB4 WILD-TYPE                                     190
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  CACNB4 MUTATED                               0
  CACNB4 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  CACNB4 MUTATED                                   0
  CACNB4 WILD-TYPE                                44
D146V3, multiclass
                                         clus
vv                                        CACNB4 MUTATED CACNB4 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"
D146V4, binary
                  cls
clus                 0   1
  CACNB4 MUTATED     2   8
  CACNB4 WILD-TYPE  84 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACNB4 MUTATED      2    8
  CACNB4 WILD-TYPE   84  154
     clus
vv    CACNB4 MUTATED CACNB4 WILD-TYPE
  NO               2               84
  YES              8              154
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CACNB4 MUTATED     6   1   0   1
  CACNB4 WILD-TYPE 165  10   7  17
D146V5, multiclass
    clus
vv   CACNB4 MUTATED CACNB4 WILD-TYPE
  R0              6              165
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CACNB4 MUTATED                                  1     0
  CACNB4 WILD-TYPE                                2    13
                  vv
clus               BLACK OR AFRICAN AMERICAN
  CACNB4 MUTATED                           1
  CACNB4 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CACNB4 MUTATED                                           1     7
  CACNB4 WILD-TYPE                                         6   186
D146V6, multiclass
                                           clus
vv                                          CACNB4 MUTATED CACNB4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       1                2
  ASIAN                                                  0               13
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  7              186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V7, binary
                  cls
clus                 0   1
  CACNB4 MUTATED     0   7
  CACNB4 WILD-TYPE   4 160
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACNB4 MUTATED      0    7
  CACNB4 WILD-TYPE    4  160
                        clus
vv                       CACNB4 MUTATED CACNB4 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              160
[1] 2 2
[1] FALSE

Clustering(147) Variable = BHLHB9 MUTATION ANALYSIS
D147V1, survival
                  sevent
clus2                0   1
  BHLHB9 MUTATED     8   0
  BHLHB9 WILD-TYPE 216  24
  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
               8              240 
  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
               0               24 
$`BHLHB9 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-BG-A0LX TCGA-BS-A0UV 
       83.67         8.22        40.11        32.55        20.19        73.25 
TCGA-D1-A103 TCGA-D1-A16Y 
       21.99        17.49 

$`BHLHB9 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        35.01        28.54        37.78        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         8.71       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74         4.44        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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
            8.22             0.56 
  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
           83.67           185.79 
  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
          27.270           29.195 
[1] "8.2 - 83.7 (27.3)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "2.5e+07"
D147V2, continuous
                  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
D147V3, 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"
D147V4, binary
                  cls
clus                 0   1
  BHLHB9 MUTATED     3   5
  BHLHB9 WILD-TYPE  83 157
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BHLHB9 MUTATED      3    5
  BHLHB9 WILD-TYPE   83  157
     clus
vv    BHLHB9 MUTATED BHLHB9 WILD-TYPE
  NO               3               83
  YES              5              157
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  BHLHB9 MUTATED     6   0   0   1
  BHLHB9 WILD-TYPE 165  11   7  17
D147V5, multiclass
    clus
vv   BHLHB9 MUTATED BHLHB9 WILD-TYPE
  R0              6              165
  R1              0               11
  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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BHLHB9 MUTATED                                  0     0
  BHLHB9 WILD-TYPE                                3    13
                  vv
clus               BLACK OR AFRICAN AMERICAN
  BHLHB9 MUTATED                           0
  BHLHB9 WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BHLHB9 MUTATED                                           1     7
  BHLHB9 WILD-TYPE                                         6   186
D147V6, multiclass
                                           clus
vv                                          BHLHB9 MUTATED BHLHB9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  0               13
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  7              186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V7, binary
                  cls
clus                 0   1
  BHLHB9 MUTATED     0   6
  BHLHB9 WILD-TYPE   4 161
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BHLHB9 MUTATED      0    6
  BHLHB9 WILD-TYPE    4  161
                        clus
vv                       BHLHB9 MUTATED BHLHB9 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              161
[1] 2 2
[1] FALSE

Clustering(148) Variable = C22ORF25 MUTATION ANALYSIS
D148V1, survival
                    sevent
clus2                  0   1
  C22ORF25 MUTATED     6   0
  C22ORF25 WILD-TYPE 218  24
  C22ORF25 MUTATED C22ORF25 WILD-TYPE 
                 6                242 
  C22ORF25 MUTATED C22ORF25 WILD-TYPE 
                 0                 24 
$`C22ORF25 MUTATED`
TCGA-A5-A0VQ TCGA-AP-A059 TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0K9 TCGA-BS-A0U8 
       15.95         8.22        40.67        32.55        11.01        97.41 

$`C22ORF25 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        35.01        28.54        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       65.88        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JZ TCGA-B5-A0K0 
       80.38        56.91        46.75        43.13        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85         8.71       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
       67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  C22ORF25 MUTATED C22ORF25 WILD-TYPE 
              8.22               0.56 
  C22ORF25 MUTATED C22ORF25 WILD-TYPE 
             97.41             185.79 
  C22ORF25 MUTATED C22ORF25 WILD-TYPE 
            24.250             29.195 
[1] "8.2 - 97.4 (24.2)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "9200000"
D148V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  C22ORF25 MUTATED                                         6
  C22ORF25 WILD-TYPE                                     194
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  C22ORF25 MUTATED                               0
  C22ORF25 WILD-TYPE                             4
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  C22ORF25 MUTATED                                   0
  C22ORF25 WILD-TYPE                                44
D148V3, multiclass
                                         clus
vv                                        C22ORF25 MUTATED C22ORF25 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"
D148V4, binary
                    cls
clus                   0   1
  C22ORF25 MUTATED     5   1
  C22ORF25 WILD-TYPE  81 161
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C22ORF25 MUTATED      5    1
  C22ORF25 WILD-TYPE   81  161
     clus
vv    C22ORF25 MUTATED C22ORF25 WILD-TYPE
  NO                 5                 81
  YES                1                161
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C22ORF25 MUTATED     2   0   0   0
  C22ORF25 WILD-TYPE 169  11   7  18
D148V5, multiclass
[1] "Remove cluster labels:" "C22ORF25 MUTATED"      
clus
  C22ORF25 MUTATED C22ORF25 WILD-TYPE 
                 2                205 
        TCGA-A5-A0G3         TCGA-A5-A0G5         TCGA-A5-A0G9 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-A5-A0GA         TCGA-A5-A0GB         TCGA-A5-A0GD 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GI 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-A5-A0GJ         TCGA-A5-A0GM         TCGA-A5-A0GN 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GQ         TCGA-A5-A0GU 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-A5-A0GV         TCGA-A5-A0GW         TCGA-A5-A0GX 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-A5-A0R6         TCGA-A5-A0R7         TCGA-A5-A0R8 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-A5-A0R9         TCGA-A5-A0RA         TCGA-A5-A0VO 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-A5-A0VP         TCGA-AP-A051         TCGA-AP-A052 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-AP-A053         TCGA-AP-A054         TCGA-AP-A056 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-AP-A05A         TCGA-AP-A05D         TCGA-AP-A05H 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-AP-A0LE         TCGA-AP-A0LF         TCGA-AP-A0LG 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LI         TCGA-AP-A0LJ 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-AP-A0LL         TCGA-AP-A0LM         TCGA-AP-A0LN 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-AP-A0LO         TCGA-AP-A0LP         TCGA-AP-A0LQ 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AP-A1DQ 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06H         TCGA-AX-A06L 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-AX-A0IS         TCGA-AX-A0IU         TCGA-AX-A0IW 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-AX-A0J0         TCGA-AX-A0J1         TCGA-AX-A1C7 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-AX-A1C8         TCGA-AX-A1CP         TCGA-AX-A2H5 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-AX-A2HF         TCGA-BG-A0LW         TCGA-BG-A0LX 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BG-A0M0         TCGA-BG-A0M2         TCGA-BG-A0M3 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BG-A0M4         TCGA-BG-A0M6         TCGA-BG-A0M7 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BG-A0M8         TCGA-BG-A0M9         TCGA-BG-A0MC 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BG-A0MG         TCGA-BG-A0MI         TCGA-BG-A0MO 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BG-A0MQ         TCGA-BG-A0MS         TCGA-BG-A0MT 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BG-A0MU         TCGA-BG-A0RY         TCGA-BG-A0VT 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BG-A0VV         TCGA-BG-A0VW         TCGA-BG-A0VX 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BG-A0VZ         TCGA-BG-A0W1         TCGA-BG-A0W2 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BG-A0YU         TCGA-BG-A0YV         TCGA-BG-A186 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BG-A187         TCGA-BG-A18A         TCGA-BG-A18B 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BG-A18C         TCGA-BK-A0C9         TCGA-BK-A0CA 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BK-A0CB         TCGA-BK-A0CC         TCGA-BK-A139 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BK-A13C         TCGA-BS-A0T9         TCGA-BS-A0TA 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BS-A0TC         TCGA-BS-A0TD         TCGA-BS-A0TE 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BS-A0TG         TCGA-BS-A0TI         TCGA-BS-A0TJ 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BS-A0U5         TCGA-BS-A0U7         TCGA-BS-A0U9 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BS-A0UA         TCGA-BS-A0UF         TCGA-BS-A0UJ 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BS-A0UL         TCGA-BS-A0UM         TCGA-BS-A0UT 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BS-A0UV         TCGA-BS-A0V6         TCGA-BS-A0V7 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-BS-A0V8         TCGA-BS-A0WQ         TCGA-D1-A0ZN 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A0ZO         TCGA-D1-A0ZP         TCGA-D1-A0ZQ 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A0ZR         TCGA-D1-A0ZS         TCGA-D1-A0ZU 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A0ZV         TCGA-D1-A0ZZ         TCGA-D1-A101 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A102         TCGA-D1-A103         TCGA-D1-A15V 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A15W         TCGA-D1-A15X         TCGA-D1-A15Z 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A160         TCGA-D1-A161         TCGA-D1-A163 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A165         TCGA-D1-A167         TCGA-D1-A168 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A169         TCGA-D1-A16B         TCGA-D1-A16D 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A16E         TCGA-D1-A16F         TCGA-D1-A16G 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A16I         TCGA-D1-A16J         TCGA-D1-A16N 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A16O         TCGA-D1-A16Q         TCGA-D1-A16R 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A16S         TCGA-D1-A16X         TCGA-D1-A16Y 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A174         TCGA-D1-A176         TCGA-D1-A177 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A17A         TCGA-D1-A17B         TCGA-D1-A17C 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A17D         TCGA-D1-A17F         TCGA-D1-A17H 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A17K         TCGA-D1-A17L         TCGA-D1-A17M 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A17N         TCGA-D1-A17Q         TCGA-D1-A17R 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A17S         TCGA-D1-A17T         TCGA-D1-A17U 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-D1-A1NU         TCGA-D1-A1NX         TCGA-DI-A0WH 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-DI-A1NN         TCGA-E6-A1LZ         TCGA-EO-A1Y5 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-EO-A1Y8         TCGA-EY-A1GS         TCGA-EY-A212 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-FI-A2D2         TCGA-FI-A2EW         TCGA-FI-A2EX 
"C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" "C22ORF25 WILD-TYPE" 
        TCGA-FI-A2F8 
"C22ORF25 WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C22ORF25 MUTATED                                  0     0
  C22ORF25 WILD-TYPE                                3    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  C22ORF25 MUTATED                           1
  C22ORF25 WILD-TYPE                        24
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C22ORF25 MUTATED                                           0     4
  C22ORF25 WILD-TYPE                                         7   189
D148V6, multiclass
                                           clus
vv                                          C22ORF25 MUTATED C22ORF25 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    0                 13
  BLACK OR AFRICAN AMERICAN                                1                 24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  7
  WHITE                                                    4                189
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V7, binary
                    cls
clus                   0   1
  C22ORF25 MUTATED     1   2
  C22ORF25 WILD-TYPE   3 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C22ORF25 MUTATED      1    2
  C22ORF25 WILD-TYPE    3  165
                        clus
vv                       C22ORF25 MUTATED C22ORF25 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO                2                165
[1] 2 2
[1] FALSE

Clustering(149) Variable = GALNT7 MUTATION ANALYSIS
D149V1, survival
                  sevent
clus2                0   1
  GALNT7 MUTATED    10   1
  GALNT7 WILD-TYPE 214  23
  GALNT7 MUTATED GALNT7 WILD-TYPE 
              11              237 
  GALNT7 MUTATED GALNT7 WILD-TYPE 
               1               23 
$`GALNT7 MUTATED`
TCGA-A5-A0GP TCGA-AP-A051 TCGA-AP-A054 TCGA-AX-A05Z TCGA-AX-A2H5 TCGA-B5-A0JY 
       46.55        83.67        23.31        46.45        71.24        32.55 
TCGA-B5-A11N TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A17Q 
       43.96        85.84        82.39        73.25         1.78 

$`GALNT7 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A056 TCGA-AP-A059 
       15.95         1.18        21.99         5.95        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       35.01        28.54        37.78        40.11        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       13.55        36.39        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        40.67        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       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        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 
       88.34        81.57        86.93        72.72        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  GALNT7 MUTATED GALNT7 WILD-TYPE 
            1.78             0.56 
  GALNT7 MUTATED GALNT7 WILD-TYPE 
           85.84           185.79 
  GALNT7 MUTATED GALNT7 WILD-TYPE 
           46.55            28.54 
[1] "1.8 - 85.8 (46.5)"  "0.6 - 185.8 (28.5)"
[1] "hr=" "1.6"
D149V2, continuous
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  GALNT7 MUTATED                                        10
  GALNT7 WILD-TYPE                                     190
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  GALNT7 MUTATED                               0
  GALNT7 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  GALNT7 MUTATED                                   1
  GALNT7 WILD-TYPE                                43
D149V3, multiclass
                                         clus
vv                                        GALNT7 MUTATED GALNT7 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"
D149V4, binary
                  cls
clus                 0   1
  GALNT7 MUTATED     1  10
  GALNT7 WILD-TYPE  85 152
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GALNT7 MUTATED      1   10
  GALNT7 WILD-TYPE   85  152
     clus
vv    GALNT7 MUTATED GALNT7 WILD-TYPE
  NO               1               85
  YES             10              152
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GALNT7 MUTATED     6   3   0   0
  GALNT7 WILD-TYPE 165   8   7  18
D149V5, multiclass
    clus
vv   GALNT7 MUTATED GALNT7 WILD-TYPE
  R0              6              165
  R1              3                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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GALNT7 MUTATED                                  0     3
  GALNT7 WILD-TYPE                                3    10
                  vv
clus               BLACK OR AFRICAN AMERICAN
  GALNT7 MUTATED                           1
  GALNT7 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GALNT7 MUTATED                                           1     5
  GALNT7 WILD-TYPE                                         6   188
D149V6, multiclass
                                           clus
vv                                          GALNT7 MUTATED GALNT7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  3               10
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  5              188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V7, binary
                  cls
clus                 0   1
  GALNT7 MUTATED     1   7
  GALNT7 WILD-TYPE   3 160
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GALNT7 MUTATED      1    7
  GALNT7 WILD-TYPE    3  160
                        clus
vv                       GALNT7 MUTATED GALNT7 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              7              160
[1] 2 2
[1] FALSE

Clustering(150) Variable = LGMN MUTATION ANALYSIS
D150V1, survival
                sevent
clus2              0   1
  LGMN MUTATED     5   2
  LGMN WILD-TYPE 219  22
  LGMN MUTATED LGMN WILD-TYPE 
             7            241 
  LGMN MUTATED LGMN WILD-TYPE 
             2             22 
$`LGMN MUTATED`
TCGA-A5-A0GA TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A05S TCGA-B5-A0JY TCGA-B5-A11E 
       17.85        86.07         8.22        13.58        32.55         8.71 
TCGA-BS-A0TG 
       77.95 

$`LGMN WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       46.95        37.02        83.51        32.78         3.22       105.37 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       35.01        28.54        37.78        40.11        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        40.67        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       11.01       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        85.55        78.21         4.80 
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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  LGMN MUTATED LGMN WILD-TYPE 
          8.22           0.56 
  LGMN MUTATED LGMN WILD-TYPE 
         86.07         185.79 
  LGMN MUTATED LGMN WILD-TYPE 
         17.85          29.33 
[1] "8.2 - 86.1 (17.9)"  "0.6 - 185.8 (29.3)"
[1] "hr=" "3.4"
D150V2, continuous
                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
D150V3, 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"
D150V4, binary
                cls
clus               0   1
  LGMN MUTATED     4   3
  LGMN WILD-TYPE  82 159
[1] "tbl2"
                cls
clus             [,1] [,2]
  LGMN MUTATED      4    3
  LGMN WILD-TYPE   82  159
     clus
vv    LGMN MUTATED LGMN WILD-TYPE
  NO             4             82
  YES            3            159
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  LGMN MUTATED     4   0   1   0
  LGMN WILD-TYPE 167  11   6  18
D150V5, multiclass
    clus
vv   LGMN MUTATED LGMN WILD-TYPE
  R0            4            167
  R1            0             11
  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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LGMN MUTATED                                  0     0
  LGMN WILD-TYPE                                3    13
                vv
clus             BLACK OR AFRICAN AMERICAN
  LGMN MUTATED                           0
  LGMN WILD-TYPE                        25
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LGMN MUTATED                                           0     7
  LGMN WILD-TYPE                                         7   186
D150V6, multiclass
                                           clus
vv                                          LGMN MUTATED LGMN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                0             13
  BLACK OR AFRICAN AMERICAN                            0             25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              7
  WHITE                                                7            186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V7, binary
                cls
clus               0   1
  LGMN MUTATED     0   4
  LGMN WILD-TYPE   4 163
[1] "tbl2"
                cls
clus             [,1] [,2]
  LGMN MUTATED      0    4
  LGMN WILD-TYPE    4  163
                        clus
vv                       LGMN MUTATED LGMN WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            4            163
[1] 2 2
[1] FALSE

Clustering(151) Variable = EPS8 MUTATION ANALYSIS
D151V1, survival
                sevent
clus2              0   1
  EPS8 MUTATED    11   1
  EPS8 WILD-TYPE 213  23
  EPS8 MUTATED EPS8 WILD-TYPE 
            12            236 
  EPS8 MUTATED EPS8 WILD-TYPE 
             1             23 
$`EPS8 MUTATED`
TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JR TCGA-B5-A0JY 
        8.22        27.12        46.45        40.11        56.91        32.55 
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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JS 
       13.55        36.39        71.24        19.36        80.38        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        40.67        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       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        43.96        40.50        32.09        33.50        27.35 
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-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       20.94        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       88.34        85.84        81.57        86.93        72.72        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  EPS8 MUTATED EPS8 WILD-TYPE 
          1.78           0.56 
  EPS8 MUTATED EPS8 WILD-TYPE 
         82.39         185.79 
  EPS8 MUTATED EPS8 WILD-TYPE 
        33.880         28.865 
[1] "1.8 - 82.4 (33.9)"  "0.6 - 185.8 (28.9)"
[1] "hr=" "1.2"
D151V2, continuous
                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
D151V3, 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"
D151V4, binary
                cls
clus               0   1
  EPS8 MUTATED     4   8
  EPS8 WILD-TYPE  82 154
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPS8 MUTATED      4    8
  EPS8 WILD-TYPE   82  154
     clus
vv    EPS8 MUTATED EPS8 WILD-TYPE
  NO             4             82
  YES            8            154
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EPS8 MUTATED     9   1   0   0
  EPS8 WILD-TYPE 162  10   7  18
D151V5, multiclass
    clus
vv   EPS8 MUTATED EPS8 WILD-TYPE
  R0            9            162
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPS8 MUTATED                                  0     1
  EPS8 WILD-TYPE                                3    12
                vv
clus             BLACK OR AFRICAN AMERICAN
  EPS8 MUTATED                           1
  EPS8 WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPS8 MUTATED                                           1     8
  EPS8 WILD-TYPE                                         6   185
D151V6, multiclass
                                           clus
vv                                          EPS8 MUTATED EPS8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                1             12
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                                8            185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V7, binary
                cls
clus               0   1
  EPS8 MUTATED     1   8
  EPS8 WILD-TYPE   3 159
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPS8 MUTATED      1    8
  EPS8 WILD-TYPE    3  159
                        clus
vv                       EPS8 MUTATED EPS8 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            8            159
[1] 2 2
[1] FALSE

Clustering(152) Variable = TGOLN2 MUTATION ANALYSIS
D152V1, survival
                  sevent
clus2                0   1
  TGOLN2 MUTATED     3   0
  TGOLN2 WILD-TYPE 221  24
  TGOLN2 MUTATED TGOLN2 WILD-TYPE 
               3              245 
  TGOLN2 MUTATED TGOLN2 WILD-TYPE 
               0               24 
$`TGOLN2 MUTATED`
TCGA-A5-A0GH TCGA-AX-A0J0 TCGA-D1-A17Q 
       74.10        40.11         1.78 

$`TGOLN2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       65.88        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       80.38        56.91        46.75        43.13        40.67        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        17.85        11.01         8.71       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        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        67.20        88.34 
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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  TGOLN2 MUTATED TGOLN2 WILD-TYPE 
            1.78             0.56 
  TGOLN2 MUTATED TGOLN2 WILD-TYPE 
           74.10           185.79 
  TGOLN2 MUTATED TGOLN2 WILD-TYPE 
           40.11            29.06 
[1] "1.8 - 74.1 (40.1)"  "0.6 - 185.8 (29.1)"
[1] "hr="     "9100000"
D152V2, continuous
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  TGOLN2 MUTATED                                         3
  TGOLN2 WILD-TYPE                                     197
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  TGOLN2 MUTATED                               0
  TGOLN2 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  TGOLN2 MUTATED                                   0
  TGOLN2 WILD-TYPE                                44
D152V3, multiclass
                                         clus
vv                                        TGOLN2 MUTATED TGOLN2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              3              197
  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"
D152V4, binary
                  cls
clus                 0   1
  TGOLN2 MUTATED     0   3
  TGOLN2 WILD-TYPE  86 159
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGOLN2 MUTATED      0    3
  TGOLN2 WILD-TYPE   86  159
     clus
vv    TGOLN2 MUTATED TGOLN2 WILD-TYPE
  NO               0               86
  YES              3              159
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TGOLN2 MUTATED     3   0   0   0
  TGOLN2 WILD-TYPE 168  11   7  18
D152V5, multiclass
    clus
vv   TGOLN2 MUTATED TGOLN2 WILD-TYPE
  R0              3              168
  R1              0               11
  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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TGOLN2 MUTATED                                  0     0
  TGOLN2 WILD-TYPE                                3    13
                  vv
clus               BLACK OR AFRICAN AMERICAN
  TGOLN2 MUTATED                           0
  TGOLN2 WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TGOLN2 MUTATED                                           0     3
  TGOLN2 WILD-TYPE                                         7   190
D152V6, multiclass
                                           clus
vv                                          TGOLN2 MUTATED TGOLN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  0               13
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                  3              190
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V7, binary
                  cls
clus                 0   1
  TGOLN2 MUTATED     0   3
  TGOLN2 WILD-TYPE   4 164
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGOLN2 MUTATED      0    3
  TGOLN2 WILD-TYPE    4  164
                        clus
vv                       TGOLN2 MUTATED TGOLN2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              164
[1] 2 2
[1] FALSE

Clustering(153) Variable = TPX2 MUTATION ANALYSIS
D153V1, survival
                sevent
clus2              0   1
  TPX2 MUTATED     6   0
  TPX2 WILD-TYPE 218  24
  TPX2 MUTATED TPX2 WILD-TYPE 
             6            242 
  TPX2 MUTATED TPX2 WILD-TYPE 
             0             24 
$`TPX2 MUTATED`
TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A11E TCGA-D1-A16Y 
        8.22        27.12        46.45        32.55         8.71        17.49 

$`TPX2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        37.78        40.11        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  TPX2 MUTATED TPX2 WILD-TYPE 
          8.22           0.56 
  TPX2 MUTATED TPX2 WILD-TYPE 
         46.45         185.79 
  TPX2 MUTATED TPX2 WILD-TYPE 
        22.305         29.510 
[1] "8.2 - 46.5 (22.3)"  "0.6 - 185.8 (29.5)"
[1] "hr="     "9200000"
D153V2, continuous
                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
D153V3, 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"
D153V4, binary
                cls
clus               0   1
  TPX2 MUTATED     2   4
  TPX2 WILD-TYPE  84 158
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPX2 MUTATED      2    4
  TPX2 WILD-TYPE   84  158
     clus
vv    TPX2 MUTATED TPX2 WILD-TYPE
  NO             2             84
  YES            4            158
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TPX2 MUTATED     2   1   0   1
  TPX2 WILD-TYPE 169  10   7  17
D153V5, multiclass
    clus
vv   TPX2 MUTATED TPX2 WILD-TYPE
  R0            2            169
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TPX2 MUTATED                                  0     0
  TPX2 WILD-TYPE                                3    13
                vv
clus             BLACK OR AFRICAN AMERICAN
  TPX2 MUTATED                           1
  TPX2 WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TPX2 MUTATED                                           0     4
  TPX2 WILD-TYPE                                         7   189
D153V6, multiclass
                                           clus
vv                                          TPX2 MUTATED TPX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                0             13
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              7
  WHITE                                                4            189
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V7, binary
                cls
clus               0   1
  TPX2 MUTATED     1   2
  TPX2 WILD-TYPE   3 165
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPX2 MUTATED      1    2
  TPX2 WILD-TYPE    3  165
                        clus
vv                       TPX2 MUTATED TPX2 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            2            165
[1] 2 2
[1] FALSE

Clustering(154) Variable = C14ORF118 MUTATION ANALYSIS
D154V1, survival
                     sevent
clus2                   0   1
  C14ORF118 MUTATED    15   0
  C14ORF118 WILD-TYPE 209  24
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                 15                 233 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                  0                  24 
$`C14ORF118 MUTATED`
TCGA-A5-A0GP TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AP-A0LT TCGA-AX-A05Z 
       46.55        86.07         8.22        27.12        49.22        46.45 
TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11J TCGA-B5-A11Y TCGA-BS-A0UF TCGA-D1-A16X 
       40.11        32.55        54.44        18.41        85.84         3.65 
TCGA-D1-A16Y TCGA-D1-A17B TCGA-D1-A17Q 
       17.49         7.00         1.78 

$`C14ORF118 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        68.35        72.03        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       34.98        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       37.78        65.88        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        17.85        11.01         8.71       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17C TCGA-D1-A17D 
       19.53        30.15        18.02         1.58         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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
               1.78                0.56 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
              86.07              185.79 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
              32.55               29.06 
[1] "1.8 - 86.1 (32.5)"  "0.6 - 185.8 (29.1)"
[1] "hr="     "2.7e+07"
D154V2, continuous
                     vv
clus                  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  C14ORF118 MUTATED                                        15
  C14ORF118 WILD-TYPE                                     185
                     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
D154V3, multiclass
                                         clus
vv                                        C14ORF118 MUTATED C14ORF118 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"
D154V4, binary
                     cls
clus                    0   1
  C14ORF118 MUTATED     4  11
  C14ORF118 WILD-TYPE  82 151
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF118 MUTATED      4   11
  C14ORF118 WILD-TYPE   82  151
     clus
vv    C14ORF118 MUTATED C14ORF118 WILD-TYPE
  NO                  4                  82
  YES                11                 151
[1] 2 2
[1] FALSE
                     vv
clus                   R0  R1  R2  RX
  C14ORF118 MUTATED    10   1   0   1
  C14ORF118 WILD-TYPE 161  10   7  17
D154V5, multiclass
    clus
vv   C14ORF118 MUTATED C14ORF118 WILD-TYPE
  R0                10                 161
  R1                 1                  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"
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF118 MUTATED                                  0     2
  C14ORF118 WILD-TYPE                                3    11
                     vv
clus                  BLACK OR AFRICAN AMERICAN
  C14ORF118 MUTATED                           1
  C14ORF118 WILD-TYPE                        24
                     vv
clus                  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C14ORF118 MUTATED                                           0    11
  C14ORF118 WILD-TYPE                                         7   182
D154V6, multiclass
                                           clus
vv                                          C14ORF118 MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                 0
  WHITE                                                    11
                                           clus
vv                                          C14ORF118 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            3
  ASIAN                                                      11
  BLACK OR AFRICAN AMERICAN                                  24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                   7
  WHITE                                                     182
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V7, binary
                     cls
clus                    0   1
  C14ORF118 MUTATED     1   8
  C14ORF118 WILD-TYPE   3 159
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF118 MUTATED      1    8
  C14ORF118 WILD-TYPE    3  159
                        clus
vv                       C14ORF118 MUTATED C14ORF118 WILD-TYPE
  HISPANIC OR LATINO                     1                   3
  NOT HISPANIC OR LATINO                 8                 159
[1] 2 2
[1] FALSE

Clustering(155) Variable = SLC34A3 MUTATION ANALYSIS
D155V1, survival
                   sevent
clus2                 0   1
  SLC34A3 MUTATED     6   0
  SLC34A3 WILD-TYPE 218  24
  SLC34A3 MUTATED SLC34A3 WILD-TYPE 
                6               242 
  SLC34A3 MUTATED SLC34A3 WILD-TYPE 
                0                24 
$`SLC34A3 MUTATED`
TCGA-AP-A059 TCGA-AP-A0LM TCGA-B5-A11H TCGA-BS-A0UV TCGA-D1-A163 TCGA-D1-A17Q 
        8.22        27.12        88.34        73.25        32.58         1.78 

$`SLC34A3 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        35.01        28.54        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       65.88        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       80.38        56.91        46.75        43.13        40.67        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        17.85        11.01         8.71       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
        3.68        29.33         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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  SLC34A3 MUTATED SLC34A3 WILD-TYPE 
             1.78              0.56 
  SLC34A3 MUTATED SLC34A3 WILD-TYPE 
            88.34            185.79 
  SLC34A3 MUTATED SLC34A3 WILD-TYPE 
           29.850            29.195 
[1] "1.8 - 88.3 (29.9)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "9200000"
D155V2, continuous
                   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
D155V3, 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"
D155V4, binary
                   cls
clus                  0   1
  SLC34A3 MUTATED     3   3
  SLC34A3 WILD-TYPE  83 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC34A3 MUTATED      3    3
  SLC34A3 WILD-TYPE   83  159
     clus
vv    SLC34A3 MUTATED SLC34A3 WILD-TYPE
  NO                3                83
  YES               3               159
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC34A3 MUTATED     5   0   0   0
  SLC34A3 WILD-TYPE 166  11   7  18
D155V5, multiclass
    clus
vv   SLC34A3 MUTATED SLC34A3 WILD-TYPE
  R0               5               166
  R1               0                11
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC34A3 MUTATED                                  0     0
  SLC34A3 WILD-TYPE                                3    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  SLC34A3 MUTATED                           1
  SLC34A3 WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC34A3 MUTATED                                           1     4
  SLC34A3 WILD-TYPE                                         6   189
D155V6, multiclass
                                           clus
vv                                          SLC34A3 MUTATED SLC34A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   0                13
  BLACK OR AFRICAN AMERICAN                               1                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 6
  WHITE                                                   4               189
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V7, binary
                   cls
clus                  0   1
  SLC34A3 MUTATED     0   4
  SLC34A3 WILD-TYPE   4 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC34A3 MUTATED      0    4
  SLC34A3 WILD-TYPE    4  163
                        clus
vv                       SLC34A3 MUTATED SLC34A3 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               4               163
[1] 2 2
[1] FALSE

Clustering(156) Variable = ZNF662 MUTATION ANALYSIS
D156V1, survival
                  sevent
clus2                0   1
  ZNF662 MUTATED    13   0
  ZNF662 WILD-TYPE 211  24
  ZNF662 MUTATED ZNF662 WILD-TYPE 
              13              235 
  ZNF662 MUTATED ZNF662 WILD-TYPE 
               0               24 
$`ZNF662 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       83.67        86.07         8.22        27.12        46.45        40.11 
TCGA-B5-A11E TCGA-B5-A11N TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A17Q 
        8.71        43.96        85.84        73.25        21.99         1.78 
TCGA-E6-A1LZ 
       48.36 

$`ZNF662 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       28.54        37.78        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       40.67        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
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 
       40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        67.20        88.34 
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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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-EO-A1Y5 
       22.92        13.22        18.25        16.31        35.38        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  ZNF662 MUTATED ZNF662 WILD-TYPE 
            1.78             0.56 
  ZNF662 MUTATED ZNF662 WILD-TYPE 
           86.07           185.79 
  ZNF662 MUTATED ZNF662 WILD-TYPE 
           43.96            28.67 
[1] "1.8 - 86.1 (44.0)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.7e+07"
D156V2, continuous
                  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
D156V3, 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"
D156V4, binary
                  cls
clus                 0   1
  ZNF662 MUTATED     5   8
  ZNF662 WILD-TYPE  81 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF662 MUTATED      5    8
  ZNF662 WILD-TYPE   81  154
     clus
vv    ZNF662 MUTATED ZNF662 WILD-TYPE
  NO               5               81
  YES              8              154
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF662 MUTATED    10   1   0   0
  ZNF662 WILD-TYPE 161  10   7  18
D156V5, multiclass
    clus
vv   ZNF662 MUTATED ZNF662 WILD-TYPE
  R0             10              161
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF662 MUTATED                                  0     1
  ZNF662 WILD-TYPE                                3    12
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ZNF662 MUTATED                           2
  ZNF662 WILD-TYPE                        23
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF662 MUTATED                                           1     8
  ZNF662 WILD-TYPE                                         6   185
D156V6, multiclass
                                           clus
vv                                          ZNF662 MUTATED ZNF662 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  1               12
  BLACK OR AFRICAN AMERICAN                              2               23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  8              185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V7, binary
                  cls
clus                 0   1
  ZNF662 MUTATED     1   7
  ZNF662 WILD-TYPE   3 160
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF662 MUTATED      1    7
  ZNF662 WILD-TYPE    3  160
                        clus
vv                       ZNF662 MUTATED ZNF662 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              7              160
[1] 2 2
[1] FALSE

Clustering(157) Variable = ZDBF2 MUTATION ANALYSIS
D157V1, survival
                 sevent
clus2               0   1
  ZDBF2 MUTATED    18   0
  ZDBF2 WILD-TYPE 206  24
  ZDBF2 MUTATED ZDBF2 WILD-TYPE 
             18             230 
  ZDBF2 MUTATED ZDBF2 WILD-TYPE 
              0              24 
$`ZDBF2 MUTATED`
TCGA-A5-A0GH TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z 
       74.10        83.67        86.07         8.22        27.12        46.45 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-BG-A18C 
       40.11        65.88        32.55         8.71        43.96        15.45 
TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A17Q 
       85.84        73.25        21.99         3.65        17.49         1.78 

$`ZDBF2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A 
       15.95         1.18        21.99         5.95        23.31        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        45.53        36.89         7.86        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        31.73        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        41.95        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        68.35        72.03        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       34.98        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       37.78        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       80.38        56.91        46.75        43.13        40.67        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        17.85        11.01       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        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        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 
       67.20        88.34        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74         4.44        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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  ZDBF2 MUTATED ZDBF2 WILD-TYPE 
           1.78            0.56 
  ZDBF2 MUTATED ZDBF2 WILD-TYPE 
          86.07          185.79 
  ZDBF2 MUTATED ZDBF2 WILD-TYPE 
         36.330          28.865 
[1] "1.8 - 86.1 (36.3)"  "0.6 - 185.8 (28.9)"
[1] "hr="     "7.5e+07"
D157V2, continuous
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZDBF2 MUTATED                                        18
  ZDBF2 WILD-TYPE                                     182
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  ZDBF2 MUTATED                               0
  ZDBF2 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZDBF2 MUTATED                                   0
  ZDBF2 WILD-TYPE                                44
D157V3, multiclass
                                         clus
vv                                        ZDBF2 MUTATED ZDBF2 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"
D157V4, binary
                 cls
clus                0   1
  ZDBF2 MUTATED     4  14
  ZDBF2 WILD-TYPE  82 148
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZDBF2 MUTATED      4   14
  ZDBF2 WILD-TYPE   82  148
     clus
vv    ZDBF2 MUTATED ZDBF2 WILD-TYPE
  NO              4              82
  YES            14             148
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZDBF2 MUTATED    12   1   0   2
  ZDBF2 WILD-TYPE 159  10   7  16
D157V5, multiclass
    clus
vv   ZDBF2 MUTATED ZDBF2 WILD-TYPE
  R0            12             159
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZDBF2 MUTATED                                  0     1
  ZDBF2 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  ZDBF2 MUTATED                           1
  ZDBF2 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZDBF2 MUTATED                                           1    14
  ZDBF2 WILD-TYPE                                         6   179
D157V6, multiclass
                                           clus
vv                                          ZDBF2 MUTATED ZDBF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                14             179
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V7, binary
                 cls
clus                0   1
  ZDBF2 MUTATED     1  11
  ZDBF2 WILD-TYPE   3 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZDBF2 MUTATED      1   11
  ZDBF2 WILD-TYPE    3  156
                        clus
vv                       ZDBF2 MUTATED ZDBF2 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            11             156
[1] 2 2
[1] FALSE

Clustering(158) Variable = SFRP4 MUTATION ANALYSIS
D158V1, survival
                 sevent
clus2               0   1
  SFRP4 MUTATED     8   0
  SFRP4 WILD-TYPE 216  24
  SFRP4 MUTATED SFRP4 WILD-TYPE 
              8             240 
  SFRP4 MUTATED SFRP4 WILD-TYPE 
              0              24 
$`SFRP4 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AX-A05Z TCGA-B5-A11E TCGA-BG-A0VZ TCGA-BS-A0UV 
       83.67        86.07        46.45         8.71        28.54        73.25 
TCGA-D1-A16Y TCGA-DI-A0WH 
       17.49        16.31 

$`SFRP4 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        37.78        40.11        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        46.75        43.13        40.67        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        17.85        11.01       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0W1 TCGA-BG-A0W2 
       24.39        26.66        16.34        34.29        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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-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-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       13.22        18.25        35.38        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  SFRP4 MUTATED SFRP4 WILD-TYPE 
           8.71            0.56 
  SFRP4 MUTATED SFRP4 WILD-TYPE 
          86.07          185.79 
  SFRP4 MUTATED SFRP4 WILD-TYPE 
         37.495          29.195 
[1] "8.7 - 86.1 (37.5)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "2.6e+07"
D158V2, continuous
                 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
D158V3, 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"
D158V4, binary
                 cls
clus                0   1
  SFRP4 MUTATED     3   5
  SFRP4 WILD-TYPE  83 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRP4 MUTATED      3    5
  SFRP4 WILD-TYPE   83  157
     clus
vv    SFRP4 MUTATED SFRP4 WILD-TYPE
  NO              3              83
  YES             5             157
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SFRP4 MUTATED     5   1   0   1
  SFRP4 WILD-TYPE 166  10   7  17
D158V5, multiclass
    clus
vv   SFRP4 MUTATED SFRP4 WILD-TYPE
  R0             5             166
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SFRP4 MUTATED                                  0     0
  SFRP4 WILD-TYPE                                3    13
                 vv
clus              BLACK OR AFRICAN AMERICAN
  SFRP4 MUTATED                           0
  SFRP4 WILD-TYPE                        25
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SFRP4 MUTATED                                           1     6
  SFRP4 WILD-TYPE                                         6   187
D158V6, multiclass
                                           clus
vv                                          SFRP4 MUTATED SFRP4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 0              13
  BLACK OR AFRICAN AMERICAN                             0              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                 6             187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V7, binary
                 cls
clus                0   1
  SFRP4 MUTATED     1   4
  SFRP4 WILD-TYPE   3 163
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRP4 MUTATED      1    4
  SFRP4 WILD-TYPE    3  163
                        clus
vv                       SFRP4 MUTATED SFRP4 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             4             163
[1] 2 2
[1] FALSE

Clustering(159) Variable = CCDC146 MUTATION ANALYSIS
D159V1, survival
                   sevent
clus2                 0   1
  CCDC146 MUTATED    14   0
  CCDC146 WILD-TYPE 210  24
  CCDC146 MUTATED CCDC146 WILD-TYPE 
               14               234 
  CCDC146 MUTATED CCDC146 WILD-TYPE 
                0                24 
$`CCDC146 MUTATED`
TCGA-A5-A0GP TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       46.55        86.07         8.22        27.12        46.45        40.11 
TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-BS-A0UF TCGA-BS-A0UV 
       65.88        32.55         8.71        43.96        85.84        73.25 
TCGA-D1-A16X TCGA-D1-A17Q 
        3.65         1.78 

$`CCDC146 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       28.54        37.78        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        17.85        11.01       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        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  CCDC146 MUTATED CCDC146 WILD-TYPE 
             1.78              0.56 
  CCDC146 MUTATED CCDC146 WILD-TYPE 
            86.07            185.79 
  CCDC146 MUTATED CCDC146 WILD-TYPE 
           42.035            28.655 
[1] "1.8 - 86.1 (42.0)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.7e+07"
D159V2, continuous
                   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
D159V3, 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"
D159V4, binary
                   cls
clus                  0   1
  CCDC146 MUTATED     3  11
  CCDC146 WILD-TYPE  83 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC146 MUTATED      3   11
  CCDC146 WILD-TYPE   83  151
     clus
vv    CCDC146 MUTATED CCDC146 WILD-TYPE
  NO                3                83
  YES              11               151
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC146 MUTATED    10   1   0   0
  CCDC146 WILD-TYPE 161  10   7  18
D159V5, multiclass
    clus
vv   CCDC146 MUTATED CCDC146 WILD-TYPE
  R0              10               161
  R1               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC146 MUTATED                                  0     2
  CCDC146 WILD-TYPE                                3    11
                   vv
clus                BLACK OR AFRICAN AMERICAN
  CCDC146 MUTATED                           1
  CCDC146 WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC146 MUTATED                                           1     9
  CCDC146 WILD-TYPE                                         6   184
D159V6, multiclass
                                           clus
vv                                          CCDC146 MUTATED CCDC146 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   2                11
  BLACK OR AFRICAN AMERICAN                               1                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 6
  WHITE                                                   9               184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V7, binary
                   cls
clus                  0   1
  CCDC146 MUTATED     1   8
  CCDC146 WILD-TYPE   3 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC146 MUTATED      1    8
  CCDC146 WILD-TYPE    3  159
                        clus
vv                       CCDC146 MUTATED CCDC146 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               8               159
[1] 2 2
[1] FALSE

Clustering(160) Variable = C7ORF60 MUTATION ANALYSIS
D160V1, survival
                   sevent
clus2                 0   1
  C7ORF60 MUTATED    10   0
  C7ORF60 WILD-TYPE 214  24
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
               10               238 
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
                0                24 
$`C7ORF60 MUTATED`
TCGA-A5-A0GI TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z 
       57.53        83.67        86.07         8.22        27.12        46.45 
TCGA-AX-A0J0 TCGA-BG-A0MQ TCGA-D1-A16Y TCGA-D1-A17Q 
       40.11        39.32        17.49         1.78 

$`C7ORF60 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37        74.10        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A 
       15.95         1.18        21.99         5.95        23.31        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        45.53        36.89         7.86        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        31.73        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        41.95        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        68.35        72.03        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       34.98        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       37.78        65.88        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       17.88        13.74        17.10        17.85        11.01         8.71 
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 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MS TCGA-BG-A0MT 
       41.52        48.56        23.47        43.04        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        67.20        88.34 
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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
             1.78              0.56 
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
            86.07            185.79 
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
           39.715            28.865 
[1] "1.8 - 86.1 (39.7)"  "0.6 - 185.8 (28.9)"
[1] "hr="     "2.6e+07"
D160V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  C7ORF60 MUTATED                                        10
  C7ORF60 WILD-TYPE                                     190
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  C7ORF60 MUTATED                               0
  C7ORF60 WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  C7ORF60 MUTATED                                   0
  C7ORF60 WILD-TYPE                                44
D160V3, multiclass
                                         clus
vv                                        C7ORF60 MUTATED C7ORF60 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"
D160V4, binary
                   cls
clus                  0   1
  C7ORF60 MUTATED     5   5
  C7ORF60 WILD-TYPE  81 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF60 MUTATED      5    5
  C7ORF60 WILD-TYPE   81  157
     clus
vv    C7ORF60 MUTATED C7ORF60 WILD-TYPE
  NO                5                81
  YES               5               157
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  C7ORF60 MUTATED     8   1   0   1
  C7ORF60 WILD-TYPE 163  10   7  17
D160V5, multiclass
    clus
vv   C7ORF60 MUTATED C7ORF60 WILD-TYPE
  R0               8               163
  R1               1                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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C7ORF60 MUTATED                                  0     0
  C7ORF60 WILD-TYPE                                3    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  C7ORF60 MUTATED                           1
  C7ORF60 WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C7ORF60 MUTATED                                           0     8
  C7ORF60 WILD-TYPE                                         7   185
D160V6, multiclass
                                           clus
vv                                          C7ORF60 MUTATED C7ORF60 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   0                13
  BLACK OR AFRICAN AMERICAN                               1                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 7
  WHITE                                                   8               185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V7, binary
                   cls
clus                  0   1
  C7ORF60 MUTATED     1   6
  C7ORF60 WILD-TYPE   3 161
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF60 MUTATED      1    6
  C7ORF60 WILD-TYPE    3  161
                        clus
vv                       C7ORF60 MUTATED C7ORF60 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               6               161
[1] 2 2
[1] FALSE

Clustering(161) Variable = ZNF649 MUTATION ANALYSIS
D161V1, survival
                  sevent
clus2                0   1
  ZNF649 MUTATED    14   0
  ZNF649 WILD-TYPE 210  24
  ZNF649 MUTATED ZNF649 WILD-TYPE 
              14              234 
  ZNF649 MUTATED ZNF649 WILD-TYPE 
               0               24 
$`ZNF649 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       83.67        86.07         8.22        27.12        46.45        40.11 
TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A0K2 TCGA-BS-A0TC TCGA-D1-A103 TCGA-D1-A16X 
       65.88        32.55        25.91        85.55        21.99         3.65 
TCGA-D1-A16Y TCGA-D1-A17Q 
       17.49         1.78 

$`ZNF649 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       28.54        37.78        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.64        28.34        30.51        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         8.71       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  ZNF649 MUTATED ZNF649 WILD-TYPE 
            1.78             0.56 
  ZNF649 MUTATED ZNF649 WILD-TYPE 
           86.07           185.79 
  ZNF649 MUTATED ZNF649 WILD-TYPE 
          29.835           29.195 
[1] "1.8 - 86.1 (29.8)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "2.7e+07"
D161V2, continuous
                  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
D161V3, 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"
D161V4, binary
                  cls
clus                 0   1
  ZNF649 MUTATED     4  10
  ZNF649 WILD-TYPE  82 152
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF649 MUTATED      4   10
  ZNF649 WILD-TYPE   82  152
     clus
vv    ZNF649 MUTATED ZNF649 WILD-TYPE
  NO               4               82
  YES             10              152
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF649 MUTATED    10   1   0   1
  ZNF649 WILD-TYPE 161  10   7  17
D161V5, multiclass
    clus
vv   ZNF649 MUTATED ZNF649 WILD-TYPE
  R0             10              161
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF649 MUTATED                                  0     1
  ZNF649 WILD-TYPE                                3    12
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ZNF649 MUTATED                           1
  ZNF649 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF649 MUTATED                                           0    11
  ZNF649 WILD-TYPE                                         7   182
D161V6, multiclass
                                           clus
vv                                          ZNF649 MUTATED ZNF649 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  1               12
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                 11              182
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V7, binary
                  cls
clus                 0   1
  ZNF649 MUTATED     1   8
  ZNF649 WILD-TYPE   3 159
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF649 MUTATED      1    8
  ZNF649 WILD-TYPE    3  159
                        clus
vv                       ZNF649 MUTATED ZNF649 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              8              159
[1] 2 2
[1] FALSE

Clustering(162) Variable = RASSF9 MUTATION ANALYSIS
D162V1, survival
                  sevent
clus2                0   1
  RASSF9 MUTATED     9   0
  RASSF9 WILD-TYPE 215  24
  RASSF9 MUTATED RASSF9 WILD-TYPE 
               9              239 
  RASSF9 MUTATED RASSF9 WILD-TYPE 
               0               24 
$`RASSF9 MUTATED`
TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-BS-A0UJ 
       86.07        27.12        46.45        40.11        32.55        82.39 
TCGA-BS-A0UM TCGA-BS-A0UV TCGA-D1-A17Q 
       86.93        73.25         1.78 

$`RASSF9 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        40.67        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        85.84        81.57        72.72 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  RASSF9 MUTATED RASSF9 WILD-TYPE 
            1.78             0.56 
  RASSF9 MUTATED RASSF9 WILD-TYPE 
           86.93           185.79 
  RASSF9 MUTATED RASSF9 WILD-TYPE 
           46.45            28.64 
[1] "1.8 - 86.9 (46.5)"  "0.6 - 185.8 (28.6)"
[1] "hr="     "2.6e+07"
D162V2, continuous
                  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
D162V3, 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"
D162V4, binary
                  cls
clus                 0   1
  RASSF9 MUTATED     2   7
  RASSF9 WILD-TYPE  84 155
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASSF9 MUTATED      2    7
  RASSF9 WILD-TYPE   84  155
     clus
vv    RASSF9 MUTATED RASSF9 WILD-TYPE
  NO               2               84
  YES              7              155
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  RASSF9 MUTATED     7   1   0   0
  RASSF9 WILD-TYPE 164  10   7  18
D162V5, multiclass
    clus
vv   RASSF9 MUTATED RASSF9 WILD-TYPE
  R0              7              164
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RASSF9 MUTATED                                  0     1
  RASSF9 WILD-TYPE                                3    12
                  vv
clus               BLACK OR AFRICAN AMERICAN
  RASSF9 MUTATED                           1
  RASSF9 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RASSF9 MUTATED                                           1     5
  RASSF9 WILD-TYPE                                         6   188
D162V6, multiclass
                                           clus
vv                                          RASSF9 MUTATED RASSF9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  1               12
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  5              188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V7, binary
                  cls
clus                 0   1
  RASSF9 MUTATED     1   5
  RASSF9 WILD-TYPE   3 162
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASSF9 MUTATED      1    5
  RASSF9 WILD-TYPE    3  162
                        clus
vv                       RASSF9 MUTATED RASSF9 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              5              162
[1] 2 2
[1] FALSE

Clustering(163) Variable = NIPA2 MUTATION ANALYSIS
D163V1, survival
                 sevent
clus2               0   1
  NIPA2 MUTATED     8   0
  NIPA2 WILD-TYPE 216  24
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              8             240 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              0              24 
$`NIPA2 MUTATED`
TCGA-A5-A0GP TCGA-AP-A059 TCGA-AX-A0J1 TCGA-B5-A11Y TCGA-BS-A0UF TCGA-BS-A0UJ 
       46.55         8.22        65.88        18.41        85.84        82.39 
TCGA-D1-A15X TCGA-D1-A17A 
       29.88         1.58 

$`NIPA2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        35.01        28.54        37.78        40.11 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        46.75        43.13        40.67        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         8.71       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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-A17B TCGA-D1-A17C TCGA-D1-A17D 
       19.53        30.15        18.02         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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  NIPA2 MUTATED NIPA2 WILD-TYPE 
           1.58            0.56 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
          85.84          185.79 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
         38.215          28.865 
[1] "1.6 - 85.8 (38.2)"  "0.6 - 185.8 (28.9)"
[1] "hr="     "2.6e+07"
D163V2, continuous
                 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
D163V3, 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"
D163V4, binary
                 cls
clus                0   1
  NIPA2 MUTATED     2   6
  NIPA2 WILD-TYPE  84 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPA2 MUTATED      2    6
  NIPA2 WILD-TYPE   84  156
     clus
vv    NIPA2 MUTATED NIPA2 WILD-TYPE
  NO              2              84
  YES             6             156
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NIPA2 MUTATED     7   0   0   0
  NIPA2 WILD-TYPE 164  11   7  18
D163V5, multiclass
    clus
vv   NIPA2 MUTATED NIPA2 WILD-TYPE
  R0             7             164
  R1             0              11
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NIPA2 MUTATED                                  0     3
  NIPA2 WILD-TYPE                                3    10
                 vv
clus              BLACK OR AFRICAN AMERICAN
  NIPA2 MUTATED                           0
  NIPA2 WILD-TYPE                        25
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NIPA2 MUTATED                                           0     5
  NIPA2 WILD-TYPE                                         7   188
D163V6, multiclass
                                           clus
vv                                          NIPA2 MUTATED NIPA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 3              10
  BLACK OR AFRICAN AMERICAN                             0              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                 5             188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V7, binary
                 cls
clus                0   1
  NIPA2 MUTATED     0   7
  NIPA2 WILD-TYPE   4 160
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPA2 MUTATED      0    7
  NIPA2 WILD-TYPE    4  160
                        clus
vv                       NIPA2 MUTATED NIPA2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             160
[1] 2 2
[1] FALSE

Clustering(164) Variable = FILIP1 MUTATION ANALYSIS
D164V1, survival
                  sevent
clus2                0   1
  FILIP1 MUTATED    16   0
  FILIP1 WILD-TYPE 208  24
  FILIP1 MUTATED FILIP1 WILD-TYPE 
              16              232 
  FILIP1 MUTATED FILIP1 WILD-TYPE 
               0               24 
$`FILIP1 MUTATED`
TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A0LM TCGA-AP-A0LP TCGA-AX-A05Z 
       42.35        83.67        86.07        27.12        61.64        46.45 
TCGA-AX-A06B TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11H TCGA-B5-A11R 
       53.92        40.11        32.55         8.71        88.34        33.50 
TCGA-BG-A0VW TCGA-BS-A0UF TCGA-D1-A103 TCGA-D1-A15X 
       16.34        85.84        21.99        29.88 

$`FILIP1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A059 
       15.95         1.18        21.99         5.95        23.31         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        83.97        82.52        33.40 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       80.78        49.22        25.08        41.95        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        68.35        72.03        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       34.98        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       65.88        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       80.38        56.91        46.75        43.13        40.67        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I 
       17.10        17.85        11.01       185.79       113.36        75.72 
TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11S 
       54.44        44.78        43.96        40.50        32.09        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z 
       22.55         1.74         4.44        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  FILIP1 MUTATED FILIP1 WILD-TYPE 
            8.71             0.56 
  FILIP1 MUTATED FILIP1 WILD-TYPE 
           88.34           185.79 
  FILIP1 MUTATED FILIP1 WILD-TYPE 
           41.23            28.54 
[1] "8.7 - 88.3 (41.2)"  "0.6 - 185.8 (28.5)"
[1] "hr="     "7.6e+07"
D164V2, continuous
                  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
D164V3, 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"
D164V4, binary
                  cls
clus                 0   1
  FILIP1 MUTATED     8   8
  FILIP1 WILD-TYPE  78 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FILIP1 MUTATED      8    8
  FILIP1 WILD-TYPE   78  154
     clus
vv    FILIP1 MUTATED FILIP1 WILD-TYPE
  NO               8               78
  YES              8              154
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FILIP1 MUTATED    11   1   0   0
  FILIP1 WILD-TYPE 160  10   7  18
D164V5, multiclass
    clus
vv   FILIP1 MUTATED FILIP1 WILD-TYPE
  R0             11              160
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FILIP1 MUTATED                                  0     1
  FILIP1 WILD-TYPE                                3    12
                  vv
clus               BLACK OR AFRICAN AMERICAN
  FILIP1 MUTATED                           2
  FILIP1 WILD-TYPE                        23
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FILIP1 MUTATED                                           0    12
  FILIP1 WILD-TYPE                                         7   181
D164V6, multiclass
                                           clus
vv                                          FILIP1 MUTATED FILIP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  1               12
  BLACK OR AFRICAN AMERICAN                              2               23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                 12              181
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V7, binary
                  cls
clus                 0   1
  FILIP1 MUTATED     1   7
  FILIP1 WILD-TYPE   3 160
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FILIP1 MUTATED      1    7
  FILIP1 WILD-TYPE    3  160
                        clus
vv                       FILIP1 MUTATED FILIP1 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              7              160
[1] 2 2
[1] FALSE

Clustering(165) Variable = PHKA2 MUTATION ANALYSIS
D165V1, survival
                 sevent
clus2               0   1
  PHKA2 MUTATED    16   0
  PHKA2 WILD-TYPE 208  24
  PHKA2 MUTATED PHKA2 WILD-TYPE 
             16             232 
  PHKA2 MUTATED PHKA2 WILD-TYPE 
              0              24 
$`PHKA2 MUTATED`
TCGA-A5-A0G3 TCGA-A5-A0GP TCGA-AP-A051 TCGA-AP-A0LG TCGA-AP-A0LM TCGA-AX-A0J1 
       46.95        46.55        83.67        63.16        27.12        65.88 
TCGA-B5-A0JR TCGA-B5-A0K9 TCGA-B5-A11E TCGA-BG-A0MQ TCGA-BS-A0UF TCGA-BS-A0UJ 
       56.91        11.01         8.71        39.32        85.84        82.39 
TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A167 TCGA-D1-A17Q 
       73.25        21.99        15.72         1.78 

$`PHKA2 WILD-TYPE`
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         3.22       105.37 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GQ 
       74.10        57.53        65.75        60.53        60.53        38.37 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.59        24.62        29.06        11.97        42.35        15.95 
TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        1.18        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37         3.39        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        31.73        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        41.95        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       28.54        37.78        40.11        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       71.24        19.36        80.38        46.75        43.13        40.67 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A11F TCGA-B5-A11G 
       17.88        13.74        17.10        17.85       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.04        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        81.57        86.93 
TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       72.72        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  PHKA2 MUTATED PHKA2 WILD-TYPE 
           1.78            0.56 
  PHKA2 MUTATED PHKA2 WILD-TYPE 
          85.84          185.79 
  PHKA2 MUTATED PHKA2 WILD-TYPE 
         46.750          28.655 
[1] "1.8 - 85.8 (46.8)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "7.6e+07"
D165V2, continuous
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  PHKA2 MUTATED                                        15
  PHKA2 WILD-TYPE                                     185
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  PHKA2 MUTATED                               0
  PHKA2 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  PHKA2 MUTATED                                   1
  PHKA2 WILD-TYPE                                43
D165V3, multiclass
                                         clus
vv                                        PHKA2 MUTATED PHKA2 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"
D165V4, binary
                 cls
clus                0   1
  PHKA2 MUTATED     6  10
  PHKA2 WILD-TYPE  80 152
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKA2 MUTATED      6   10
  PHKA2 WILD-TYPE   80  152
     clus
vv    PHKA2 MUTATED PHKA2 WILD-TYPE
  NO              6              80
  YES            10             152
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PHKA2 MUTATED    13   0   0   0
  PHKA2 WILD-TYPE 158  11   7  18
D165V5, multiclass
    clus
vv   PHKA2 MUTATED PHKA2 WILD-TYPE
  R0            13             158
  R1             0              11
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PHKA2 MUTATED                                  0     3
  PHKA2 WILD-TYPE                                3    10
                 vv
clus              BLACK OR AFRICAN AMERICAN
  PHKA2 MUTATED                           2
  PHKA2 WILD-TYPE                        23
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PHKA2 MUTATED                                           1    10
  PHKA2 WILD-TYPE                                         6   183
D165V6, multiclass
                                           clus
vv                                          PHKA2 MUTATED PHKA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 3              10
  BLACK OR AFRICAN AMERICAN                             2              23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                10             183
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V7, binary
                 cls
clus                0   1
  PHKA2 MUTATED     0   9
  PHKA2 WILD-TYPE   4 158
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKA2 MUTATED      0    9
  PHKA2 WILD-TYPE    4  158
                        clus
vv                       PHKA2 MUTATED PHKA2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             158
[1] 2 2
[1] FALSE

Clustering(166) Variable = COBLL1 MUTATION ANALYSIS
D166V1, survival
                  sevent
clus2                0   1
  COBLL1 MUTATED    15   0
  COBLL1 WILD-TYPE 209  24
  COBLL1 MUTATED COBLL1 WILD-TYPE 
              15              233 
  COBLL1 MUTATED COBLL1 WILD-TYPE 
               0               24 
$`COBLL1 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LF TCGA-AP-A0LM TCGA-AX-A05Z 
       83.67        86.07         8.22         3.39        27.12        46.45 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0UF TCGA-BS-A0UJ 
       40.11        65.88        32.55         8.71        85.84        82.39 
TCGA-D1-A0ZO TCGA-D1-A103 TCGA-D1-A17Q 
       19.79        21.99         1.78 

$`COBLL1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        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        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        31.73        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        41.95        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        68.35        72.03        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       34.98        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       37.78        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       80.38        56.91        46.75        43.13        40.67        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        17.85        11.01       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        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-A102 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  COBLL1 MUTATED COBLL1 WILD-TYPE 
            1.78             0.56 
  COBLL1 MUTATED COBLL1 WILD-TYPE 
           86.07           185.79 
  COBLL1 MUTATED COBLL1 WILD-TYPE 
           32.55            29.06 
[1] "1.8 - 86.1 (32.5)"  "0.6 - 185.8 (29.1)"
[1] "hr="     "2.7e+07"
D166V2, continuous
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  COBLL1 MUTATED                                        15
  COBLL1 WILD-TYPE                                     185
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  COBLL1 MUTATED                               0
  COBLL1 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  COBLL1 MUTATED                                   0
  COBLL1 WILD-TYPE                                44
D166V3, multiclass
                                         clus
vv                                        COBLL1 MUTATED COBLL1 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"
D166V4, binary
                  cls
clus                 0   1
  COBLL1 MUTATED     4  11
  COBLL1 WILD-TYPE  82 151
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COBLL1 MUTATED      4   11
  COBLL1 WILD-TYPE   82  151
     clus
vv    COBLL1 MUTATED COBLL1 WILD-TYPE
  NO               4               82
  YES             11              151
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  COBLL1 MUTATED    11   1   1   0
  COBLL1 WILD-TYPE 160  10   6  18
D166V5, multiclass
    clus
vv   COBLL1 MUTATED COBLL1 WILD-TYPE
  R0             11              160
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COBLL1 MUTATED                                  0     2
  COBLL1 WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  COBLL1 MUTATED                           1
  COBLL1 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  COBLL1 MUTATED                                           0    11
  COBLL1 WILD-TYPE                                         7   182
D166V6, multiclass
                                           clus
vv                                          COBLL1 MUTATED COBLL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                 11              182
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V7, binary
                  cls
clus                 0   1
  COBLL1 MUTATED     1   9
  COBLL1 WILD-TYPE   3 158
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COBLL1 MUTATED      1    9
  COBLL1 WILD-TYPE    3  158
                        clus
vv                       COBLL1 MUTATED COBLL1 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              9              158
[1] 2 2
[1] FALSE

Clustering(167) Variable = AGPAT9 MUTATION ANALYSIS
D167V1, survival
                  sevent
clus2                0   1
  AGPAT9 MUTATED     8   0
  AGPAT9 WILD-TYPE 216  24
  AGPAT9 MUTATED AGPAT9 WILD-TYPE 
               8              240 
  AGPAT9 MUTATED AGPAT9 WILD-TYPE 
               0               24 
$`AGPAT9 MUTATED`
TCGA-AX-A05Z TCGA-AX-A0J1 TCGA-B5-A0JY TCGA-B5-A11H TCGA-BS-A0TC TCGA-BS-A0UF 
       46.45        65.88        32.55        88.34        85.55        85.84 
TCGA-D1-A101 TCGA-D1-A103 
        1.74        21.99 

$`AGPAT9 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89         7.86        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
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        41.95        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       68.35        72.03        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       40.11        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       80.38        56.91        46.75        43.13        40.67        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         8.71       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W 
       28.67        23.93        22.55         4.44        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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  AGPAT9 MUTATED AGPAT9 WILD-TYPE 
            1.74             0.56 
  AGPAT9 MUTATED AGPAT9 WILD-TYPE 
           88.34           185.79 
  AGPAT9 MUTATED AGPAT9 WILD-TYPE 
          56.165           28.655 
[1] "1.7 - 88.3 (56.2)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.6e+07"
D167V2, continuous
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AGPAT9 MUTATED                                         8
  AGPAT9 WILD-TYPE                                     192
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  AGPAT9 MUTATED                               0
  AGPAT9 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  AGPAT9 MUTATED                                   0
  AGPAT9 WILD-TYPE                                44
D167V3, multiclass
                                         clus
vv                                        AGPAT9 MUTATED AGPAT9 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"
D167V4, binary
                  cls
clus                 0   1
  AGPAT9 MUTATED     0   8
  AGPAT9 WILD-TYPE  86 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AGPAT9 MUTATED      0    8
  AGPAT9 WILD-TYPE   86  154
     clus
vv    AGPAT9 MUTATED AGPAT9 WILD-TYPE
  NO               0               86
  YES              8              154
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  AGPAT9 MUTATED     4   1   0   1
  AGPAT9 WILD-TYPE 167  10   7  17
D167V5, multiclass
    clus
vv   AGPAT9 MUTATED AGPAT9 WILD-TYPE
  R0              4              167
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AGPAT9 MUTATED                                  0     2
  AGPAT9 WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  AGPAT9 MUTATED                           0
  AGPAT9 WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AGPAT9 MUTATED                                           0     5
  AGPAT9 WILD-TYPE                                         7   188
D167V6, multiclass
                                           clus
vv                                          AGPAT9 MUTATED AGPAT9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                  5              188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V7, binary
                  cls
clus                 0   1
  AGPAT9 MUTATED     1   5
  AGPAT9 WILD-TYPE   3 162
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AGPAT9 MUTATED      1    5
  AGPAT9 WILD-TYPE    3  162
                        clus
vv                       AGPAT9 MUTATED AGPAT9 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              5              162
[1] 2 2
[1] FALSE

Clustering(168) Variable = NOP56 MUTATION ANALYSIS
D168V1, survival
                 sevent
clus2               0   1
  NOP56 MUTATED    11   0
  NOP56 WILD-TYPE 213  24
  NOP56 MUTATED NOP56 WILD-TYPE 
             11             237 
  NOP56 MUTATED NOP56 WILD-TYPE 
              0              24 
$`NOP56 MUTATED`
TCGA-AP-A059 TCGA-AP-A0LD TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-B5-A11E TCGA-B5-A11H 
        8.22       117.99        27.12        40.11         8.71        88.34 
TCGA-BG-A0M0 TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A101 TCGA-D1-A16X 
       19.33        85.84        73.25         1.74         3.65 

$`NOP56 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LE TCGA-AP-A0LF 
        7.86        20.91        48.79       125.42       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       46.75        43.13        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J 
       17.85        11.01       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       88.34        82.39        81.57        86.93        72.72        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  NOP56 MUTATED NOP56 WILD-TYPE 
           1.74            0.56 
  NOP56 MUTATED NOP56 WILD-TYPE 
         117.99          185.79 
  NOP56 MUTATED NOP56 WILD-TYPE 
          27.12           29.33 
[1] "1.7 - 118.0 (27.1)" "0.6 - 185.8 (29.3)"
[1] "hr="     "2.6e+07"
D168V2, continuous
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  NOP56 MUTATED                                        11
  NOP56 WILD-TYPE                                     189
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  NOP56 MUTATED                               0
  NOP56 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  NOP56 MUTATED                                   0
  NOP56 WILD-TYPE                                44
D168V3, multiclass
                                         clus
vv                                        NOP56 MUTATED NOP56 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"
D168V4, binary
                 cls
clus                0   1
  NOP56 MUTATED     3   8
  NOP56 WILD-TYPE  83 154
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOP56 MUTATED      3    8
  NOP56 WILD-TYPE   83  154
     clus
vv    NOP56 MUTATED NOP56 WILD-TYPE
  NO              3              83
  YES             8             154
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NOP56 MUTATED     8   0   0   1
  NOP56 WILD-TYPE 163  11   7  17
D168V5, multiclass
    clus
vv   NOP56 MUTATED NOP56 WILD-TYPE
  R0             8             163
  R1             0              11
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOP56 MUTATED                                  0     1
  NOP56 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  NOP56 MUTATED                           1
  NOP56 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NOP56 MUTATED                                           1     8
  NOP56 WILD-TYPE                                         6   185
D168V6, multiclass
                                           clus
vv                                          NOP56 MUTATED NOP56 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                 8             185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V7, binary
                 cls
clus                0   1
  NOP56 MUTATED     0   7
  NOP56 WILD-TYPE   4 160
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOP56 MUTATED      0    7
  NOP56 WILD-TYPE    4  160
                        clus
vv                       NOP56 MUTATED NOP56 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             160
[1] 2 2
[1] FALSE

Clustering(169) Variable = RBL2 MUTATION ANALYSIS
D169V1, survival
                sevent
clus2              0   1
  RBL2 MUTATED    11   1
  RBL2 WILD-TYPE 213  23
  RBL2 MUTATED RBL2 WILD-TYPE 
            12            236 
  RBL2 MUTATED RBL2 WILD-TYPE 
             1             23 
$`RBL2 MUTATED`
TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J1 TCGA-B5-A11E 
       83.67        23.31        27.12        46.45        65.88         8.71 
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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A056 
       42.35        15.95         1.18        21.99         5.95        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        40.11        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       43.13        40.67        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       11.01       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       77.95        61.87        96.49        30.74        97.41        67.20 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       88.34        82.39        81.57        86.93        72.72        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        21.99        39.48        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-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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  RBL2 MUTATED RBL2 WILD-TYPE 
          3.65           0.56 
  RBL2 MUTATED RBL2 WILD-TYPE 
         85.84         185.79 
  RBL2 MUTATED RBL2 WILD-TYPE 
        38.265         28.865 
[1] "3.6 - 85.8 (38.3)"  "0.6 - 185.8 (28.9)"
[1] "hr=" "1.4"
D169V2, continuous
                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"
D169V4, binary
                cls
clus               0   1
  RBL2 MUTATED     4   8
  RBL2 WILD-TYPE  82 154
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED      4    8
  RBL2 WILD-TYPE   82  154
     clus
vv    RBL2 MUTATED RBL2 WILD-TYPE
  NO             4             82
  YES            8            154
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RBL2 MUTATED     8   2   0   1
  RBL2 WILD-TYPE 163   9   7  17
D169V5, multiclass
    clus
vv   RBL2 MUTATED RBL2 WILD-TYPE
  R0            8            163
  R1            2              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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBL2 MUTATED                                  0     2
  RBL2 WILD-TYPE                                3    11
                vv
clus             BLACK OR AFRICAN AMERICAN
  RBL2 MUTATED                           1
  RBL2 WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RBL2 MUTATED                                           1     7
  RBL2 WILD-TYPE                                         6   186
D169V6, multiclass
                                           clus
vv                                          RBL2 MUTATED RBL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                2             11
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                                7            186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V7, binary
                cls
clus               0   1
  RBL2 MUTATED     1   8
  RBL2 WILD-TYPE   3 159
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED      1    8
  RBL2 WILD-TYPE    3  159
                        clus
vv                       RBL2 MUTATED RBL2 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            8            159
[1] 2 2
[1] FALSE

Clustering(170) Variable = ABCC6 MUTATION ANALYSIS
D170V1, survival
                 sevent
clus2               0   1
  ABCC6 MUTATED    10   2
  ABCC6 WILD-TYPE 214  22
  ABCC6 MUTATED ABCC6 WILD-TYPE 
             12             236 
  ABCC6 MUTATED ABCC6 WILD-TYPE 
              2              22 
$`ABCC6 MUTATED`
TCGA-A5-A0VP TCGA-AP-A056 TCGA-AP-A0LH TCGA-AP-A0LM TCGA-AP-A0LP TCGA-AX-A05S 
       42.35        86.07        36.36        27.12        61.64        13.58 
TCGA-AX-A05Z TCGA-B5-A0JY TCGA-BS-A0WQ TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A16X 
       46.45        32.55        66.48        21.99        30.08         3.65 

$`ABCC6 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       63.16        97.71        31.73        83.97        82.52        33.40 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05T TCGA-AX-A05U 
       80.78        49.22        25.08        41.95        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       68.35        72.03        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       40.11        65.88        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        17.85        11.01         8.71       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        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        67.20        88.34 
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-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       62.79        63.58        49.55        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74         4.44        39.48        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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  ABCC6 MUTATED ABCC6 WILD-TYPE 
           3.65            0.56 
  ABCC6 MUTATED ABCC6 WILD-TYPE 
          86.07          185.79 
  ABCC6 MUTATED ABCC6 WILD-TYPE 
         34.455          28.655 
[1] "3.6 - 86.1 (34.5)"  "0.6 - 185.8 (28.7)"
[1] "hr=" "1.6"
D170V2, continuous
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ABCC6 MUTATED                                        11
  ABCC6 WILD-TYPE                                     189
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  ABCC6 MUTATED                               1
  ABCC6 WILD-TYPE                             3
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  ABCC6 MUTATED                                   0
  ABCC6 WILD-TYPE                                44
D170V3, multiclass
                                         clus
vv                                        ABCC6 MUTATED ABCC6 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA            11             189
  MIXED SEROUS AND ENDOMETRIOID                       1               3
  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"
D170V4, binary
                 cls
clus                0   1
  ABCC6 MUTATED     7   5
  ABCC6 WILD-TYPE  79 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC6 MUTATED      7    5
  ABCC6 WILD-TYPE   79  157
     clus
vv    ABCC6 MUTATED ABCC6 WILD-TYPE
  NO              7              79
  YES             5             157
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ABCC6 MUTATED     8   1   1   1
  ABCC6 WILD-TYPE 163  10   6  17
D170V5, multiclass
    clus
vv   ABCC6 MUTATED ABCC6 WILD-TYPE
  R0             8             163
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABCC6 MUTATED                                  0     1
  ABCC6 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  ABCC6 MUTATED                           1
  ABCC6 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCC6 MUTATED                                           0     9
  ABCC6 WILD-TYPE                                         7   184
D170V6, multiclass
                                           clus
vv                                          ABCC6 MUTATED ABCC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                 9             184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V7, binary
                 cls
clus                0   1
  ABCC6 MUTATED     1   7
  ABCC6 WILD-TYPE   3 160
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC6 MUTATED      1    7
  ABCC6 WILD-TYPE    3  160
                        clus
vv                       ABCC6 MUTATED ABCC6 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             7             160
[1] 2 2
[1] FALSE

Clustering(171) Variable = CCDC104 MUTATION ANALYSIS
D171V1, survival
                   sevent
clus2                 0   1
  CCDC104 MUTATED    10   0
  CCDC104 WILD-TYPE 214  24
  CCDC104 MUTATED CCDC104 WILD-TYPE 
               10               238 
  CCDC104 MUTATED CCDC104 WILD-TYPE 
                0                24 
$`CCDC104 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11J 
       83.67        86.07        40.11        32.55         8.71        54.44 
TCGA-BG-A0M4 TCGA-BS-A0UF TCGA-D1-A16X TCGA-D1-A17Q 
       34.98        85.84         3.65         1.78 

$`CCDC104 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        35.01        28.54        37.78        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       20.94        35.21         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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-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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  CCDC104 MUTATED CCDC104 WILD-TYPE 
             1.78              0.56 
  CCDC104 MUTATED CCDC104 WILD-TYPE 
            86.07            185.79 
  CCDC104 MUTATED CCDC104 WILD-TYPE 
           37.545            28.655 
[1] "1.8 - 86.1 (37.5)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.6e+07"
D171V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CCDC104 MUTATED                                        10
  CCDC104 WILD-TYPE                                     190
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  CCDC104 MUTATED                               0
  CCDC104 WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  CCDC104 MUTATED                                   0
  CCDC104 WILD-TYPE                                44
D171V3, multiclass
                                         clus
vv                                        CCDC104 MUTATED CCDC104 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"
D171V4, binary
                   cls
clus                  0   1
  CCDC104 MUTATED     2   8
  CCDC104 WILD-TYPE  84 154
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC104 MUTATED      2    8
  CCDC104 WILD-TYPE   84  154
     clus
vv    CCDC104 MUTATED CCDC104 WILD-TYPE
  NO                2                84
  YES               8               154
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC104 MUTATED     7   0   0   0
  CCDC104 WILD-TYPE 164  11   7  18
D171V5, multiclass
    clus
vv   CCDC104 MUTATED CCDC104 WILD-TYPE
  R0               7               164
  R1               0                11
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC104 MUTATED                                  0     1
  CCDC104 WILD-TYPE                                3    12
                   vv
clus                BLACK OR AFRICAN AMERICAN
  CCDC104 MUTATED                           0
  CCDC104 WILD-TYPE                        25
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC104 MUTATED                                           0     9
  CCDC104 WILD-TYPE                                         7   184
D171V6, multiclass
                                           clus
vv                                          CCDC104 MUTATED CCDC104 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                12
  BLACK OR AFRICAN AMERICAN                               0                25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 7
  WHITE                                                   9               184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V7, binary
                   cls
clus                  0   1
  CCDC104 MUTATED     0   5
  CCDC104 WILD-TYPE   4 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC104 MUTATED      0    5
  CCDC104 WILD-TYPE    4  162
                        clus
vv                       CCDC104 MUTATED CCDC104 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               5               162
[1] 2 2
[1] FALSE

Clustering(172) Variable = MLL2 MUTATION ANALYSIS
D172V1, survival
                sevent
clus2              0   1
  MLL2 MUTATED    32   1
  MLL2 WILD-TYPE 192  23
  MLL2 MUTATED MLL2 WILD-TYPE 
            33            215 
  MLL2 MUTATED MLL2 WILD-TYPE 
             1             23 
$`MLL2 MUTATED`
TCGA-A5-A0GA TCGA-A5-A0GH TCGA-A5-A0GP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 
       17.85        74.10        46.55        83.67        86.07         8.22 
TCGA-AP-A0LD TCGA-AP-A0LG TCGA-AP-A0LM TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A0J0 
      117.99        63.16        27.12        35.34        66.58        40.11 
TCGA-AX-A0J1 TCGA-B5-A0JT TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11J TCGA-BG-A0MS 
       65.88        43.13        32.55         8.71        54.44        30.81 
TCGA-BG-A0VW TCGA-BG-A0W2 TCGA-BG-A18B TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0UA 
       16.34        56.58        15.45        23.47        85.55        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A15X TCGA-D1-A160 
       85.84        82.39        73.25        21.99        29.88         3.68 
TCGA-D1-A17H TCGA-D1-A17Q TCGA-E6-A1LZ 
       28.01         1.78        48.36 

$`MLL2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       46.95        37.02        83.51        32.78         3.22       105.37 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GQ TCGA-A5-A0GU 
       57.53        65.75        60.53        60.53        38.37        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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        11.97        42.35        15.95         1.18 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       21.99         5.95        23.31        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LE 
       36.89         7.86        20.91        48.79       125.42       110.37 
TCGA-AP-A0LF TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
        3.39        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A062 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       45.99        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       28.54        37.78        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JV TCGA-B5-A0JZ 
       19.36        80.38        56.91        46.75        40.67        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        17.85        11.01       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       75.72        44.78        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       39.32        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       34.29        28.54        52.83        14.83        12.56        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-A0TD 
        6.21        10.22        10.16        24.99        46.95        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-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 
       97.41        67.20        81.57        86.93        72.72        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A161 
        1.74         4.44        39.48        30.08         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-A17K TCGA-D1-A17L TCGA-D1-A17M 
        0.99        30.44         1.28        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-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       18.25        16.31        35.38        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  MLL2 MUTATED MLL2 WILD-TYPE 
          1.78           0.56 
  MLL2 MUTATED MLL2 WILD-TYPE 
        117.99         185.79 
  MLL2 MUTATED MLL2 WILD-TYPE 
         43.13          28.34 
[1] "1.8 - 118.0 (43.1)" "0.6 - 185.8 (28.3)"
[1] "hr=" "4.8"
D172V2, continuous
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MLL2 MUTATED                                        31
  MLL2 WILD-TYPE                                     169
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  MLL2 MUTATED                               0
  MLL2 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  MLL2 MUTATED                                   2
  MLL2 WILD-TYPE                                42
D172V3, multiclass
                                         clus
vv                                        MLL2 MUTATED MLL2 WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA           31            169
  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"
D172V4, binary
                cls
clus               0   1
  MLL2 MUTATED    11  22
  MLL2 WILD-TYPE  75 140
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     11   22
  MLL2 WILD-TYPE   75  140
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO            11             75
  YES           22            140
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MLL2 MUTATED    25   1   0   3
  MLL2 WILD-TYPE 146  10   7  15
D172V5, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  R0           25            146
  R1            1             10
  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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL2 MUTATED                                  1     4
  MLL2 WILD-TYPE                                2     9
                vv
clus             BLACK OR AFRICAN AMERICAN
  MLL2 MUTATED                           2
  MLL2 WILD-TYPE                        23
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MLL2 MUTATED                                           2    24
  MLL2 WILD-TYPE                                         5   169
D172V6, multiclass
                                           clus
vv                                          MLL2 MUTATED MLL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     1              2
  ASIAN                                                4              9
  BLACK OR AFRICAN AMERICAN                            2             23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            2              5
  WHITE                                               24            169
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V7, binary
                cls
clus               0   1
  MLL2 MUTATED     1  22
  MLL2 WILD-TYPE   3 145
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      1   22
  MLL2 WILD-TYPE    3  145
                        clus
vv                       MLL2 MUTATED MLL2 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           22            145
[1] 2 2
[1] FALSE

Clustering(173) Variable = SSH2 MUTATION ANALYSIS
D173V1, survival
                sevent
clus2              0   1
  SSH2 MUTATED    12   0
  SSH2 WILD-TYPE 212  24
  SSH2 MUTATED SSH2 WILD-TYPE 
            12            236 
  SSH2 MUTATED SSH2 WILD-TYPE 
             0             24 
$`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         8.22        49.22        46.45 
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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A 
        1.18        83.67        21.99         5.95        23.31        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        45.53        36.89         7.86        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        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        41.95        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        68.35        72.03        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       34.98        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       37.78        40.11        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       40.67        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       24.99        46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 
       88.34        81.57        86.93        72.72        73.25        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z 
        1.74         4.44        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-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-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  SSH2 MUTATED SSH2 WILD-TYPE 
          1.78           0.56 
  SSH2 MUTATED SSH2 WILD-TYPE 
         86.07         185.79 
  SSH2 MUTATED SSH2 WILD-TYPE 
        46.500         28.655 
[1] "1.8 - 86.1 (46.5)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.7e+07"
D173V2, continuous
                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
D173V3, 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"
D173V4, binary
                cls
clus               0   1
  SSH2 MUTATED     5   7
  SSH2 WILD-TYPE  81 155
[1] "tbl2"
                cls
clus             [,1] [,2]
  SSH2 MUTATED      5    7
  SSH2 WILD-TYPE   81  155
     clus
vv    SSH2 MUTATED SSH2 WILD-TYPE
  NO             5             81
  YES            7            155
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SSH2 MUTATED    11   1   0   0
  SSH2 WILD-TYPE 160  10   7  18
D173V5, multiclass
    clus
vv   SSH2 MUTATED SSH2 WILD-TYPE
  R0           11            160
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SSH2 MUTATED                                  0     4
  SSH2 WILD-TYPE                                3     9
                vv
clus             BLACK OR AFRICAN AMERICAN
  SSH2 MUTATED                           0
  SSH2 WILD-TYPE                        25
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SSH2 MUTATED                                           0     6
  SSH2 WILD-TYPE                                         7   187
D173V6, multiclass
                                           clus
vv                                          SSH2 MUTATED SSH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                4              9
  BLACK OR AFRICAN AMERICAN                            0             25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              7
  WHITE                                                6            187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V7, binary
                cls
clus               0   1
  SSH2 MUTATED     2   8
  SSH2 WILD-TYPE   2 159
[1] "tbl2"
                cls
clus             [,1] [,2]
  SSH2 MUTATED      2    8
  SSH2 WILD-TYPE    2  159
                        clus
vv                       SSH2 MUTATED SSH2 WILD-TYPE
  HISPANIC OR LATINO                2              2
  NOT HISPANIC OR LATINO            8            159
[1] 2 2
[1] FALSE

Clustering(174) Variable = ZNF709 MUTATION ANALYSIS
D174V1, survival
                  sevent
clus2                0   1
  ZNF709 MUTATED    12   0
  ZNF709 WILD-TYPE 212  24
  ZNF709 MUTATED ZNF709 WILD-TYPE 
              12              236 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               0               24 
$`ZNF709 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A11E 
       83.67        86.07        27.12        46.45        40.11         8.71 
TCGA-B5-A11N TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A174 
       43.96        85.55        85.84        73.25        21.99        19.53 

$`ZNF709 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        65.88        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       43.13        40.67        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       11.01       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        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        23.47        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        67.20        88.34 
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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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-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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  ZNF709 MUTATED ZNF709 WILD-TYPE 
            8.71             0.56 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
           86.07           185.79 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
          45.205           28.655 
[1] "8.7 - 86.1 (45.2)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.7e+07"
D174V2, continuous
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZNF709 MUTATED                                        12
  ZNF709 WILD-TYPE                                     188
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ZNF709 MUTATED                               0
  ZNF709 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZNF709 MUTATED                                   0
  ZNF709 WILD-TYPE                                44
D174V3, multiclass
                                         clus
vv                                        ZNF709 MUTATED ZNF709 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"
D174V4, binary
                  cls
clus                 0   1
  ZNF709 MUTATED     4   8
  ZNF709 WILD-TYPE  82 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      4    8
  ZNF709 WILD-TYPE   82  154
     clus
vv    ZNF709 MUTATED ZNF709 WILD-TYPE
  NO               4               82
  YES              8              154
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF709 MUTATED     9   1   0   0
  ZNF709 WILD-TYPE 162  10   7  18
D174V5, multiclass
    clus
vv   ZNF709 MUTATED ZNF709 WILD-TYPE
  R0              9              162
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF709 MUTATED                                  0     2
  ZNF709 WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ZNF709 MUTATED                           1
  ZNF709 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF709 MUTATED                                           1     7
  ZNF709 WILD-TYPE                                         6   186
D174V6, multiclass
                                           clus
vv                                          ZNF709 MUTATED ZNF709 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  7              186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V7, binary
                  cls
clus                 0   1
  ZNF709 MUTATED     1   6
  ZNF709 WILD-TYPE   3 161
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      1    6
  ZNF709 WILD-TYPE    3  161
                        clus
vv                       ZNF709 MUTATED ZNF709 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              6              161
[1] 2 2
[1] FALSE

Clustering(175) Variable = BRDT MUTATION ANALYSIS
D175V1, survival
                sevent
clus2              0   1
  BRDT MUTATED    14   0
  BRDT WILD-TYPE 210  24
  BRDT MUTATED BRDT WILD-TYPE 
            14            234 
  BRDT MUTATED BRDT WILD-TYPE 
             0             24 
$`BRDT MUTATED`
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY 
       86.07         8.22        27.12        46.45        40.11        32.55 
TCGA-B5-A11E TCGA-B5-A11N TCGA-BK-A0C9 TCGA-BS-A0TC TCGA-BS-A0UF TCGA-BS-A0UV 
        8.71        43.96        35.90        85.55        85.84        73.25 
TCGA-D1-A103 TCGA-D1-A17N 
       21.99         1.51 

$`BRDT WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       35.01        28.54        37.78        65.88        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        40.67        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
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 
       40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        13.78 
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-A0T9 TCGA-BS-A0TA 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74         4.44        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-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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  BRDT MUTATED BRDT WILD-TYPE 
          1.51           0.56 
  BRDT MUTATED BRDT WILD-TYPE 
         86.07         185.79 
  BRDT MUTATED BRDT WILD-TYPE 
        38.005         28.655 
[1] "1.5 - 86.1 (38.0)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.7e+07"
D175V2, continuous
                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
D175V3, 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"
D175V4, binary
                cls
clus               0   1
  BRDT MUTATED     3  11
  BRDT WILD-TYPE  83 151
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRDT MUTATED      3   11
  BRDT WILD-TYPE   83  151
     clus
vv    BRDT MUTATED BRDT WILD-TYPE
  NO             3             83
  YES           11            151
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BRDT MUTATED    10   1   0   0
  BRDT WILD-TYPE 161  10   7  18
D175V5, multiclass
    clus
vv   BRDT MUTATED BRDT WILD-TYPE
  R0           10            161
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRDT MUTATED                                  0     2
  BRDT WILD-TYPE                                3    11
                vv
clus             BLACK OR AFRICAN AMERICAN
  BRDT MUTATED                           1
  BRDT WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BRDT MUTATED                                           1     8
  BRDT WILD-TYPE                                         6   185
D175V6, multiclass
                                           clus
vv                                          BRDT MUTATED BRDT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                2             11
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                                8            185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V7, binary
                cls
clus               0   1
  BRDT MUTATED     1   8
  BRDT WILD-TYPE   3 159
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRDT MUTATED      1    8
  BRDT WILD-TYPE    3  159
                        clus
vv                       BRDT MUTATED BRDT WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            8            159
[1] 2 2
[1] FALSE

Clustering(176) Variable = SH3BGRL MUTATION ANALYSIS
D176V1, survival
                   sevent
clus2                 0   1
  SH3BGRL MUTATED     6   0
  SH3BGRL WILD-TYPE 218  24
  SH3BGRL MUTATED SH3BGRL WILD-TYPE 
                6               242 
  SH3BGRL MUTATED SH3BGRL WILD-TYPE 
                0                24 
$`SH3BGRL MUTATED`
TCGA-A5-A0GP TCGA-B5-A0JY TCGA-B5-A11E TCGA-BG-A0M3 TCGA-BS-A0UF TCGA-BS-A0UV 
       46.55        32.55         8.71        35.21        85.84        73.25 

$`SH3BGRL WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       40.11        65.88        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        17.85        11.01       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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-A0M4 TCGA-BG-A0M6 
       18.61        20.19        19.33        20.94        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  SH3BGRL MUTATED SH3BGRL WILD-TYPE 
             8.71              0.56 
  SH3BGRL MUTATED SH3BGRL WILD-TYPE 
            85.84            185.79 
  SH3BGRL MUTATED SH3BGRL WILD-TYPE 
           40.880            28.655 
[1] "8.7 - 85.8 (40.9)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.5e+07"
D176V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SH3BGRL MUTATED                                         6
  SH3BGRL WILD-TYPE                                     194
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  SH3BGRL MUTATED                               0
  SH3BGRL WILD-TYPE                             4
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  SH3BGRL MUTATED                                   0
  SH3BGRL WILD-TYPE                                44
D176V3, multiclass
                                         clus
vv                                        SH3BGRL MUTATED SH3BGRL 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"
D176V4, binary
                   cls
clus                  0   1
  SH3BGRL MUTATED     1   5
  SH3BGRL WILD-TYPE  85 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SH3BGRL MUTATED      1    5
  SH3BGRL WILD-TYPE   85  157
     clus
vv    SH3BGRL MUTATED SH3BGRL WILD-TYPE
  NO                1                85
  YES               5               157
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SH3BGRL MUTATED     4   0   0   0
  SH3BGRL WILD-TYPE 167  11   7  18
D176V5, multiclass
    clus
vv   SH3BGRL MUTATED SH3BGRL WILD-TYPE
  R0               4               167
  R1               0                11
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SH3BGRL MUTATED                                  0     2
  SH3BGRL WILD-TYPE                                3    11
                   vv
clus                BLACK OR AFRICAN AMERICAN
  SH3BGRL MUTATED                           0
  SH3BGRL WILD-TYPE                        25
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SH3BGRL MUTATED                                           1     3
  SH3BGRL WILD-TYPE                                         6   190
D176V6, multiclass
                                           clus
vv                                          SH3BGRL MUTATED SH3BGRL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   2                11
  BLACK OR AFRICAN AMERICAN                               0                25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 6
  WHITE                                                   3               190
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V7, binary
                   cls
clus                  0   1
  SH3BGRL MUTATED     0   4
  SH3BGRL WILD-TYPE   4 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SH3BGRL MUTATED      0    4
  SH3BGRL WILD-TYPE    4  163
                        clus
vv                       SH3BGRL MUTATED SH3BGRL WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               4               163
[1] 2 2
[1] FALSE

Clustering(177) Variable = MLH3 MUTATION ANALYSIS
D177V1, survival
                sevent
clus2              0   1
  MLH3 MUTATED    16   1
  MLH3 WILD-TYPE 208  23
  MLH3 MUTATED MLH3 WILD-TYPE 
            17            231 
  MLH3 MUTATED MLH3 WILD-TYPE 
             1             23 
$`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         8.22        27.12        46.45 
TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A0K2 TCGA-B5-A11R TCGA-BS-A0UF TCGA-BS-A0UJ 
       40.11        32.55        25.91        33.50        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05A 
       15.95         1.18        83.67        21.99         5.95        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        45.53        36.89         7.86        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        31.73        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        41.95        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        68.35        72.03        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       34.98        53.92        27.39        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 
       37.78        65.88        16.96        13.55        36.39        71.24 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV 
       19.36        80.38        56.91        46.75        43.13        40.67 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.64        28.34        30.51        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         8.71       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       32.09        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        28.27        41.52        48.56        23.47 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74         4.44        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-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-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN 
       24.30         2.33        13.22        18.25        16.31        35.38 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  MLH3 MUTATED MLH3 WILD-TYPE 
          1.78           0.56 
  MLH3 MUTATED MLH3 WILD-TYPE 
         86.07         185.79 
  MLH3 MUTATED MLH3 WILD-TYPE 
         29.88          29.06 
[1] "1.8 - 86.1 (29.9)"  "0.6 - 185.8 (29.1)"
[1] "hr=" "1.7"
D177V2, continuous
                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
D177V3, 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"
D177V4, binary
                cls
clus               0   1
  MLH3 MUTATED     6  11
  MLH3 WILD-TYPE  80 151
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH3 MUTATED      6   11
  MLH3 WILD-TYPE   80  151
     clus
vv    MLH3 MUTATED MLH3 WILD-TYPE
  NO             6             80
  YES           11            151
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MLH3 MUTATED    12   2   0   0
  MLH3 WILD-TYPE 159   9   7  18
D177V5, multiclass
    clus
vv   MLH3 MUTATED MLH3 WILD-TYPE
  R0           12            159
  R1            2              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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLH3 MUTATED                                  0     3
  MLH3 WILD-TYPE                                3    10
                vv
clus             BLACK OR AFRICAN AMERICAN
  MLH3 MUTATED                           2
  MLH3 WILD-TYPE                        23
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MLH3 MUTATED                                           0    11
  MLH3 WILD-TYPE                                         7   182
D177V6, multiclass
                                           clus
vv                                          MLH3 MUTATED MLH3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                3             10
  BLACK OR AFRICAN AMERICAN                            2             23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              7
  WHITE                                               11            182
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V7, binary
                cls
clus               0   1
  MLH3 MUTATED     1  11
  MLH3 WILD-TYPE   3 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH3 MUTATED      1   11
  MLH3 WILD-TYPE    3  156
                        clus
vv                       MLH3 MUTATED MLH3 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           11            156
[1] 2 2
[1] FALSE

Clustering(178) Variable = CCDC150 MUTATION ANALYSIS
D178V1, survival
                   sevent
clus2                 0   1
  CCDC150 MUTATED    12   0
  CCDC150 WILD-TYPE 212  24
  CCDC150 MUTATED CCDC150 WILD-TYPE 
               12               236 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
                0                24 
$`CCDC150 MUTATED`
TCGA-A5-A0GQ TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-B5-A11H TCGA-BG-A0M9 
       38.37        86.07        27.12        40.11        88.34        28.27 
TCGA-BS-A0UF TCGA-D1-A103 TCGA-D1-A15X TCGA-D1-A16F TCGA-D1-A177 TCGA-D1-A17Q 
       85.84        21.99        29.88         2.63        18.02         1.78 

$`CCDC150 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       46.55        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       46.75        43.13        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I 
       17.85        11.01         8.71       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       36.49        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        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 
       67.20        88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        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-A17A 
       18.67         3.65        17.49        19.53        30.15         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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  CCDC150 MUTATED CCDC150 WILD-TYPE 
             1.78              0.56 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
            88.34            185.79 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
           29.075            29.195 
[1] "1.8 - 88.3 (29.1)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "2.6e+07"
D178V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  CCDC150 MUTATED                                        11
  CCDC150 WILD-TYPE                                     189
                   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
D178V3, multiclass
                                         clus
vv                                        CCDC150 MUTATED CCDC150 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"
D178V4, binary
                   cls
clus                  0   1
  CCDC150 MUTATED     4   8
  CCDC150 WILD-TYPE  82 154
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      4    8
  CCDC150 WILD-TYPE   82  154
     clus
vv    CCDC150 MUTATED CCDC150 WILD-TYPE
  NO                4                82
  YES               8               154
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CCDC150 MUTATED    11   0   0   0
  CCDC150 WILD-TYPE 160  11   7  18
D178V5, multiclass
    clus
vv   CCDC150 MUTATED CCDC150 WILD-TYPE
  R0              11               160
  R1               0                11
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC150 MUTATED                                  0     1
  CCDC150 WILD-TYPE                                3    12
                   vv
clus                BLACK OR AFRICAN AMERICAN
  CCDC150 MUTATED                           1
  CCDC150 WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC150 MUTATED                                           0    10
  CCDC150 WILD-TYPE                                         7   183
D178V6, multiclass
                                           clus
vv                                          CCDC150 MUTATED CCDC150 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                12
  BLACK OR AFRICAN AMERICAN                               1                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 7
  WHITE                                                  10               183
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V7, binary
                   cls
clus                  0   1
  CCDC150 MUTATED     0   9
  CCDC150 WILD-TYPE   4 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      0    9
  CCDC150 WILD-TYPE    4  158
                        clus
vv                       CCDC150 MUTATED CCDC150 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               9               158
[1] 2 2
[1] FALSE

Clustering(179) Variable = NT5C3 MUTATION ANALYSIS
D179V1, survival
                 sevent
clus2               0   1
  NT5C3 MUTATED     7   0
  NT5C3 WILD-TYPE 217  24
  NT5C3 MUTATED NT5C3 WILD-TYPE 
              7             241 
  NT5C3 MUTATED NT5C3 WILD-TYPE 
              0              24 
$`NT5C3 MUTATED`
TCGA-A5-A0GP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AX-A05Z TCGA-AX-A0J0 
       46.55        83.67        86.07         8.22        46.45        40.11 
TCGA-BS-A0UF 
       85.84 

$`NT5C3 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A 
       15.95         1.18        21.99         5.95        23.31        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        45.53        36.89         7.86        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       28.54        37.78        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       40.67        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        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 
       67.20        88.34        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        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  NT5C3 MUTATED NT5C3 WILD-TYPE 
           8.22            0.56 
  NT5C3 MUTATED NT5C3 WILD-TYPE 
          86.07          185.79 
  NT5C3 MUTATED NT5C3 WILD-TYPE 
          46.55           28.64 
[1] "8.2 - 86.1 (46.5)"  "0.6 - 185.8 (28.6)"
[1] "hr="     "2.6e+07"
D179V2, continuous
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  NT5C3 MUTATED                                         7
  NT5C3 WILD-TYPE                                     193
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  NT5C3 MUTATED                               0
  NT5C3 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  NT5C3 MUTATED                                   0
  NT5C3 WILD-TYPE                                44
D179V3, multiclass
                                         clus
vv                                        NT5C3 MUTATED NT5C3 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"
D179V4, binary
                 cls
clus                0   1
  NT5C3 MUTATED     3   4
  NT5C3 WILD-TYPE  83 158
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NT5C3 MUTATED      3    4
  NT5C3 WILD-TYPE   83  158
     clus
vv    NT5C3 MUTATED NT5C3 WILD-TYPE
  NO              3              83
  YES             4             158
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NT5C3 MUTATED     6   1   0   0
  NT5C3 WILD-TYPE 165  10   7  18
D179V5, multiclass
    clus
vv   NT5C3 MUTATED NT5C3 WILD-TYPE
  R0             6             165
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NT5C3 MUTATED                                  0     2
  NT5C3 WILD-TYPE                                3    11
                 vv
clus              BLACK OR AFRICAN AMERICAN
  NT5C3 MUTATED                           0
  NT5C3 WILD-TYPE                        25
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NT5C3 MUTATED                                           0     4
  NT5C3 WILD-TYPE                                         7   189
D179V6, multiclass
                                           clus
vv                                          NT5C3 MUTATED NT5C3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 2              11
  BLACK OR AFRICAN AMERICAN                             0              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                 4             189
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V7, binary
                 cls
clus                0   1
  NT5C3 MUTATED     1   4
  NT5C3 WILD-TYPE   3 163
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NT5C3 MUTATED      1    4
  NT5C3 WILD-TYPE    3  163
                        clus
vv                       NT5C3 MUTATED NT5C3 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             4             163
[1] 2 2
[1] FALSE

Clustering(180) Variable = APAF1 MUTATION ANALYSIS
D180V1, survival
                 sevent
clus2               0   1
  APAF1 MUTATED    12   1
  APAF1 WILD-TYPE 212  23
  APAF1 MUTATED APAF1 WILD-TYPE 
             13             235 
  APAF1 MUTATED APAF1 WILD-TYPE 
              1              23 
$`APAF1 MUTATED`
TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AX-A05Z TCGA-B5-A0JR TCGA-B5-A0JY 
       83.67        23.31        86.07        46.45        56.91        32.55 
TCGA-B5-A11E TCGA-BG-A0MS TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A103 
        8.71        30.81        85.84        82.39        73.25        21.99 
TCGA-D1-A17Q 
        1.78 

$`APAF1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A059 
       42.35        15.95         1.18        21.99         5.95         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       35.01        28.54        37.78        40.11        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JS 
       13.55        36.39        71.24        19.36        80.38        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        40.67        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
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 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
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        39.32        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        67.20        88.34 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        86.93        72.72        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  APAF1 MUTATED APAF1 WILD-TYPE 
           1.78            0.56 
  APAF1 MUTATED APAF1 WILD-TYPE 
          86.07          185.79 
  APAF1 MUTATED APAF1 WILD-TYPE 
          46.45           28.64 
[1] "1.8 - 86.1 (46.5)"  "0.6 - 185.8 (28.6)"
[1] "hr=" "1.7"
D180V2, continuous
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  APAF1 MUTATED                                        13
  APAF1 WILD-TYPE                                     187
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  APAF1 MUTATED                               0
  APAF1 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  APAF1 MUTATED                                   0
  APAF1 WILD-TYPE                                44
D180V3, multiclass
                                         clus
vv                                        APAF1 MUTATED APAF1 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"
D180V4, binary
                 cls
clus                0   1
  APAF1 MUTATED     3  10
  APAF1 WILD-TYPE  83 152
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APAF1 MUTATED      3   10
  APAF1 WILD-TYPE   83  152
     clus
vv    APAF1 MUTATED APAF1 WILD-TYPE
  NO              3              83
  YES            10             152
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  APAF1 MUTATED     8   2   0   0
  APAF1 WILD-TYPE 163   9   7  18
D180V5, multiclass
    clus
vv   APAF1 MUTATED APAF1 WILD-TYPE
  R0             8             163
  R1             2               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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APAF1 MUTATED                                  0     2
  APAF1 WILD-TYPE                                3    11
                 vv
clus              BLACK OR AFRICAN AMERICAN
  APAF1 MUTATED                           0
  APAF1 WILD-TYPE                        25
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  APAF1 MUTATED                                           1     9
  APAF1 WILD-TYPE                                         6   184
D180V6, multiclass
                                           clus
vv                                          APAF1 MUTATED APAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 2              11
  BLACK OR AFRICAN AMERICAN                             0              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                 9             184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V7, binary
                 cls
clus                0   1
  APAF1 MUTATED     1   7
  APAF1 WILD-TYPE   3 160
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APAF1 MUTATED      1    7
  APAF1 WILD-TYPE    3  160
                        clus
vv                       APAF1 MUTATED APAF1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             7             160
[1] 2 2
[1] FALSE

Clustering(181) Variable = KANK4 MUTATION ANALYSIS
D181V1, survival
                 sevent
clus2               0   1
  KANK4 MUTATED    10   1
  KANK4 WILD-TYPE 214  23
  KANK4 MUTATED KANK4 WILD-TYPE 
             11             237 
  KANK4 MUTATED KANK4 WILD-TYPE 
              1              23 
$`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         8.71        43.96        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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        37.78        40.11        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        46.75        43.13        40.67        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        17.85        11.01       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        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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-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-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-A17S 
       28.08        26.37        10.22         1.51         1.78        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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  KANK4 MUTATED KANK4 WILD-TYPE 
           2.63            0.56 
  KANK4 MUTATED KANK4 WILD-TYPE 
          86.07          185.79 
  KANK4 MUTATED KANK4 WILD-TYPE 
          27.12           29.33 
[1] "2.6 - 86.1 (27.1)"  "0.6 - 185.8 (29.3)"
[1] "hr=" "1"  
D181V2, continuous
                 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
D181V3, 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"
D181V4, binary
                 cls
clus                0   1
  KANK4 MUTATED     5   6
  KANK4 WILD-TYPE  81 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK4 MUTATED      5    6
  KANK4 WILD-TYPE   81  156
     clus
vv    KANK4 MUTATED KANK4 WILD-TYPE
  NO              5              81
  YES             6             156
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KANK4 MUTATED     9   0   0   0
  KANK4 WILD-TYPE 162  11   7  18
D181V5, multiclass
    clus
vv   KANK4 MUTATED KANK4 WILD-TYPE
  R0             9             162
  R1             0              11
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KANK4 MUTATED                                  0     0
  KANK4 WILD-TYPE                                3    13
                 vv
clus              BLACK OR AFRICAN AMERICAN
  KANK4 MUTATED                           1
  KANK4 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KANK4 MUTATED                                           1     9
  KANK4 WILD-TYPE                                         6   184
D181V6, multiclass
                                           clus
vv                                          KANK4 MUTATED KANK4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 0              13
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                 9             184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V7, binary
                 cls
clus                0   1
  KANK4 MUTATED     0   6
  KANK4 WILD-TYPE   4 161
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK4 MUTATED      0    6
  KANK4 WILD-TYPE    4  161
                        clus
vv                       KANK4 MUTATED KANK4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             161
[1] 2 2
[1] FALSE

Clustering(182) Variable = NRIP1 MUTATION ANALYSIS
D182V1, survival
                 sevent
clus2               0   1
  NRIP1 MUTATED    13   0
  NRIP1 WILD-TYPE 211  24
  NRIP1 MUTATED NRIP1 WILD-TYPE 
             13             235 
  NRIP1 MUTATED NRIP1 WILD-TYPE 
              0              24 
$`NRIP1 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AP-A0LT TCGA-AX-A0J0 TCGA-AX-A0J1 
       83.67         8.22        27.12        49.22        40.11        65.88 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A16X TCGA-D1-A17Q 
       32.55         8.71        85.84        73.25         3.65         1.78 
TCGA-EY-A1GS 
       15.09 

$`NRIP1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       35.01        28.54        37.78        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       17.88        13.74        17.10        17.85        11.01       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        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        67.20        88.34 
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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        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-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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.92        10.78         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  NRIP1 MUTATED NRIP1 WILD-TYPE 
           1.78            0.56 
  NRIP1 MUTATED NRIP1 WILD-TYPE 
          85.84          185.79 
  NRIP1 MUTATED NRIP1 WILD-TYPE 
          32.55           29.06 
[1] "1.8 - 85.8 (32.5)"  "0.6 - 185.8 (29.1)"
[1] "hr="     "2.7e+07"
D182V2, continuous
                 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
D182V3, 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"
D182V4, binary
                 cls
clus                0   1
  NRIP1 MUTATED     4   9
  NRIP1 WILD-TYPE  82 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NRIP1 MUTATED      4    9
  NRIP1 WILD-TYPE   82  153
     clus
vv    NRIP1 MUTATED NRIP1 WILD-TYPE
  NO              4              82
  YES             9             153
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NRIP1 MUTATED    10   0   1   0
  NRIP1 WILD-TYPE 161  11   6  18
D182V5, multiclass
    clus
vv   NRIP1 MUTATED NRIP1 WILD-TYPE
  R0            10             161
  R1             0              11
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NRIP1 MUTATED                                  0     1
  NRIP1 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  NRIP1 MUTATED                           2
  NRIP1 WILD-TYPE                        23
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NRIP1 MUTATED                                           1     9
  NRIP1 WILD-TYPE                                         6   184
D182V6, multiclass
                                           clus
vv                                          NRIP1 MUTATED NRIP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             2              23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                 9             184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V7, binary
                 cls
clus                0   1
  NRIP1 MUTATED     0   8
  NRIP1 WILD-TYPE   4 159
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NRIP1 MUTATED      0    8
  NRIP1 WILD-TYPE    4  159
                        clus
vv                       NRIP1 MUTATED NRIP1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             159
[1] 2 2
[1] FALSE

Clustering(183) Variable = GTF2H1 MUTATION ANALYSIS
D183V1, survival
                  sevent
clus2                0   1
  GTF2H1 MUTATED     8   0
  GTF2H1 WILD-TYPE 216  24
  GTF2H1 MUTATED GTF2H1 WILD-TYPE 
               8              240 
  GTF2H1 MUTATED GTF2H1 WILD-TYPE 
               0               24 
$`GTF2H1 MUTATED`
TCGA-A5-A0GH TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J1 TCGA-B5-A0K9 TCGA-BS-A0UJ 
       74.10        27.12        46.45        65.88        11.01        82.39 
TCGA-D1-A103 TCGA-D1-A17Q 
       21.99         1.78 

$`GTF2H1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        40.11        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       46.75        43.13        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85         8.71       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        85.84        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74         4.44        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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  GTF2H1 MUTATED GTF2H1 WILD-TYPE 
            1.78             0.56 
  GTF2H1 MUTATED GTF2H1 WILD-TYPE 
           82.39           185.79 
  GTF2H1 MUTATED GTF2H1 WILD-TYPE 
          36.785           29.195 
[1] "1.8 - 82.4 (36.8)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "2.6e+07"
D183V2, continuous
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  GTF2H1 MUTATED                                         8
  GTF2H1 WILD-TYPE                                     192
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  GTF2H1 MUTATED                               0
  GTF2H1 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  GTF2H1 MUTATED                                   0
  GTF2H1 WILD-TYPE                                44
D183V3, multiclass
                                         clus
vv                                        GTF2H1 MUTATED GTF2H1 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"
D183V4, binary
                  cls
clus                 0   1
  GTF2H1 MUTATED     2   6
  GTF2H1 WILD-TYPE  84 156
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF2H1 MUTATED      2    6
  GTF2H1 WILD-TYPE   84  156
     clus
vv    GTF2H1 MUTATED GTF2H1 WILD-TYPE
  NO               2               84
  YES              6              156
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GTF2H1 MUTATED     6   1   0   0
  GTF2H1 WILD-TYPE 165  10   7  18
D183V5, multiclass
    clus
vv   GTF2H1 MUTATED GTF2H1 WILD-TYPE
  R0              6              165
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GTF2H1 MUTATED                                  0     1
  GTF2H1 WILD-TYPE                                3    12
                  vv
clus               BLACK OR AFRICAN AMERICAN
  GTF2H1 MUTATED                           1
  GTF2H1 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GTF2H1 MUTATED                                           0     5
  GTF2H1 WILD-TYPE                                         7   188
D183V6, multiclass
                                           clus
vv                                          GTF2H1 MUTATED GTF2H1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  1               12
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                  5              188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V7, binary
                  cls
clus                 0   1
  GTF2H1 MUTATED     1   5
  GTF2H1 WILD-TYPE   3 162
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF2H1 MUTATED      1    5
  GTF2H1 WILD-TYPE    3  162
                        clus
vv                       GTF2H1 MUTATED GTF2H1 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              5              162
[1] 2 2
[1] FALSE

Clustering(184) Variable = ASXL2 MUTATION ANALYSIS
D184V1, survival
                 sevent
clus2               0   1
  ASXL2 MUTATED    14   0
  ASXL2 WILD-TYPE 210  24
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             14             234 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
              0              24 
$`ASXL2 MUTATED`
TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A1CP 
       83.67        86.07         8.22        27.12        46.45        36.39 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11H TCGA-BS-A0UJ TCGA-BS-A0UV TCGA-D1-A103 
       32.55         8.71        88.34        82.39        73.25        21.99 
TCGA-D1-A174 TCGA-D1-A17Q 
       19.53         1.78 

$`ASXL2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 
       28.54        37.78        40.11        65.88        16.96        13.55 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       17.88        13.74        17.10        17.85        11.01       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        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        36.49        28.27        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  ASXL2 MUTATED ASXL2 WILD-TYPE 
           1.78            0.56 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
          88.34          185.79 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
         34.470          28.865 
[1] "1.8 - 88.3 (34.5)"  "0.6 - 185.8 (28.9)"
[1] "hr="     "2.7e+07"
D184V2, continuous
                 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
D184V3, 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"
D184V4, binary
                 cls
clus                0   1
  ASXL2 MUTATED     5   9
  ASXL2 WILD-TYPE  81 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED      5    9
  ASXL2 WILD-TYPE   81  153
     clus
vv    ASXL2 MUTATED ASXL2 WILD-TYPE
  NO              5              81
  YES             9             153
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ASXL2 MUTATED     9   2   0   0
  ASXL2 WILD-TYPE 162   9   7  18
D184V5, multiclass
    clus
vv   ASXL2 MUTATED ASXL2 WILD-TYPE
  R0             9             162
  R1             2               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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASXL2 MUTATED                                  0     1
  ASXL2 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  ASXL2 MUTATED                           1
  ASXL2 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ASXL2 MUTATED                                           1    10
  ASXL2 WILD-TYPE                                         6   183
D184V6, multiclass
                                           clus
vv                                          ASXL2 MUTATED ASXL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               6
  WHITE                                                10             183
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V7, binary
                 cls
clus                0   1
  ASXL2 MUTATED     1   7
  ASXL2 WILD-TYPE   3 160
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED      1    7
  ASXL2 WILD-TYPE    3  160
                        clus
vv                       ASXL2 MUTATED ASXL2 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             7             160
[1] 2 2
[1] FALSE

Clustering(185) Variable = ZNF611 MUTATION ANALYSIS
D185V1, survival
                  sevent
clus2                0   1
  ZNF611 MUTATED    11   1
  ZNF611 WILD-TYPE 213  23
  ZNF611 MUTATED ZNF611 WILD-TYPE 
              12              236 
  ZNF611 MUTATED ZNF611 WILD-TYPE 
               1               23 
$`ZNF611 MUTATED`
TCGA-A5-A0GP TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       46.55        23.31         8.22        27.12        46.45        40.11 
TCGA-B5-A11I TCGA-B5-A11N TCGA-BS-A0UF TCGA-D1-A103 TCGA-D1-A163 TCGA-D1-A17Q 
       75.72        43.96        85.84        21.99        32.58         1.78 

$`ZNF611 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A056 
       15.95         1.18        83.67        21.99         5.95        86.07 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       28.54        37.78        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       40.67        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11M 
        8.71       185.79       113.36        88.34        54.44        44.78 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        67.20        88.34 
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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
        3.68        29.33         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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  ZNF611 MUTATED ZNF611 WILD-TYPE 
            1.78             0.56 
  ZNF611 MUTATED ZNF611 WILD-TYPE 
           85.84           185.79 
  ZNF611 MUTATED ZNF611 WILD-TYPE 
          36.345           28.865 
[1] "1.8 - 85.8 (36.3)"  "0.6 - 185.8 (28.9)"
[1] "hr=" "1.3"
D185V2, continuous
                  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
D185V3, 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"
D185V4, binary
                  cls
clus                 0   1
  ZNF611 MUTATED     4   8
  ZNF611 WILD-TYPE  82 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF611 MUTATED      4    8
  ZNF611 WILD-TYPE   82  154
     clus
vv    ZNF611 MUTATED ZNF611 WILD-TYPE
  NO               4               82
  YES              8              154
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF611 MUTATED     8   2   0   0
  ZNF611 WILD-TYPE 163   9   7  18
D185V5, multiclass
    clus
vv   ZNF611 MUTATED ZNF611 WILD-TYPE
  R0              8              163
  R1              2                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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF611 MUTATED                                  0     2
  ZNF611 WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ZNF611 MUTATED                           2
  ZNF611 WILD-TYPE                        23
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF611 MUTATED                                           0     7
  ZNF611 WILD-TYPE                                         7   186
D185V6, multiclass
                                           clus
vv                                          ZNF611 MUTATED ZNF611 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              2               23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                  7              186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V7, binary
                  cls
clus                 0   1
  ZNF611 MUTATED     1   8
  ZNF611 WILD-TYPE   3 159
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF611 MUTATED      1    8
  ZNF611 WILD-TYPE    3  159
                        clus
vv                       ZNF611 MUTATED ZNF611 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              8              159
[1] 2 2
[1] FALSE

Clustering(186) Variable = SUN3 MUTATION ANALYSIS
D186V1, survival
                sevent
clus2              0   1
  SUN3 MUTATED     6   0
  SUN3 WILD-TYPE 218  24
  SUN3 MUTATED SUN3 WILD-TYPE 
             6            242 
  SUN3 MUTATED SUN3 WILD-TYPE 
             0             24 
$`SUN3 MUTATED`
TCGA-A5-A0VQ TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-BS-A0UF 
       15.95        27.12        46.45        40.11        32.55        85.84 

$`SUN3 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        40.67        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  SUN3 MUTATED SUN3 WILD-TYPE 
         15.95           0.56 
  SUN3 MUTATED SUN3 WILD-TYPE 
         85.84         185.79 
  SUN3 MUTATED SUN3 WILD-TYPE 
        36.330         28.865 
[1] "15.9 - 85.8 (36.3)" "0.6 - 185.8 (28.9)"
[1] "hr="     "2.5e+07"
D186V2, continuous
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SUN3 MUTATED                                         6
  SUN3 WILD-TYPE                                     194
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  SUN3 MUTATED                               0
  SUN3 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  SUN3 MUTATED                                   0
  SUN3 WILD-TYPE                                44
D186V3, multiclass
                                         clus
vv                                        SUN3 MUTATED SUN3 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"
D186V4, binary
                cls
clus               0   1
  SUN3 MUTATED     2   4
  SUN3 WILD-TYPE  84 158
[1] "tbl2"
                cls
clus             [,1] [,2]
  SUN3 MUTATED      2    4
  SUN3 WILD-TYPE   84  158
     clus
vv    SUN3 MUTATED SUN3 WILD-TYPE
  NO             2             84
  YES            4            158
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SUN3 MUTATED     4   1   0   0
  SUN3 WILD-TYPE 167  10   7  18
D186V5, multiclass
    clus
vv   SUN3 MUTATED SUN3 WILD-TYPE
  R0            4            167
  R1            1             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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SUN3 MUTATED                                  0     1
  SUN3 WILD-TYPE                                3    12
                vv
clus             BLACK OR AFRICAN AMERICAN
  SUN3 MUTATED                           1
  SUN3 WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SUN3 MUTATED                                           0     2
  SUN3 WILD-TYPE                                         7   191
D186V6, multiclass
                                           clus
vv                                          SUN3 MUTATED SUN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                1             12
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              7
  WHITE                                                2            191
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V7, binary
                cls
clus               0   1
  SUN3 MUTATED     2   2
  SUN3 WILD-TYPE   2 165
[1] "tbl2"
                cls
clus             [,1] [,2]
  SUN3 MUTATED      2    2
  SUN3 WILD-TYPE    2  165
                        clus
vv                       SUN3 MUTATED SUN3 WILD-TYPE
  HISPANIC OR LATINO                2              2
  NOT HISPANIC OR LATINO            2            165
[1] 2 2
[1] FALSE

Clustering(187) Variable = ZNF195 MUTATION ANALYSIS
D187V1, survival
                  sevent
clus2                0   1
  ZNF195 MUTATED    11   0
  ZNF195 WILD-TYPE 213  24
  ZNF195 MUTATED ZNF195 WILD-TYPE 
              11              237 
  ZNF195 MUTATED ZNF195 WILD-TYPE 
               0               24 
$`ZNF195 MUTATED`
TCGA-A5-A0GW TCGA-AP-A056 TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11E 
       23.21        86.07        46.45        40.11        32.55         8.71 
TCGA-BS-A0UF TCGA-BS-A0UV TCGA-D1-A103 TCGA-D1-A16J TCGA-D1-A17Q 
       85.84        73.25        21.99        29.92         1.78 

$`ZNF195 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 
       46.55        38.37        28.27        20.81        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        40.67        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       11.01       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        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 
       67.20        88.34        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74         4.44        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-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-EY-A212 TCGA-FI-A2D2 
       48.36        10.92        10.78        15.09         3.62        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  ZNF195 MUTATED ZNF195 WILD-TYPE 
            1.78             0.56 
  ZNF195 MUTATED ZNF195 WILD-TYPE 
           86.07           185.79 
  ZNF195 MUTATED ZNF195 WILD-TYPE 
           32.55            28.67 
[1] "1.8 - 86.1 (32.5)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.6e+07"
D187V2, continuous
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  ZNF195 MUTATED                                        11
  ZNF195 WILD-TYPE                                     189
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  ZNF195 MUTATED                               0
  ZNF195 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  ZNF195 MUTATED                                   0
  ZNF195 WILD-TYPE                                44
D187V3, multiclass
                                         clus
vv                                        ZNF195 MUTATED ZNF195 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"
D187V4, binary
                  cls
clus                 0   1
  ZNF195 MUTATED     3   8
  ZNF195 WILD-TYPE  83 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF195 MUTATED      3    8
  ZNF195 WILD-TYPE   83  154
     clus
vv    ZNF195 MUTATED ZNF195 WILD-TYPE
  NO               3               83
  YES              8              154
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF195 MUTATED     8   1   0   0
  ZNF195 WILD-TYPE 163  10   7  18
D187V5, multiclass
    clus
vv   ZNF195 MUTATED ZNF195 WILD-TYPE
  R0              8              163
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF195 MUTATED                                  0     2
  ZNF195 WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  ZNF195 MUTATED                           0
  ZNF195 WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF195 MUTATED                                           1     7
  ZNF195 WILD-TYPE                                         6   186
D187V6, multiclass
                                           clus
vv                                          ZNF195 MUTATED ZNF195 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  7              186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V7, binary
                  cls
clus                 0   1
  ZNF195 MUTATED     1   7
  ZNF195 WILD-TYPE   3 160
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF195 MUTATED      1    7
  ZNF195 WILD-TYPE    3  160
                        clus
vv                       ZNF195 MUTATED ZNF195 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              7              160
[1] 2 2
[1] FALSE

Clustering(188) Variable = EXOSC9 MUTATION ANALYSIS
D188V1, survival
                  sevent
clus2                0   1
  EXOSC9 MUTATED    10   0
  EXOSC9 WILD-TYPE 214  24
  EXOSC9 MUTATED EXOSC9 WILD-TYPE 
              10              238 
  EXOSC9 MUTATED EXOSC9 WILD-TYPE 
               0               24 
$`EXOSC9 MUTATED`
TCGA-A5-A0VP TCGA-AP-A056 TCGA-AX-A05Z TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-B5-A0JY 
       42.35        86.07        46.45        40.11        65.88        32.55 
TCGA-B5-A0K9 TCGA-BS-A0UV TCGA-D1-A0ZO TCGA-D1-A17Q 
       11.01        73.25        19.79         1.78 

$`EXOSC9 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 
       60.66        35.01        28.54        37.78        16.96        13.55 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       36.39        71.24        19.36        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       43.13        40.67        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A11E 
       23.01        17.88        13.74        17.10        17.85         8.71 
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 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       88.34        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 
       62.79        63.58        49.55        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  EXOSC9 MUTATED EXOSC9 WILD-TYPE 
            1.78             0.56 
  EXOSC9 MUTATED EXOSC9 WILD-TYPE 
           86.07           185.79 
  EXOSC9 MUTATED EXOSC9 WILD-TYPE 
          41.230           28.655 
[1] "1.8 - 86.1 (41.2)"  "0.6 - 185.8 (28.7)"
[1] "hr="     "2.6e+07"
D188V2, continuous
                  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
D188V3, 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"
D188V4, binary
                  cls
clus                 0   1
  EXOSC9 MUTATED     3   7
  EXOSC9 WILD-TYPE  83 155
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EXOSC9 MUTATED      3    7
  EXOSC9 WILD-TYPE   83  155
     clus
vv    EXOSC9 MUTATED EXOSC9 WILD-TYPE
  NO               3               83
  YES              7              155
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  EXOSC9 MUTATED     7   1   0   0
  EXOSC9 WILD-TYPE 164  10   7  18
D188V5, multiclass
    clus
vv   EXOSC9 MUTATED EXOSC9 WILD-TYPE
  R0              7              164
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EXOSC9 MUTATED                                  0     0
  EXOSC9 WILD-TYPE                                3    13
                  vv
clus               BLACK OR AFRICAN AMERICAN
  EXOSC9 MUTATED                           0
  EXOSC9 WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EXOSC9 MUTATED                                           1     8
  EXOSC9 WILD-TYPE                                         6   185
D188V6, multiclass
                                           clus
vv                                          EXOSC9 MUTATED EXOSC9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  0               13
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  8              185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V7, binary
                  cls
clus                 0   1
  EXOSC9 MUTATED     1   6
  EXOSC9 WILD-TYPE   3 161
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EXOSC9 MUTATED      1    6
  EXOSC9 WILD-TYPE    3  161
                        clus
vv                       EXOSC9 MUTATED EXOSC9 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              6              161
[1] 2 2
[1] FALSE

Clustering(189) Variable = MFN2 MUTATION ANALYSIS
D189V1, survival
                sevent
clus2              0   1
  MFN2 MUTATED     9   0
  MFN2 WILD-TYPE 215  24
  MFN2 MUTATED MFN2 WILD-TYPE 
             9            239 
  MFN2 MUTATED MFN2 WILD-TYPE 
             0             24 
$`MFN2 MUTATED`
TCGA-A5-A0VQ TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-B5-A0JY TCGA-B5-A11R TCGA-BG-A0MQ 
       15.95        27.12        40.11        32.55        33.50        39.32 
TCGA-D1-A103 TCGA-D1-A176 TCGA-DI-A0WH 
       21.99        30.15        16.31 

$`MFN2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       27.39        60.66        35.01        28.54        37.78        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN 
       16.96        13.55        36.39        71.24        19.36        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 
       56.91        46.75        43.13        40.67        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         8.71       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        43.96        40.50        32.09 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       24.99        46.95        23.47        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 
       67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74         4.44        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-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       19.53        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-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS 
       18.25        35.38        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  MFN2 MUTATED MFN2 WILD-TYPE 
         15.95           0.56 
  MFN2 MUTATED MFN2 WILD-TYPE 
         40.11         185.79 
  MFN2 MUTATED MFN2 WILD-TYPE 
         30.15          29.06 
[1] "15.9 - 40.1 (30.1)" "0.6 - 185.8 (29.1)"
[1] "hr="     "2.6e+07"
D189V2, continuous
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MFN2 MUTATED                                         9
  MFN2 WILD-TYPE                                     191
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  MFN2 MUTATED                               0
  MFN2 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  MFN2 MUTATED                                   0
  MFN2 WILD-TYPE                                44
D189V3, multiclass
                                         clus
vv                                        MFN2 MUTATED MFN2 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"
D189V4, binary
                cls
clus               0   1
  MFN2 MUTATED     4   5
  MFN2 WILD-TYPE  82 157
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN2 MUTATED      4    5
  MFN2 WILD-TYPE   82  157
     clus
vv    MFN2 MUTATED MFN2 WILD-TYPE
  NO             4             82
  YES            5            157
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MFN2 MUTATED     7   0   0   0
  MFN2 WILD-TYPE 164  11   7  18
D189V5, multiclass
    clus
vv   MFN2 MUTATED MFN2 WILD-TYPE
  R0            7            164
  R1            0             11
  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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MFN2 MUTATED                                  0     0
  MFN2 WILD-TYPE                                3    13
                vv
clus             BLACK OR AFRICAN AMERICAN
  MFN2 MUTATED                           2
  MFN2 WILD-TYPE                        23
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MFN2 MUTATED                                           0     6
  MFN2 WILD-TYPE                                         7   187
D189V6, multiclass
                                           clus
vv                                          MFN2 MUTATED MFN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                0             13
  BLACK OR AFRICAN AMERICAN                            2             23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              7
  WHITE                                                6            187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D189V7, binary
                cls
clus               0   1
  MFN2 MUTATED     1   5
  MFN2 WILD-TYPE   3 162
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN2 MUTATED      1    5
  MFN2 WILD-TYPE    3  162
                        clus
vv                       MFN2 MUTATED MFN2 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            5            162
[1] 2 2
[1] FALSE

Clustering(190) Variable = LIMA1 MUTATION ANALYSIS
D190V1, survival
                 sevent
clus2               0   1
  LIMA1 MUTATED     8   0
  LIMA1 WILD-TYPE 216  24
  LIMA1 MUTATED LIMA1 WILD-TYPE 
              8             240 
  LIMA1 MUTATED LIMA1 WILD-TYPE 
              0              24 
$`LIMA1 MUTATED`
TCGA-AP-A051 TCGA-AP-A059 TCGA-B5-A0JY TCGA-B5-A11E TCGA-BG-A0M8 TCGA-BS-A0UF 
       83.67         8.22        32.55         8.71        36.49        85.84 
TCGA-D1-A103 TCGA-D1-A160 
       21.99         3.68 

$`LIMA1 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       42.35        15.95         1.18        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 
       27.39        60.66        35.01        28.54        37.78        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       65.88        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ 
       80.38        56.91        46.75        43.13        40.67        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        17.85        11.01       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        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       33.50        27.35        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       38.37        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74         4.44        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       30.08        29.88         1.91        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        48.36        10.92        10.78 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       15.09         3.62        36.00        59.01         9.07        25.02 

  LIMA1 MUTATED LIMA1 WILD-TYPE 
           3.68            0.56 
  LIMA1 MUTATED LIMA1 WILD-TYPE 
          85.84          185.79 
  LIMA1 MUTATED LIMA1 WILD-TYPE 
         27.270          29.195 
[1] "3.7 - 85.8 (27.3)"  "0.6 - 185.8 (29.2)"
[1] "hr="     "2.5e+07"
D190V2, continuous
                 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
D190V3, 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"
D190V4, binary
                 cls
clus                0   1
  LIMA1 MUTATED     2   6
  LIMA1 WILD-TYPE  84 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LIMA1 MUTATED      2    6
  LIMA1 WILD-TYPE   84  156
     clus
vv    LIMA1 MUTATED LIMA1 WILD-TYPE
  NO              2              84
  YES             6             156
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LIMA1 MUTATED     6   0   0   0
  LIMA1 WILD-TYPE 165  11   7  18
D190V5, multiclass
    clus
vv   LIMA1 MUTATED LIMA1 WILD-TYPE
  R0             6             165
  R1             0              11
  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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LIMA1 MUTATED                                  0     1
  LIMA1 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  LIMA1 MUTATED                           0
  LIMA1 WILD-TYPE                        25
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LIMA1 MUTATED                                           0     7
  LIMA1 WILD-TYPE                                         7   186
D190V6, multiclass
                                           clus
vv                                          LIMA1 MUTATED LIMA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             0              25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                 7             186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D190V7, binary
                 cls
clus                0   1
  LIMA1 MUTATED     0   5
  LIMA1 WILD-TYPE   4 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LIMA1 MUTATED      0    5
  LIMA1 WILD-TYPE    4  162
                        clus
vv                       LIMA1 MUTATED LIMA1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             162
[1] 2 2
[1] FALSE

Clustering(191) Variable = PTPN12 MUTATION ANALYSIS
D191V1, survival
                  sevent
clus2                0   1
  PTPN12 MUTATED     9   1
  PTPN12 WILD-TYPE 215  23
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              10              238 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
               1               23 
$`PTPN12 MUTATED`
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-AP-A059 TCGA-AX-A05Z TCGA-B5-A0JY TCGA-B5-A11E 
       17.85        32.78         8.22        46.45        32.55         8.71 
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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       46.95        37.02        83.51         3.22       105.37        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.59        24.62        29.06        11.97        42.35        15.95 
TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        1.18        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L 
       45.99        66.58        34.98        53.92        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       35.01        28.54        37.78        40.11        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        40.67        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       11.01       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        43.96        40.50        32.09        33.50        27.35 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       28.27        41.52        48.56        23.47        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        23.47        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        67.20        88.34 
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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        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-EY-A212 
       35.38        48.36        10.92        10.78        15.09         3.62 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       36.00        59.01         9.07        25.02 

  PTPN12 MUTATED PTPN12 WILD-TYPE 
            8.22             0.56 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
           85.84           185.79 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
          32.665           28.865 
[1] "8.2 - 85.8 (32.7)"  "0.6 - 185.8 (28.9)"
[1] "hr=" "1"  
D191V2, continuous
                  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
D191V3, 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"
D191V4, binary
                  cls
clus                 0   1
  PTPN12 MUTATED     2   8
  PTPN12 WILD-TYPE  84 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED      2    8
  PTPN12 WILD-TYPE   84  154
     clus
vv    PTPN12 MUTATED PTPN12 WILD-TYPE
  NO               2               84
  YES              8              154
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PTPN12 MUTATED     7   1   0   0
  PTPN12 WILD-TYPE 164  10   7  18
D191V5, multiclass
    clus
vv   PTPN12 MUTATED PTPN12 WILD-TYPE
  R0              7              164
  R1              1               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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPN12 MUTATED                                  0     2
  PTPN12 WILD-TYPE                                3    11
                  vv
clus               BLACK OR AFRICAN AMERICAN
  PTPN12 MUTATED                           0
  PTPN12 WILD-TYPE                        25
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTPN12 MUTATED                                           0     7
  PTPN12 WILD-TYPE                                         7   186
D191V6, multiclass
                                           clus
vv                                          PTPN12 MUTATED PTPN12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  2               11
  BLACK OR AFRICAN AMERICAN                              0               25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                7
  WHITE                                                  7              186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D191V7, binary
                  cls
clus                 0   1
  PTPN12 MUTATED     1   6
  PTPN12 WILD-TYPE   3 161
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED      1    6
  PTPN12 WILD-TYPE    3  161
                        clus
vv                       PTPN12 MUTATED PTPN12 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              6              161
[1] 2 2
[1] FALSE

Clustering(192) Variable = MTF2 MUTATION ANALYSIS
D192V1, survival
                sevent
clus2              0   1
  MTF2 MUTATED     9   0
  MTF2 WILD-TYPE 215  24
  MTF2 MUTATED MTF2 WILD-TYPE 
             9            239 
  MTF2 MUTATED MTF2 WILD-TYPE 
             0             24 
$`MTF2 MUTATED`
TCGA-A5-A0GP TCGA-AP-A056 TCGA-AP-A0LM TCGA-AX-A0J0 TCGA-B5-A11E TCGA-BS-A0UF 
       46.55        86.07        27.12        40.11         8.71        85.84 
TCGA-D1-A103 TCGA-D1-A174 TCGA-D1-A17Q 
       21.99        19.53         1.78 

$`MTF2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       46.75        43.13        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01       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        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y 
       27.35        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-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO 
       36.49        28.27        41.52        48.56        23.47        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        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         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.16        24.99        46.95        23.47        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        67.20        88.34        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        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74         4.44        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-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        48.36        10.92        10.78        15.09 
TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        3.62        36.00        59.01         9.07        25.02 

  MTF2 MUTATED MTF2 WILD-TYPE 
          1.78           0.56 
  MTF2 MUTATED MTF2 WILD-TYPE 
         86.07         185.79 
  MTF2 MUTATED MTF2 WILD-TYPE 
         27.12          29.33 
[1] "1.8 - 86.1 (27.1)"  "0.6 - 185.8 (29.3)"
[1] "hr="     "2.6e+07"
D192V2, continuous
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MTF2 MUTATED                                         9
  MTF2 WILD-TYPE                                     191
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  MTF2 MUTATED                               0
  MTF2 WILD-TYPE                             4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  MTF2 MUTATED                                   0
  MTF2 WILD-TYPE                                44
D192V3, multiclass
                                         clus
vv                                        MTF2 MUTATED MTF2 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"
D192V4, binary
                cls
clus               0   1
  MTF2 MUTATED     3   6
  MTF2 WILD-TYPE  83 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTF2 MUTATED      3    6
  MTF2 WILD-TYPE   83  156
     clus
vv    MTF2 MUTATED MTF2 WILD-TYPE
  NO             3             83
  YES            6            156
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MTF2 MUTATED     8   0   0   0
  MTF2 WILD-TYPE 163  11   7  18
D192V5, multiclass
    clus
vv   MTF2 MUTATED MTF2 WILD-TYPE
  R0            8            163
  R1            0             11
  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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTF2 MUTATED                                  0     2
  MTF2 WILD-TYPE                                3    11
                vv
clus             BLACK OR AFRICAN AMERICAN
  MTF2 MUTATED                           1
  MTF2 WILD-TYPE                        24
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MTF2 MUTATED                                           0     6
  MTF2 WILD-TYPE                                         7   187
D192V6, multiclass
                                           clus
vv                                          MTF2 MUTATED MTF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                2             11
  BLACK OR AFRICAN AMERICAN                            1             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              7
  WHITE                                                6            187
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D192V7, binary
                cls
clus               0   1
  MTF2 MUTATED     0   6
  MTF2 WILD-TYPE   4 161
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTF2 MUTATED      0    6
  MTF2 WILD-TYPE    4  161
                        clus
vv                       MTF2 MUTATED MTF2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            161
[1] 2 2
[1] FALSE

Clustering(193) Variable = MLL4 MUTATION ANALYSIS
D193V1, survival
                sevent
clus2              0   1
  MLL4 MUTATED    30   0
  MLL4 WILD-TYPE 194  24
  MLL4 MUTATED MLL4 WILD-TYPE 
            30            218 
  MLL4 MUTATED MLL4 WILD-TYPE 
             0             24 
$`MLL4 MUTATED`
TCGA-A5-A0GI TCGA-A5-A0GP TCGA-A5-A0VP TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 
       57.53        46.55        42.35        83.67        86.07         8.22 
TCGA-AP-A0LE TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A06H TCGA-B5-A11E TCGA-B5-A11G 
      110.37        27.12        46.45        27.39         8.71       113.36 
TCGA-B5-A11J TCGA-B5-A11Y TCGA-BG-A0MQ TCGA-BK-A0CB TCGA-BS-A0UF TCGA-BS-A0UM 
       54.44        18.41        39.32         6.21        85.84        86.93 
TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-D1-A0ZS TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15X 
       73.25        62.79         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-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GQ 
      105.37        74.10        65.75        60.53        60.53        38.37 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VQ TCGA-AJ-A23M 
       19.59        24.62        29.06        11.97        15.95         1.18 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       21.99         5.95        23.31        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89         7.86        20.91        48.79       125.42       117.99 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06L 
       35.34        45.99        66.58        34.98        53.92        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 
       35.01        28.54        37.78        40.11        65.88        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       46.75        43.13        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11M 
       17.85        11.01       185.79        88.34        75.72        44.78 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       48.56        23.47        43.04        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        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 
       10.22        10.16        24.99        46.95        23.47        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        67.20        88.34        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       72.72        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
        4.44        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-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
       17.49         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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  MLL4 MUTATED MLL4 WILD-TYPE 
          1.58           0.56 
  MLL4 MUTATED MLL4 WILD-TYPE 
        113.36         185.79 
  MLL4 MUTATED MLL4 WILD-TYPE 
        30.015         28.865 
[1] "1.6 - 113.4 (30.0)" "0.6 - 185.8 (28.9)"
[1] "hr="     "8.2e+07"
D193V2, continuous
                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
D193V3, 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"
D193V4, binary
                cls
clus               0   1
  MLL4 MUTATED    11  19
  MLL4 WILD-TYPE  75 143
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     11   19
  MLL4 WILD-TYPE   75  143
     clus
vv    MLL4 MUTATED MLL4 WILD-TYPE
  NO            11             75
  YES           19            143
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MLL4 MUTATED    23   2   0   1
  MLL4 WILD-TYPE 148   9   7  17
D193V5, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  R0           23            148
  R1            2              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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL4 MUTATED                                  1     3
  MLL4 WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN
  MLL4 MUTATED                           2
  MLL4 WILD-TYPE                        23
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MLL4 MUTATED                                           1    22
  MLL4 WILD-TYPE                                         6   171
D193V6, multiclass
                                           clus
vv                                          MLL4 MUTATED MLL4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     1              2
  ASIAN                                                3             10
  BLACK OR AFRICAN AMERICAN                            2             23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              6
  WHITE                                               22            171
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D193V7, binary
                cls
clus               0   1
  MLL4 MUTATED     1  21
  MLL4 WILD-TYPE   3 146
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED      1   21
  MLL4 WILD-TYPE    3  146
                        clus
vv                       MLL4 MUTATED MLL4 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           21            146
[1] 2 2
[1] FALSE

Clustering(194) Variable = C1ORF101 MUTATION ANALYSIS
D194V1, survival
                    sevent
clus2                  0   1
  C1ORF101 MUTATED    12   0
  C1ORF101 WILD-TYPE 212  24
  C1ORF101 MUTATED C1ORF101 WILD-TYPE 
                12                236 
  C1ORF101 MUTATED C1ORF101 WILD-TYPE 
                 0                 24 
$`C1ORF101 MUTATED`
TCGA-A5-A0GP TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A0LM TCGA-AX-A05Z TCGA-AX-A0J0 
       46.55        86.07         8.22        27.12        46.45        40.11 
TCGA-B5-A0K6 TCGA-BG-A0LX TCGA-BK-A0C9 TCGA-BS-A0TC TCGA-BS-A0UV TCGA-D1-A16Y 
       13.74        20.19        35.90        85.55        73.25        17.49 

$`C1ORF101 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
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        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P 
       39.42        57.80        45.53        36.89         7.86        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        31.73        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        41.95        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       66.58        34.98        53.92        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       28.54        37.78        65.88        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       40.67        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       23.01        17.88        17.10        17.85        11.01         8.71 
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 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        13.78 
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-A0T9 TCGA-BS-A0TA 
        6.21        10.22        10.16        24.99        46.95        23.47 
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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
       22.92        13.22        18.25        16.31        35.38        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
       10.92        10.78        15.09         3.62        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 
        9.07        25.02 

  C1ORF101 MUTATED C1ORF101 WILD-TYPE 
              8.22               0.56 
  C1ORF101 MUTATED C1ORF101 WILD-TYPE 
             86.07             185.79 
  C1ORF101 MUTATED C1ORF101 WILD-TYPE 
            38.005             28.865 
[1] "8.2 - 86.1 (38.0)"  "0.6 - 185.8 (28.9)"
[1] "hr="     "2.6e+07"
D194V2, continuous
                    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
D194V3, 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"
D194V4, binary
                    cls
clus                   0   1
  C1ORF101 MUTATED     4   8
  C1ORF101 WILD-TYPE  82 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF101 MUTATED      4    8
  C1ORF101 WILD-TYPE   82  154
     clus
vv    C1ORF101 MUTATED C1ORF101 WILD-TYPE
  NO                 4                 82
  YES                8                154
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C1ORF101 MUTATED     9   1   0   1
  C1ORF101 WILD-TYPE 162  10   7  17
D194V5, multiclass
    clus
vv   C1ORF101 MUTATED C1ORF101 WILD-TYPE
  R0                9                162
  R1                1                 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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF101 MUTATED                                  0     2
  C1ORF101 WILD-TYPE                                3    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  C1ORF101 MUTATED                           1
  C1ORF101 WILD-TYPE                        24
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C1ORF101 MUTATED                                           1     7
  C1ORF101 WILD-TYPE                                         6   186
D194V6, multiclass
                                           clus
vv                                          C1ORF101 MUTATED C1ORF101 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    2                 11
  BLACK OR AFRICAN AMERICAN                                1                 24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  6
  WHITE                                                    7                186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D194V7, binary
                    cls
clus                   0   1
  C1ORF101 MUTATED     1   8
  C1ORF101 WILD-TYPE   3 159
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF101 MUTATED      1    8
  C1ORF101 WILD-TYPE    3  159
                        clus
vv                       C1ORF101 MUTATED C1ORF101 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO                8                159
[1] 2 2
[1] FALSE

Clustering(195) Variable = MBOAT2 MUTATION ANALYSIS
D195V1, survival
                  sevent
clus2                0   1
  MBOAT2 MUTATED     7   0
  MBOAT2 WILD-TYPE 217  24
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               7              241 
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               0               24 
$`MBOAT2 MUTATED`
TCGA-AP-A056 TCGA-AX-A0J0 TCGA-BS-A0UV TCGA-D1-A16X TCGA-D1-A17M TCGA-D1-A17Q 
       86.07        40.11        73.25         3.65        10.22         1.78 
TCGA-FI-A2EW 
       59.01 

$`MBOAT2 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       42.35        15.95         1.18        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        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        41.95        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       53.92        27.39        60.66        35.01        28.54        37.78 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF 
       65.88        16.96        13.55        36.39        71.24        19.36 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY 
       80.38        56.91        46.75        43.13        40.67        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        17.85        11.01         8.71       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        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC 
       34.98         7.92        38.37        36.49        28.27        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        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         6.21        10.22        10.16        24.99        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        67.20        88.34 
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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        49.55        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-A17N TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       28.08        26.37         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        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EX 
       10.92        10.78        15.09         3.62        36.00         9.07 
TCGA-FI-A2F8 
       25.02 

  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
            1.78             0.56 
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
           86.07           185.79 
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
           40.11            29.06 
[1] "1.8 - 86.1 (40.1)"  "0.6 - 185.8 (29.1)"
[1] "hr="     "2.6e+07"
D195V2, continuous
                  vv
clus               ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  MBOAT2 MUTATED                                         6
  MBOAT2 WILD-TYPE                                     194
                  vv
clus               MIXED SEROUS AND ENDOMETRIOID
  MBOAT2 MUTATED                               0
  MBOAT2 WILD-TYPE                             4
                  vv
clus               SEROUS ENDOMETRIAL ADENOCARCINOMA
  MBOAT2 MUTATED                                   1
  MBOAT2 WILD-TYPE                                43
D195V3, multiclass
                                         clus
vv                                        MBOAT2 MUTATED MBOAT2 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"
D195V4, binary
                  cls
clus                 0   1
  MBOAT2 MUTATED     2   5
  MBOAT2 WILD-TYPE  84 157
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MBOAT2 MUTATED      2    5
  MBOAT2 WILD-TYPE   84  157
     clus
vv    MBOAT2 MUTATED MBOAT2 WILD-TYPE
  NO               2               84
  YES              5              157
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MBOAT2 MUTATED     7   0   0   0
  MBOAT2 WILD-TYPE 164  11   7  18
D195V5, multiclass
    clus
vv   MBOAT2 MUTATED MBOAT2 WILD-TYPE
  R0              7              164
  R1              0               11
  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"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MBOAT2 MUTATED                                  0     0
  MBOAT2 WILD-TYPE                                3    13
                  vv
clus               BLACK OR AFRICAN AMERICAN
  MBOAT2 MUTATED                           1
  MBOAT2 WILD-TYPE                        24
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MBOAT2 MUTATED                                           1     5
  MBOAT2 WILD-TYPE                                         6   188
D195V6, multiclass
                                           clus
vv                                          MBOAT2 MUTATED MBOAT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                       0                3
  ASIAN                                                  0               13
  BLACK OR AFRICAN AMERICAN                              1               24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                6
  WHITE                                                  5              188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D195V7, binary
                  cls
clus                 0   1
  MBOAT2 MUTATED     0   5
  MBOAT2 WILD-TYPE   4 162
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MBOAT2 MUTATED      0    5
  MBOAT2 WILD-TYPE    4  162
                        clus
vv                       MBOAT2 MUTATED MBOAT2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              162
[1] 2 2
[1] FALSE

Clustering(196) Variable = CHD4 MUTATION ANALYSIS
D196V1, survival
                sevent
clus2              0   1
  CHD4 MUTATED    30   5
  CHD4 WILD-TYPE 194  19
  CHD4 MUTATED CHD4 WILD-TYPE 
            35            213 
  CHD4 MUTATED CHD4 WILD-TYPE 
             5             19 
$`CHD4 MUTATED`
TCGA-A5-A0R8 TCGA-AP-A051 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
       19.59        83.67        86.07         8.22        39.42        57.80 
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        65.88 
TCGA-B5-A0JY TCGA-B5-A11E TCGA-B5-A11N TCGA-B5-A11Z TCGA-BG-A0MG TCGA-BG-A0MI 
       32.55         8.71        43.96        17.36        48.56        23.47 
TCGA-BG-A0MQ TCGA-BG-A0VV TCGA-BG-A2AE TCGA-BK-A0CB TCGA-BK-A13C TCGA-BS-A0T9 
       39.32        26.66        23.70         6.21        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        36.00 

$`CHD4 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP 
       19.96        17.59        24.62        29.06        11.97        42.35 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05J 
       15.95         1.18        21.99         5.95        23.31        36.89 
TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
        7.86        20.91       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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        41.95 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
       35.01        28.54        37.78        16.96        13.55        36.39 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       71.24        19.36        80.38        56.91        46.75        43.13 
TCGA-B5-A0JV TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       40.67        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       17.88        13.74        17.10        17.85        11.01       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        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       19.59        18.41        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-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MO TCGA-BG-A0MS 
       38.37        36.49        28.27        41.52        43.04        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        24.39        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BK-A0CA 
       14.73        14.01        15.45        15.45        35.90        34.98 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BS-A0TA TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       10.22        10.16        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT 
       88.34        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-A0ZO 
       62.79        63.58        49.55        66.48        16.83        19.79 
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-A102 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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-A16F TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.36        37.51         2.63        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-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       19.53        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-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 
       16.31        35.38        48.36        10.78        15.09         3.62 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       59.01         9.07        25.02 

  CHD4 MUTATED CHD4 WILD-TYPE 
          1.78           0.56 
  CHD4 MUTATED CHD4 WILD-TYPE 
         86.07         185.79 
  CHD4 MUTATED CHD4 WILD-TYPE 
         36.00          28.54 
[1] "1.8 - 86.1 (36.0)"  "0.6 - 185.8 (28.5)"
[1] "hr=" "1.4"
D196V2, continuous
                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
D196V3, 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"
D196V4, binary
                cls
clus               0   1
  CHD4 MUTATED    10  25
  CHD4 WILD-TYPE  76 137
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD4 MUTATED     10   25
  CHD4 WILD-TYPE   76  137
     clus
vv    CHD4 MUTATED CHD4 WILD-TYPE
  NO            10             76
  YES           25            137
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CHD4 MUTATED    26   1   1   2
  CHD4 WILD-TYPE 145  10   6  16
D196V5, multiclass
    clus
vv   CHD4 MUTATED CHD4 WILD-TYPE
  R0           26            145
  R1            1             10
  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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHD4 MUTATED                                  0     1
  CHD4 WILD-TYPE                                3    12
                vv
clus             BLACK OR AFRICAN AMERICAN
  CHD4 MUTATED                           3
  CHD4 WILD-TYPE                        22
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CHD4 MUTATED                                           2    28
  CHD4 WILD-TYPE                                         5   165
D196V6, multiclass
                                           clus
vv                                          CHD4 MUTATED CHD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                     0              3
  ASIAN                                                1             12
  BLACK OR AFRICAN AMERICAN                            3             22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            2              5
  WHITE                                               28            165
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D196V7, binary
                cls
clus               0   1
  CHD4 MUTATED     0  22
  CHD4 WILD-TYPE   4 145
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD4 MUTATED      0   22
  CHD4 WILD-TYPE    4  145
                        clus
vv                       CHD4 MUTATED CHD4 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           22            145
[1] 2 2
[1] FALSE

Clustering(197) Variable = SESN3 MUTATION ANALYSIS
D197V1, survival
                 sevent
clus2               0   1
  SESN3 MUTATED    13   0
  SESN3 WILD-TYPE 211  24
  SESN3 MUTATED SESN3 WILD-TYPE 
             13             235 
  SESN3 MUTATED SESN3 WILD-TYPE 
              0              24 
$`SESN3 MUTATED`
TCGA-A5-A0VP TCGA-AP-A056 TCGA-AX-A05Z TCGA-AX-A0J1 TCGA-B5-A0JZ TCGA-B5-A11E 
       42.35        86.07        46.45        65.88        28.64         8.71 
TCGA-B5-A11G TCGA-BS-A0UF TCGA-D1-A0ZO TCGA-D1-A0ZS TCGA-D1-A16X TCGA-D1-A174 
      113.36        85.84        19.79         4.87         3.65        19.53 
TCGA-D1-A17Q 
        1.78 

$`SESN3 WILD-TYPE`
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
       46.95        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
       19.96        17.59        19.59        24.62        29.06        11.97 
TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       15.95         1.18        83.67        21.99         5.95        23.31 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        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 
       41.95        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H 
       35.34        45.99        66.58        34.98        53.92        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A1C7 
       60.66        35.01        28.54        37.78        40.11        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR 
       13.55        36.39        71.24        19.36        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0K0 TCGA-B5-A0K1 
       46.75        43.13        40.67        32.55        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M 
       11.01       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-A11U 
       43.96        40.50        32.09        33.50        27.35        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        48.56        23.47        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
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         6.21        10.22        10.16        24.99 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        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 
       62.79        63.58        49.55        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        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-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       18.67        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        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       10.78        15.09         3.62        36.00        59.01         9.07 
TCGA-FI-A2F8 
       25.02 

  SESN3 MUTATED SESN3 WILD-TYPE 
           1.78            0.56 
  SESN3 MUTATED SESN3 WILD-TYPE 
         113.36          185.79 
  SESN3 MUTATED SESN3 WILD-TYPE 
          28.64           29.33 
[1] "1.8 - 113.4 (28.6)" "0.6 - 185.8 (29.3)"
[1] "hr="     "2.6e+07"
D197V2, continuous
                 vv
clus              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  SESN3 MUTATED                                        13
  SESN3 WILD-TYPE                                     187
                 vv
clus              MIXED SEROUS AND ENDOMETRIOID
  SESN3 MUTATED                               0
  SESN3 WILD-TYPE                             4
                 vv
clus              SEROUS ENDOMETRIAL ADENOCARCINOMA
  SESN3 MUTATED                                   0
  SESN3 WILD-TYPE                                44
D197V3, multiclass
                                         clus
vv                                        SESN3 MUTATED SESN3 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"
D197V4, binary
                 cls
clus                0   1
  SESN3 MUTATED     5   8
  SESN3 WILD-TYPE  81 154
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SESN3 MUTATED      5    8
  SESN3 WILD-TYPE   81  154
     clus
vv    SESN3 MUTATED SESN3 WILD-TYPE
  NO              5              81
  YES             8             154
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SESN3 MUTATED     9   1   0   0
  SESN3 WILD-TYPE 162  10   7  18
D197V5, multiclass
    clus
vv   SESN3 MUTATED SESN3 WILD-TYPE
  R0             9             162
  R1             1              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"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SESN3 MUTATED                                  0     1
  SESN3 WILD-TYPE                                3    12
                 vv
clus              BLACK OR AFRICAN AMERICAN
  SESN3 MUTATED                           1
  SESN3 WILD-TYPE                        24
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SESN3 MUTATED                                           0    10
  SESN3 WILD-TYPE                                         7   183
D197V6, multiclass
                                           clus
vv                                          SESN3 MUTATED SESN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                      0               3
  ASIAN                                                 1              12
  BLACK OR AFRICAN AMERICAN                             1              24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               7
  WHITE                                                10             183
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D197V7, binary
                 cls
clus                0   1
  SESN3 MUTATED     1   8
  SESN3 WILD-TYPE   3 159
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SESN3 MUTATED      1    8
  SESN3 WILD-TYPE    3  159
                        clus
vv                       SESN3 MUTATED SESN3 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             8             159
[1] 2 2
[1] FALSE
