[1] "ofn"        "-oTBLCA-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/BLCA-TP/22506467/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/22811975/transformed.cor.cli.txt"

nPatients in clinical file=412, in cluster file=395, common to both=395
[1]  81 395
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           196            199 
  TP53 MUTATED TP53 WILD-TYPE 
           196            199 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           70           325 
  RB1 MUTATED RB1 WILD-TYPE 
           70           325 
[1] "ELF3 MUTATION ANALYSIS"
[1] 3
  ELF3 MUTATED ELF3 WILD-TYPE 
            46            349 
  ELF3 MUTATED ELF3 WILD-TYPE 
            46            349 
[1] "TSC1 MUTATION ANALYSIS"
[1] 3
  TSC1 MUTATED TSC1 WILD-TYPE 
            33            362 
  TSC1 MUTATED TSC1 WILD-TYPE 
            33            362 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              86              309 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              86              309 
[1] "RHOB MUTATION ANALYSIS"
[1] 3
  RHOB MUTATED RHOB WILD-TYPE 
            26            369 
  RHOB MUTATED RHOB WILD-TYPE 
            26            369 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
            103             292 
  KDM6A MUTATED KDM6A WILD-TYPE 
            103             292 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              26              369 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              26              369 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              97              298 
  ARID1A MUTATED ARID1A WILD-TYPE 
              97              298 
[1] "STAG2 MUTATION ANALYSIS"
[1] 3
  STAG2 MUTATED STAG2 WILD-TYPE 
             56             339 
  STAG2 MUTATED STAG2 WILD-TYPE 
             56             339 
[1] "ZFP36L1 MUTATION ANALYSIS"
[1] 3
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
               25               370 
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
               25               370 
[1] "CDKN1A MUTATION ANALYSIS"
[1] 3
  CDKN1A MUTATED CDKN1A WILD-TYPE 
              35              360 
  CDKN1A MUTATED CDKN1A WILD-TYPE 
              35              360 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
             61             334 
  EP300 MUTATED EP300 WILD-TYPE 
             61             334 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
           114            281 
  MLL2 MUTATED MLL2 WILD-TYPE 
           114            281 
[1] "FGFR3 MUTATION ANALYSIS"
[1] 3
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             56             339 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             56             339 
[1] "ERCC2 MUTATION ANALYSIS"
[1] 3
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             38             357 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             38             357 
[1] "CREBBP MUTATION ANALYSIS"
[1] 3
  CREBBP MUTATED CREBBP WILD-TYPE 
              48              347 
  CREBBP MUTATED CREBBP WILD-TYPE 
              48              347 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            17            378 
  HRAS MUTATED HRAS WILD-TYPE 
            17            378 
[1] "FOXA1 MUTATION ANALYSIS"
[1] 3
  FOXA1 MUTATED FOXA1 WILD-TYPE 
             14             381 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
             14             381 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            13            382 
  KRAS MUTATED KRAS WILD-TYPE 
            13            382 
[1] "RHOA MUTATION ANALYSIS"
[1] 3
  RHOA MUTATED RHOA WILD-TYPE 
            18            377 
  RHOA MUTATED RHOA WILD-TYPE 
            18            377 
[1] "KIAA1267 MUTATION ANALYSIS"
[1] 3
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                24                371 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                24                371 
[1] "MLL MUTATION ANALYSIS"
[1] 3
  MLL MUTATED MLL WILD-TYPE 
           44           351 
  MLL MUTATED MLL WILD-TYPE 
           44           351 
[1] "FAT1 MUTATION ANALYSIS"
[1] 3
  FAT1 MUTATED FAT1 WILD-TYPE 
            50            345 
  FAT1 MUTATED FAT1 WILD-TYPE 
            50            345 
[1] "KLF5 MUTATION ANALYSIS"
[1] 3
  KLF5 MUTATED KLF5 WILD-TYPE 
            23            372 
  KLF5 MUTATED KLF5 WILD-TYPE 
            23            372 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            14            381 
  PTEN MUTATED PTEN WILD-TYPE 
            14            381 
[1] "C3ORF70 MUTATION ANALYSIS"
[1] 3
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
               17               378 
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
               17               378 
[1] "PSIP1 MUTATION ANALYSIS"
[1] 3
  PSIP1 MUTATED PSIP1 WILD-TYPE 
             20             375 
  PSIP1 MUTATED PSIP1 WILD-TYPE 
             20             375 
[1] "MLL3 MUTATION ANALYSIS"
[1] 3
  MLL3 MUTATED MLL3 WILD-TYPE 
            74            321 
  MLL3 MUTATED MLL3 WILD-TYPE 
            74            321 
[1] "ASXL2 MUTATION ANALYSIS"
[1] 3
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             36             359 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             36             359 
[1] "ZBTB7B MUTATION ANALYSIS"
[1] 3
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
              11              384 
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
              11              384 
[1] "RXRA MUTATION ANALYSIS"
[1] 3
  RXRA MUTATED RXRA WILD-TYPE 
            24            371 
  RXRA MUTATED RXRA WILD-TYPE 
            24            371 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             30             365 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             30             365 
[1] "RBM10 MUTATION ANALYSIS"
[1] 3
  RBM10 MUTATED RBM10 WILD-TYPE 
             22             373 
  RBM10 MUTATED RBM10 WILD-TYPE 
             22             373 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              24              371 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              24              371 
[1] "CUL1 MUTATION ANALYSIS"
[1] 3
  CUL1 MUTATED CUL1 WILD-TYPE 
            19            376 
  CUL1 MUTATED CUL1 WILD-TYPE 
            19            376 
[1] "HLA-A MUTATION ANALYSIS"
[1] 3
  HLA-A MUTATED HLA-A WILD-TYPE 
              5             390 
  HLA-A MUTATED HLA-A WILD-TYPE 
              5             390 
[1] "GNA13 MUTATION ANALYSIS"
[1] 3
  GNA13 MUTATED GNA13 WILD-TYPE 
             12             383 
  GNA13 MUTATED GNA13 WILD-TYPE 
             12             383 
[1] "NUDT11 MUTATION ANALYSIS"
[1] 3
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               7              388 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               7              388 
[1] "MBD1 MUTATION ANALYSIS"
[1] 3
  MBD1 MUTATED MBD1 WILD-TYPE 
            12            383 
  MBD1 MUTATED MBD1 WILD-TYPE 
            12            383 
[1] "SCARF2 MUTATION ANALYSIS"
[1] 3
  SCARF2 MUTATED SCARF2 WILD-TYPE 
               8              387 
  SCARF2 MUTATED SCARF2 WILD-TYPE 
               8              387 
[1] "FOXQ1 MUTATION ANALYSIS"
[1] 3
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
             14             381 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
             14             381 
[1] "FAM47C MUTATION ANALYSIS"
[1] 3
  FAM47C MUTATED FAM47C WILD-TYPE 
              21              374 
  FAM47C MUTATED FAM47C WILD-TYPE 
              21              374 
[1] "METTL3 MUTATION ANALYSIS"
[1] 3
  METTL3 MUTATED METTL3 WILD-TYPE 
              17              378 
  METTL3 MUTATED METTL3 WILD-TYPE 
              17              378 
[1] "ZNF185 MUTATION ANALYSIS"
[1] 3
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               5              390 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               5              390 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             48             347 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             48             347 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           53           342 
  ATM MUTATED ATM WILD-TYPE 
           53           342 
[1] "UNC93B1 MUTATION ANALYSIS"
[1] 3
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                7               388 
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                7               388 
[1] "SF1 MUTATION ANALYSIS"
[1] 3
  SF1 MUTATED SF1 WILD-TYPE 
           10           385 
  SF1 MUTATED SF1 WILD-TYPE 
           10           385 
[1] "BCL2L1 MUTATION ANALYSIS"
[1] 3
  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
               4              391 
  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
               4              391 
[1] "DNAH6 MUTATION ANALYSIS"
[1] 3
  DNAH6 MUTATED DNAH6 WILD-TYPE 
             16             379 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
             16             379 
[1] "HES1 MUTATION ANALYSIS"
[1] 3
  HES1 MUTATED HES1 WILD-TYPE 
            11            384 
  HES1 MUTATED HES1 WILD-TYPE 
            11            384 
[1] "ERBB3 MUTATION ANALYSIS"
[1] 3
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             41             354 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             41             354 
[1] "TXNIP MUTATION ANALYSIS"
[1] 3
  TXNIP MUTATED TXNIP WILD-TYPE 
             17             378 
  TXNIP MUTATED TXNIP WILD-TYPE 
             17             378 
[1] "THRAP3 MUTATION ANALYSIS"
[1] 3
  THRAP3 MUTATED THRAP3 WILD-TYPE 
              14              381 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
              14              381 
[1] "SPTAN1 MUTATION ANALYSIS"
[1] 3
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
              45              350 
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
              45              350 
[1] "ARID1B MUTATION ANALYSIS"
[1] 3
  ARID1B MUTATED ARID1B WILD-TYPE 
              23              372 
  ARID1B MUTATED ARID1B WILD-TYPE 
              23              372 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             7            388 
  NRAS MUTATED NRAS WILD-TYPE 
             7            388 
[1] "RPTN MUTATION ANALYSIS"
[1] 3
  RPTN MUTATED RPTN WILD-TYPE 
            15            380 
  RPTN MUTATED RPTN WILD-TYPE 
            15            380 
[1] "RAI1 MUTATION ANALYSIS"
[1] 3
  RAI1 MUTATED RAI1 WILD-TYPE 
            21            374 
  RAI1 MUTATED RAI1 WILD-TYPE 
            21            374 
[1] "TMCO4 MUTATION ANALYSIS"
[1] 3
  TMCO4 MUTATED TMCO4 WILD-TYPE 
             12             383 
  TMCO4 MUTATED TMCO4 WILD-TYPE 
             12             383 
[1] "CNOT1 MUTATION ANALYSIS"
[1] 3
  CNOT1 MUTATED CNOT1 WILD-TYPE 
             21             374 
  CNOT1 MUTATED CNOT1 WILD-TYPE 
             21             374 
[1] "PARD3 MUTATION ANALYSIS"
[1] 3
  PARD3 MUTATED PARD3 WILD-TYPE 
             22             373 
  PARD3 MUTATED PARD3 WILD-TYPE 
             22             373 
[1] "EZR MUTATION ANALYSIS"
[1] 3
  EZR MUTATED EZR WILD-TYPE 
           12           383 
  EZR MUTATED EZR WILD-TYPE 
           12           383 
[1] "MOAP1 MUTATION ANALYSIS"
[1] 3
  MOAP1 MUTATED MOAP1 WILD-TYPE 
              7             388 
  MOAP1 MUTATED MOAP1 WILD-TYPE 
              7             388 
[1] "SF3B1 MUTATION ANALYSIS"
[1] 3
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             24             371 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             24             371 
[1] "RUNX1 MUTATION ANALYSIS"
[1] 3
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             13             382 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             13             382 
[1] "MEGF8 MUTATION ANALYSIS"
[1] 3
  MEGF8 MUTATED MEGF8 WILD-TYPE 
             20             375 
  MEGF8 MUTATED MEGF8 WILD-TYPE 
             20             375 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
             14             381 
  CASP8 MUTATED CASP8 WILD-TYPE 
             14             381 
[1] "DAZAP1 MUTATION ANALYSIS"
[1] 3
  DAZAP1 MUTATED DAZAP1 WILD-TYPE 
               6              389 
  DAZAP1 MUTATED DAZAP1 WILD-TYPE 
               6              389 
[1] "USP28 MUTATION ANALYSIS"
[1] 3
  USP28 MUTATED USP28 WILD-TYPE 
             13             382 
  USP28 MUTATED USP28 WILD-TYPE 
             13             382 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             27             368 
  SETD2 MUTATED SETD2 WILD-TYPE 
             27             368 
[1] "EME1 MUTATION ANALYSIS"
[1] 3
  EME1 MUTATED EME1 WILD-TYPE 
             5            390 
  EME1 MUTATED EME1 WILD-TYPE 
             5            390 
[1] "ADC MUTATION ANALYSIS"
[1] 3
  ADC MUTATED ADC WILD-TYPE 
            5           390 
  ADC MUTATED ADC WILD-TYPE 
            5           390 
[1] "CNOT3 MUTATION ANALYSIS"
[1] 3
  CNOT3 MUTATED CNOT3 WILD-TYPE 
             10             385 
  CNOT3 MUTATED CNOT3 WILD-TYPE 
             10             385 
[1] "SSH3 MUTATION ANALYSIS"
[1] 3
  SSH3 MUTATED SSH3 WILD-TYPE 
            15            380 
  SSH3 MUTATED SSH3 WILD-TYPE 
            15            380 
[1] "AHR MUTATION ANALYSIS"
[1] 3
  AHR MUTATED AHR WILD-TYPE 
           22           373 
  AHR MUTATED AHR WILD-TYPE 
           22           373 
[1] "EIF4A2 MUTATION ANALYSIS"
[1] 3
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
              11              384 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
              11              384 
[1] "EPHA2 MUTATION ANALYSIS"
[1] 3
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             19             376 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             19             376 
[1] "OGDH MUTATION ANALYSIS"
[1] 3
  OGDH MUTATED OGDH WILD-TYPE 
            19            376 
  OGDH MUTATED OGDH WILD-TYPE 
            19            376 
[1] "POU3F1 MUTATION ANALYSIS"
[1] 3
  POU3F1 MUTATED POU3F1 WILD-TYPE 
               3              392 
  POU3F1 MUTATED POU3F1 WILD-TYPE 
               3              392 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 395 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=157,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=206,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=69,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 395 columns, 1 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"              "PATHOLOGIC_STAGE"           
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
 [9] "NUMBER_PACK_YEARS_SMOKED"    "NUMBER_OF_LYMPH_NODES"      
[11] "RACE"                        "ETHNICITY"                  
YEARS_TO_BIRTH, nv=52, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1   3 112 190  57 
[1] "table(vv)"
vv
T0+T1+T2       T3       T4 
     116      190       57 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1   3 112 190  57 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1+T2       T3       T4 
     116      190       57 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
225  46  75   8 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
225  46  75   8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
225  46  75   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
225  46  75   8 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=69, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=20, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  TP53 MUTATED   108  88
  TP53 WILD-TYPE 109  87
  TP53 MUTATED TP53 WILD-TYPE 
           196            196 
  TP53 MUTATED TP53 WILD-TYPE 
            88             87 
$`TP53 MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A2LD TCGA-BT-A3PJ 
       16.27        16.77        15.12        26.14        20.48        25.94 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A1AC 
        8.98         2.04        18.48         2.14        16.70       130.88 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 
       87.32         8.22        50.27        23.21         9.67        66.05 
TCGA-DK-A3X2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA74 
       17.98        36.66        38.24       165.73        13.64        56.15 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       20.32        15.35         0.92         1.22        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       60.66        24.30        23.41        19.79        12.85        27.35 
TCGA-FD-A5BR TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       26.73         6.15        12.69        12.36        31.07        17.23 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       33.01        17.62        70.32        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A4AB 
       10.92        32.98        19.82        19.07         9.01         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41P TCGA-UY-A78N TCGA-UY-A9PH 
        9.14        27.68        50.56        35.97        86.83        51.32 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T3 
       15.98        34.45         4.21        21.04        26.27         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       66.64         2.10        10.82        54.90         7.63        71.57 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       86.30        18.58        13.64        30.28        94.29         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-2F-A9KP TCGA-4Z-AA7R TCGA-4Z-AA7W 
       88.87        19.69        57.90        11.97        17.16        27.62 
TCGA-4Z-AA80 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A13J TCGA-BL-A3JM 
        0.62        10.22        47.80         2.50         2.66         6.74 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA 
       19.04        12.16         5.06        14.96         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42F TCGA-CF-A1HS TCGA-CF-A47Y TCGA-CF-A5U8 
       16.18         4.67        28.41        12.56        12.26        13.12 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK 
       21.86        66.41       112.44        17.95         7.79         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-AA6Q TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A2PC 
       13.58         8.15        13.58        19.00        15.35        43.59 
TCGA-E5-A4U1 TCGA-E7-A6ME TCGA-E7-A97Q TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SO 
       38.83        24.03         8.09        12.62        22.52         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TF 
       25.74        22.98         5.36         2.70        13.35         2.27 
TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       10.85        10.65        48.00        26.93        59.31         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A6I1 
       20.12        66.02        29.36        15.81        15.91         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 
       13.91        26.70        20.98         2.20        11.31         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
       20.05        15.78         4.73        21.34        19.10         8.48 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       64.01        12.16         9.07        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI 
       15.42        11.80         1.15        15.32        15.58        12.23 
TCGA-PQ-A6FN TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       16.67        17.62        37.05        22.68        76.01        69.34 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A9SI 
       35.24        29.56        17.82         6.21         1.87        79.66 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       23.64        28.24       110.60         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-ZF-A9R0 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       56.48        22.36        13.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       20.22         2.89        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-GU-AATO 
       19.40        54.21        29.49        10.65 

$`TP53 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PK 
      108.95        33.83        12.39        14.89         8.35         9.96 
TCGA-BT-A42C TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E 
       28.70        18.58        12.92         4.90        15.12        13.58 
TCGA-DK-A1AA TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A6AV TCGA-DK-A6AW 
       19.00        46.68        17.72        21.30        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6S 
       76.60        67.36        15.68        50.70        52.01       166.03 
TCGA-DK-AA71 TCGA-DK-AA75 TCGA-E7-A541 TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
       13.64        11.18        25.58        17.98        29.16        46.78 
TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
        3.62        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FD-A6TH 
       58.92         6.28        62.86        18.81         3.06         4.31 
TCGA-FD-A6TI TCGA-FT-A61P TCGA-GC-A3BM TCGA-GU-A763 TCGA-GV-A3QF TCGA-GV-A3QK 
        9.67        11.08        21.40        32.78        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A3WU TCGA-KQ-A41N TCGA-KQ-A41Q 
        8.58        22.72        25.02         3.45        52.73        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9SV 
       14.24         1.84        33.14         3.22        14.93        12.76 
TCGA-XF-A9SW TCGA-XF-A9T2 TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAMR TCGA-XF-AAMY 
       11.90        18.90        13.74        11.31        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 
       44.32        30.94        61.45         3.88         9.63        21.11 
TCGA-ZF-AA4R TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       34.06        12.23        24.13        94.88       104.65         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 
       44.94        16.83        34.98        50.04        41.75        51.16 
TCGA-4Z-AA83 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX 
       66.54        17.42        40.08         7.33         6.58        13.15 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20V TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F0 
       17.88        19.50         5.06        17.56        36.43         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
        2.93        23.01        12.79        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU 
       12.62        12.00        12.10        11.87        13.08         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       29.79         1.84        18.41        16.14        17.62        15.62 
TCGA-DK-A2I4 TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6T 
      142.78        20.81        10.55       163.30        15.02        18.81 
TCGA-DK-AA76 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       12.03        29.72         5.36        22.16         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF 
        0.56         0.66        26.96        26.24         4.24        24.66 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 
       13.68        14.07        12.95        14.37        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3N6 TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BZ 
        8.94        27.98        14.96        20.91        19.33        27.45 
TCGA-FD-A62O TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
        7.10        12.66         8.94         3.25        22.88        61.94 
TCGA-G2-A2EK TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GD-A3OP TCGA-GD-A3OQ 
       15.95         6.94        20.71        14.07         2.10         3.12 
TCGA-GU-A42R TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       18.97         7.00        14.27        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A83P TCGA-KQ-A41R TCGA-MV-A51V TCGA-S5-AA26 
       38.60        21.24        16.27        44.38        13.48        16.54 
TCGA-SY-A9G5 TCGA-UY-A9PF TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL 
       38.99         3.85        17.88        48.62        64.80        66.41 
TCGA-XF-A9SU TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC 
        5.98        16.27        92.98        27.06        75.39         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       11.97        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA56 TCGA-ZF-AA5N 
        8.61        59.38         8.52         5.52 

  TP53 MUTATED TP53 WILD-TYPE 
          0.62           0.56 
  TP53 MUTATED TP53 WILD-TYPE 
        165.73         166.03 
  TP53 MUTATED TP53 WILD-TYPE 
        17.885         16.800 
[1] "0.6 - 165.7 (17.9)" "0.6 - 166.0 (16.8)"
[1] "hr=" "1"  
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TP53 MUTATED         0       59        61       76
  TP53 WILD-TYPE       2       63        74       58
D1V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I              0              2
  STAGE II            59             63
  STAGE III           61             74
  STAGE IV            76             58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2 T3 T4
  TP53 MUTATED         52 97 28
  TP53 WILD-TYPE       64 93 29
D1V4, multiclass
          clus
vv         TP53 MUTATED TP53 WILD-TYPE
  T0+T1+T2           52             64
  T3                 97             93
  T4                 28             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TP53 MUTATED    96  25  42   7
  TP53 WILD-TYPE 129  21  33   1
D1V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           96            129
  N1           25             21
  N2           42             33
  N3            7              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                cls
clus               0   1
  TP53 MUTATED    77   6
  TP53 WILD-TYPE 112   5
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     77    6
  TP53 WILD-TYPE  112    5
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           77            112
  1            6              5
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus               0   1
  TP53 MUTATED    51 145
  TP53 WILD-TYPE  51 148
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     51  145
  TP53 WILD-TYPE   51  148
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           51             51
  MALE            145            148
[1] 2 2
[1] FALSE
D1V8, binary
                cls
clus               0   1
  TP53 MUTATED   174   7
  TP53 WILD-TYPE 176  13
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    174    7
  TP53 WILD-TYPE  176   13
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO           174            176
  YES            7             13
[1] 2 2
[1] FALSE
D1V9, continuous
D1V10, continuous
D1V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       9                        10   168
  TP53 WILD-TYPE    30                        12   149
D1V12, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                9             30
  BLACK OR AFRICAN AMERICAN           10             12
  WHITE                              168            149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, binary
                cls
clus               0   1
  TP53 MUTATED     4 173
  TP53 WILD-TYPE   4 182
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      4  173
  TP53 WILD-TYPE    4  182
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                4              4
  NOT HISPANIC OR LATINO          173            182
[1] 2 2
[1] FALSE

Clustering(2) Variable = RB1 MUTATION ANALYSIS
D2V1, survival
               sevent
clus2             0   1
  RB1 MUTATED    35  35
  RB1 WILD-TYPE 182 140
  RB1 MUTATED RB1 WILD-TYPE 
           70           322 
  RB1 MUTATED RB1 WILD-TYPE 
           35           140 
$`RB1 MUTATED`
TCGA-BT-A3PJ TCGA-CU-A0YN TCGA-DK-A3IN TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
       25.94        12.92         8.22         9.67        66.05        17.98 
TCGA-DK-AA6M TCGA-E5-A4TZ TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A43P 
       52.01        15.35        33.04         4.01        23.41        27.35 
TCGA-FD-A5C0 TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-GC-A3YS 
       18.08         6.15        12.69        12.36         4.31        24.92 
TCGA-GV-A40G TCGA-K4-A54R TCGA-KQ-A41Q TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9ST 
       19.07        27.68        46.98         3.22        34.45         4.21 
TCGA-XF-A9SW TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAML 
       11.90         2.24         2.10        13.74        10.82         7.63 
TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-ZF-AA4T TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-5N-A9KI 
       61.45        18.58        19.69        41.75        10.22         2.50 
TCGA-BL-A3JM TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A3PH TCGA-C4-A0F0 TCGA-DK-A3IL 
        6.74         5.06        17.16         4.67         1.94        13.58 
TCGA-DK-AA6T TCGA-E7-A6ME TCGA-E7-A7PW TCGA-FD-A3N5 TCGA-FD-A3SO TCGA-FD-A62N 
       18.81        24.03        13.68        22.52         5.52         2.70 
TCGA-FD-A6TF TCGA-G2-A2EL TCGA-GV-A3JX TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ 
        2.27        26.93        19.10         9.07        17.72         1.81 
TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-UY-A78L TCGA-XF-A9SG 
       15.32        13.48        12.23        16.67        37.05        48.62 
TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-AAN0 TCGA-ZF-A9RF TCGA-ZF-AA4V 
       79.66        23.64        28.24        56.48        64.08        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-GU-AATO 
       67.20        54.21        29.49        10.65 

$`RB1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C 
       26.14        14.89         8.35        20.48         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        8.98         2.04        18.58         4.90        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       13.58         2.14        19.00        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A6AV 
       87.32        17.72        50.27        21.30        23.21        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       53.29        76.60        67.36        15.68        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       38.24       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3NA 
       11.18        20.32        25.58         0.92         1.22        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       24.30        17.98        29.16        46.78        19.79        12.85 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
        3.62        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FD-A6TI 
       58.92         6.28        62.86        18.81         3.06         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D 
       31.07        17.23        11.08        33.01        17.62        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP 
       21.40        19.13        17.75        10.92        32.78        32.98 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND 
       19.82        20.28        27.35         8.58        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41N TCGA-KQ-A41O 
       25.02         3.45         2.76         9.14        52.73        50.56 
TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       35.97        14.24         1.84        33.14        86.83        51.32 
TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
       15.98        14.93        12.76        21.04        26.27        18.90 
TCGA-XF-A9T5 TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       66.64        11.31        54.90        71.57        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       44.32        30.94        86.30         3.88         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
       21.11        30.28        94.29         3.48        88.87        34.06 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       57.90        12.23        24.13        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-5N-A9KM 
       50.04         0.62        51.16        66.54        47.80        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         2.66         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       12.16        17.88        19.50        14.96         5.06         8.25 
TCGA-BT-A2LB TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F1 TCGA-C4-A0F6 
       16.18        17.56        36.43        28.41         2.93        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       12.79        12.56        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       12.16        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.19        29.79         1.84        21.86        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
      142.78         4.80         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       15.02        13.58        19.00        15.35        12.03        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         5.36        22.16         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF 
        0.56         0.66        26.96        26.24         4.24        24.66 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
        8.94        12.62        27.98        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S 
       20.91        19.33         5.36        27.45         7.10        13.35 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC 
       10.85        12.66        10.65         8.94         3.25        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       61.94        48.00        15.95        59.31         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       66.02         6.94        29.36        20.71        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07         8.94        13.91        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
       20.98         2.20        11.31        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH 
       15.78         4.73         7.00        14.27        21.34         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
       36.49         1.51        19.40        38.60        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       21.24        11.70        15.42        16.27        11.80        44.38 
TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M 
        1.15        15.58        16.54        38.99        17.62        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        69.34        35.24        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU 
        3.85         1.87        17.88        64.80        66.41         5.98 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       16.27        92.98       110.60         2.96         8.32         6.77 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG 
       31.20        35.84        21.86        28.41        13.41        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 
       47.84        20.22         2.89         8.61        60.16        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5N 
       35.41        19.40         8.52         5.52 

  RB1 MUTATED RB1 WILD-TYPE 
         1.81          0.56 
  RB1 MUTATED RB1 WILD-TYPE 
        79.66        166.03 
  RB1 MUTATED RB1 WILD-TYPE 
       16.915        17.670 
[1] "1.8 - 79.7 (16.9)"  "0.6 - 166.0 (17.7)"
[1] "hr=" "1.3"
D2V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  RB1 MUTATED         0       20        23       27
  RB1 WILD-TYPE       2      102       112      107
D2V3, multiclass
           clus
vv          RB1 MUTATED RB1 WILD-TYPE
  STAGE I             0             2
  STAGE II           20           102
  STAGE III          23           112
  STAGE IV           27           107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1+T2  T3  T4
  RB1 MUTATED         17  39  10
  RB1 WILD-TYPE       99 151  47
D2V4, multiclass
          clus
vv         RB1 MUTATED RB1 WILD-TYPE
  T0+T1+T2          17            99
  T3                39           151
  T4                10            47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  RB1 MUTATED    37   6  21   0
  RB1 WILD-TYPE 188  40  54   8
D2V5, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  N0          37           188
  N1           6            40
  N2          21            54
  N3           0             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
               cls
clus              0   1
  RB1 MUTATED    24   2
  RB1 WILD-TYPE 165   9
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     24    2
  RB1 WILD-TYPE  165    9
   clus
vv  RB1 MUTATED RB1 WILD-TYPE
  0          24           165
  1           2             9
[1] 2 2
[1] FALSE
D2V7, binary
               cls
clus              0   1
  RB1 MUTATED    15  55
  RB1 WILD-TYPE  87 238
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     15   55
  RB1 WILD-TYPE   87  238
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE          15            87
  MALE            55           238
[1] 2 2
[1] FALSE
D2V8, binary
               cls
clus              0   1
  RB1 MUTATED    60   2
  RB1 WILD-TYPE 290  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     60    2
  RB1 WILD-TYPE  290   18
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO           60           290
  YES           2            18
[1] 2 2
[1] FALSE
D2V9, continuous
D2V10, continuous
D2V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED       4                         4    60
  RB1 WILD-TYPE    35                        18   257
D2V12, multiclass
                           clus
vv                          RB1 MUTATED RB1 WILD-TYPE
  ASIAN                               4            35
  BLACK OR AFRICAN AMERICAN           4            18
  WHITE                              60           257
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, binary
               cls
clus              0   1
  RB1 MUTATED     1  66
  RB1 WILD-TYPE   7 289
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      1   66
  RB1 WILD-TYPE    7  289
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               1             7
  NOT HISPANIC OR LATINO          66           289
[1] 2 2
[1] FALSE

Clustering(3) Variable = ELF3 MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  ELF3 MUTATED    26  19
  ELF3 WILD-TYPE 191 156
  ELF3 MUTATED ELF3 WILD-TYPE 
            45            347 
  ELF3 MUTATED ELF3 WILD-TYPE 
            19            156 
$`ELF3 MUTATED`
TCGA-2F-A9KT TCGA-CF-A9FL TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-AA6L TCGA-DK-AA75 
      108.95        18.58        15.12        13.58        38.24        11.18 
TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TI TCGA-FJ-A3ZF 
       46.78        27.35        18.81         6.15         9.67        17.23 
TCGA-GU-AATP TCGA-KQ-A41N TCGA-KQ-A41O TCGA-R3-A69X TCGA-XF-AAN1 TCGA-XF-AAN2 
       32.98        52.73        50.56        14.24        30.94        61.45 
TCGA-ZF-A9R4 TCGA-5N-A9KM TCGA-BT-A20Q TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A3YL 
       30.28        17.42        19.50        12.56        12.62        29.79 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A5KF TCGA-E7-A97Q TCGA-FD-A43N TCGA-FD-A62O 
       43.59        38.83         0.66         8.09        22.98         7.10 
TCGA-G2-A2EO TCGA-GC-A3RC TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 
       59.31        15.91         8.94        26.70         2.10         2.20 
TCGA-GV-A3JV TCGA-UY-A78O TCGA-ZF-A9R0 TCGA-ZF-A9R7 TCGA-ZF-A9RG TCGA-ZF-A9RM 
       14.27        76.01        22.36        21.86        58.72        47.84 
TCGA-ZF-AA4X TCGA-ZF-AA56 TCGA-ZF-AA5N 
       67.20         8.52         5.52 

$`ELF3 WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
       16.27        16.77        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-DK-A1A5 
        8.98         2.04        12.92         4.90        18.48         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN 
       19.00        16.70       130.88        46.68        87.32         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 
       17.72        50.27        21.30        23.21         9.67        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        53.29        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       50.70        36.66        52.01       165.73       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU 
       13.64        56.15        20.32        15.35        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        1.22        33.04         4.01        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A5BR 
       17.98        29.16        19.79        12.85         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
        6.28        62.86        12.69        12.36         3.06         4.31 
TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM 
       31.07        11.08        33.01        17.62        70.32        21.40 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ 
       19.13        17.75        24.92        10.92        32.78        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       20.28        27.35         8.58        19.07        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41P 
       25.02         3.45         2.76         9.14        27.68        35.97 
TCGA-KQ-A41Q TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ 
       46.98         1.84        33.14        86.83        51.32         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
       15.98        34.45        14.93         4.21        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       13.74        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 
       91.73        98.99        44.32        86.30        18.58         3.88 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL 
        9.63        13.64        21.11        94.29         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       34.06        19.69        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       34.98        27.62        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13I 
       66.54        10.22        47.80         2.50        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        2.66         6.74         6.58        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       17.88         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       16.18         4.67        17.56        36.43        28.41         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
        2.93        23.01        12.79        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
        5.19         1.84        21.86        66.41        18.41       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       15.02        13.58        18.81        19.00        15.35        12.03 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        22.16         2.24        16.70         0.56 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
       26.96        26.24         4.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       14.07        12.95        14.37        32.02        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S 
       12.62        22.52        27.98         5.52        25.74        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62S 
       20.91        19.33         5.36        27.45         2.70        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.27        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
       22.88        61.94        48.00        15.95        26.93         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       20.12        66.02         6.94        29.36        20.71        15.81 
TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R 
       14.07        13.91         3.12        20.98        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW 
        7.63        20.05        15.78         4.73         7.00        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       19.10         8.48        36.49         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       64.01        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
        1.81        15.42        16.27        11.80        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       15.32        15.58        13.48        12.23        16.67        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A9PA 
       38.99        17.62        37.05        22.68        69.34        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         6.21         3.85         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       48.62        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW 
       28.24        16.27        92.98       110.60         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L 
        6.77        56.48        27.06        75.39         0.66        11.97 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       25.41        31.20        35.84        28.41        13.41        64.08 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 
       20.22         2.89         8.61        59.38        60.16        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-GU-AATO 
       35.41        19.40        54.21        29.49        10.65 

  ELF3 MUTATED ELF3 WILD-TYPE 
          0.66           0.56 
  ELF3 MUTATED ELF3 WILD-TYPE 
        108.95         166.03 
  ELF3 MUTATED ELF3 WILD-TYPE 
         19.50          17.56 
[1] "0.7 - 109.0 (19.5)" "0.6 - 166.0 (17.6)"
[1] "hr=" "1.2"
D3V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  ELF3 MUTATED         0       14        17       15
  ELF3 WILD-TYPE       2      108       118      119
D3V3, multiclass
           clus
vv          ELF3 MUTATED ELF3 WILD-TYPE
  STAGE I              0              2
  STAGE II            14            108
  STAGE III           17            118
  STAGE IV            15            119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  ELF3 MUTATED         17  19   8
  ELF3 WILD-TYPE       99 171  49
D3V4, multiclass
          clus
vv         ELF3 MUTATED ELF3 WILD-TYPE
  T0+T1+T2           17             99
  T3                 19            171
  T4                  8             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ELF3 MUTATED    27   5   8   1
  ELF3 WILD-TYPE 198  41  67   7
D3V5, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  N0           27            198
  N1            5             41
  N2            8             67
  N3            1              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"
D3V6, binary
                cls
clus               0   1
  ELF3 MUTATED    22   1
  ELF3 WILD-TYPE 167  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED     22    1
  ELF3 WILD-TYPE  167   10
   clus
vv  ELF3 MUTATED ELF3 WILD-TYPE
  0           22            167
  1            1             10
[1] 2 2
[1] FALSE
D3V7, binary
                cls
clus               0   1
  ELF3 MUTATED    15  31
  ELF3 WILD-TYPE  87 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED     15   31
  ELF3 WILD-TYPE   87  262
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  FEMALE           15             87
  MALE             31            262
[1] 2 2
[1] FALSE
D3V8, binary
                cls
clus               0   1
  ELF3 MUTATED    41   2
  ELF3 WILD-TYPE 309  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED     41    2
  ELF3 WILD-TYPE  309   18
     clus
vv    ELF3 MUTATED ELF3 WILD-TYPE
  NO            41            309
  YES            2             18
[1] 2 2
[1] FALSE
D3V9, continuous
D3V10, continuous
D3V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ELF3 MUTATED       4                         2    37
  ELF3 WILD-TYPE    35                        20   280
D3V12, multiclass
                           clus
vv                          ELF3 MUTATED ELF3 WILD-TYPE
  ASIAN                                4             35
  BLACK OR AFRICAN AMERICAN            2             20
  WHITE                               37            280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, binary
                cls
clus               0   1
  ELF3 MUTATED     0  45
  ELF3 WILD-TYPE   8 310
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      0   45
  ELF3 WILD-TYPE    8  310
                        clus
vv                       ELF3 MUTATED ELF3 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           45            310
[1] 2 2
[1] FALSE

Clustering(4) Variable = TSC1 MUTATION ANALYSIS
D4V1, survival
                sevent
clus2              0   1
  TSC1 MUTATED    18  14
  TSC1 WILD-TYPE 199 161
  TSC1 MUTATED TSC1 WILD-TYPE 
            32            360 
  TSC1 MUTATED TSC1 WILD-TYPE 
            14            161 
$`TSC1 MUTATED`
TCGA-BT-A42C TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A6TB TCGA-FD-A6TI 
       28.70        17.98        29.16        46.78        18.81         9.67 
TCGA-GU-AATP TCGA-GV-A3QF TCGA-XF-A9SK TCGA-XF-A9ST TCGA-XF-AAMR TCGA-ZF-A9RL 
       32.98        20.28        15.98         4.21        91.73        88.87 
TCGA-ZF-AA53 TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA83 TCGA-5N-A9KM TCGA-BT-A20P 
       57.90        50.04         0.62        66.54        17.42        17.88 
TCGA-CF-A1HR TCGA-CF-A3MG TCGA-CF-A9FF TCGA-DK-A1A3 TCGA-DK-A3WW TCGA-FD-A5BU 
       12.79        12.13        11.87        21.86        20.81        19.33 
TCGA-FD-A6TF TCGA-G2-A2EO TCGA-G2-AA3B TCGA-GD-A2C5 TCGA-GU-A766 TCGA-ZF-A9R3 
        2.27        59.31        66.02        26.70        15.78        31.20 
TCGA-ZF-AA54 TCGA-ZF-AA5H 
       19.40        29.49 

$`TSC1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SR 
       33.04         4.01        60.66        24.30        23.41        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       12.85        27.35         3.62        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
        5.69         8.25        18.08        58.92         6.28        62.86 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 
        6.15        12.69        12.36         3.06         4.31        31.07 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM 
       17.23        11.08        33.01        17.62        70.32        21.40 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ 
       19.13        17.75        24.92        10.92        32.78        19.82 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        3.45         2.76         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       35.97        46.98        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SW 
       51.32         3.22        34.45        14.93        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       13.74        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       98.99        44.32        30.94        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
        3.88         9.63        13.64        21.11        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
        3.48        34.06        19.69        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-4Z-AA87 
       34.98        27.62        41.75        51.16        10.22        47.80 
TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
        2.50        40.08         7.33         2.66         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       13.15        19.04        12.16        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
        5.06         8.25        17.16        16.18         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HS 
       36.43        28.41         1.94         2.93        23.01        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       13.97        12.59        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 
       12.10        13.08         5.19        29.79         1.84        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WX 
        7.79       142.78         4.80        13.58         8.15        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
      163.30        15.02        13.58        18.81        19.00        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       12.03        43.59        38.83        29.72         5.36        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70         0.56         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
        4.24        24.03        24.66        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       14.37         8.09        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       20.91         5.36        27.45         2.70         7.10        13.35 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC 
       10.85        12.66        10.65         8.94         3.25        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE 
       61.94        48.00        15.95        26.93         7.23        20.12 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        29.36        20.71        15.81        15.91        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        8.94        13.91         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATQ 
       11.31        18.97         7.63        20.05         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
       14.27        21.34        19.10         8.48        36.49         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
       19.40        38.60        64.01        12.16        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70        17.72         1.81        15.42        16.27        11.80 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       44.38         1.15        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        69.34        35.24        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        3.85         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 
      110.60         2.96         8.32         6.77        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R5 
       75.39         0.66        11.97        22.36        25.41        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       21.86        28.41        13.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       20.22         2.89         8.61        59.38        60.16        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
       56.35        35.41         8.52        54.21         5.52        10.65 

  TSC1 MUTATED TSC1 WILD-TYPE 
          0.62           0.56 
  TSC1 MUTATED TSC1 WILD-TYPE 
         91.73         166.03 
  TSC1 MUTATED TSC1 WILD-TYPE 
        20.545         16.995 
[1] "0.6 - 91.7 (20.5)"  "0.6 - 166.0 (17.0)"
[1] "hr=" "1.2"
D4V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TSC1 MUTATED         0       13        10       10
  TSC1 WILD-TYPE       2      109       125      124
D4V3, multiclass
           clus
vv          TSC1 MUTATED TSC1 WILD-TYPE
  STAGE I              0              2
  STAGE II            13            109
  STAGE III           10            125
  STAGE IV            10            124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  TSC1 MUTATED         12  17   2
  TSC1 WILD-TYPE      104 173  55
D4V4, multiclass
          clus
vv         TSC1 MUTATED TSC1 WILD-TYPE
  T0+T1+T2           12            104
  T3                 17            173
  T4                  2             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TSC1 MUTATED    19   2   8   0
  TSC1 WILD-TYPE 206  44  67   8
D4V5, multiclass
    clus
vv   TSC1 MUTATED TSC1 WILD-TYPE
  N0           19            206
  N1            2             44
  N2            8             67
  N3            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                cls
clus               0   1
  TSC1 MUTATED    16   2
  TSC1 WILD-TYPE 173   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC1 MUTATED     16    2
  TSC1 WILD-TYPE  173    9
   clus
vv  TSC1 MUTATED TSC1 WILD-TYPE
  0           16            173
  1            2              9
[1] 2 2
[1] FALSE
D4V7, binary
                cls
clus               0   1
  TSC1 MUTATED     8  25
  TSC1 WILD-TYPE  94 268
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC1 MUTATED      8   25
  TSC1 WILD-TYPE   94  268
        clus
vv       TSC1 MUTATED TSC1 WILD-TYPE
  FEMALE            8             94
  MALE             25            268
[1] 2 2
[1] FALSE
D4V8, binary
                cls
clus               0   1
  TSC1 MUTATED    30   0
  TSC1 WILD-TYPE 320  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC1 MUTATED     30    0
  TSC1 WILD-TYPE  320   20
     clus
vv    TSC1 MUTATED TSC1 WILD-TYPE
  NO            30            320
  YES            0             20
[1] 2 2
[1] FALSE
D4V9, continuous
D4V10, continuous
D4V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TSC1 MUTATED       4                         1    28
  TSC1 WILD-TYPE    35                        21   289
D4V12, multiclass
                           clus
vv                          TSC1 MUTATED TSC1 WILD-TYPE
  ASIAN                                4             35
  BLACK OR AFRICAN AMERICAN            1             21
  WHITE                               28            289
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, binary
                cls
clus               0   1
  TSC1 MUTATED     1  29
  TSC1 WILD-TYPE   7 326
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC1 MUTATED      1   29
  TSC1 WILD-TYPE    7  326
                        clus
vv                       TSC1 MUTATED TSC1 WILD-TYPE
  HISPANIC OR LATINO                1              7
  NOT HISPANIC OR LATINO           29            326
[1] 2 2
[1] FALSE

Clustering(5) Variable = PIK3CA MUTATION ANALYSIS
D5V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    48  37
  PIK3CA WILD-TYPE 169 138
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              85              307 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              37              138 
$`PIK3CA MUTATED`
TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A1AC 
       15.12        33.83        13.58         2.14        16.70       130.88 
TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA71 TCGA-DK-AA77 
       66.05        53.29        15.68        50.70        13.64        20.32 
TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A5BX 
        0.92        33.04        60.66        24.30        29.16         5.69 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TD TCGA-G2-A3VY TCGA-GC-A3WC TCGA-K4-A3WS 
       58.92         6.28        12.69        17.62        17.75        25.02 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-XF-A9T0 TCGA-XF-A9T8 TCGA-XF-AAN2 TCGA-ZF-A9R2 
        2.76        27.68        26.27        13.74        61.45        21.11 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KR 
        3.48        88.87        57.90        12.23        24.13       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BT-A20O 
        8.35        27.62        50.04        47.80         2.50        12.16 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-CF-A5UA TCGA-CF-A9FF TCGA-CU-A5W6 TCGA-DK-A1A6 
       19.50         5.06        12.00        11.87         1.84        66.41 
TCGA-DK-A1AG TCGA-DK-A3WW TCGA-DK-AA6Q TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       15.62        20.81        13.58        15.35        12.03        43.59 
TCGA-E7-A4IJ TCGA-FD-A3B5 TCGA-FD-A3SO TCGA-FD-A43N TCGA-G2-A2EJ TCGA-G2-A2EO 
       22.16         8.94         5.52        22.98        48.00        59.31 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A6I3 TCGA-GD-A3OP 
       66.02         6.94        20.71        15.81        13.91         2.10 
TCGA-GD-A6C6 TCGA-GU-AATQ TCGA-GV-A3JX TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A83P 
        2.20         7.00        19.10         1.51        12.16        16.27 
TCGA-SY-A9G5 TCGA-UY-A78M TCGA-XF-A8HI TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAN0 
       38.99        22.68        17.88        92.98       110.60        56.48 
TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA56 
       58.72         2.89         8.61        67.20        35.41         8.52 
TCGA-GU-AATO 
       10.65 

$`PIK3CA WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
      108.95        16.27        16.77        12.39        26.14        14.89 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
        8.35        20.48        25.94         9.96        28.70         8.98 
TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        2.04        18.58        12.92         4.90        15.12        18.48 
TCGA-DK-A1AA TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
       19.00        46.68        87.32         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 
       21.30        23.21         9.67        17.98        64.18        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S 
       67.36        36.66        38.24        52.01       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV 
       13.64        56.15        11.18        15.35        25.58         1.22 
TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
        4.01        23.41        17.98        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BY 
       27.35         3.62        26.73        53.88        10.78         8.25 
TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
       18.08        62.86        18.81         6.15        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        4.31         9.67        31.07        17.23        11.08        33.01 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 
       70.32        21.40        19.13        24.92        10.92        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       32.98        19.82        20.28        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AC TCGA-KQ-A41N TCGA-KQ-A41O 
       22.72         9.01         3.45         9.14        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       35.97        46.98        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       51.32         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       12.76        11.90        21.04        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
        2.10        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN7 
       91.73        98.99        44.32        30.94        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-AA4R 
        3.88         9.63        13.64        30.28        94.29        34.06 
TCGA-ZF-AA4T TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       19.69        11.97        94.88        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       34.98         0.62        41.75        51.16        66.54        10.22 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       17.42        40.08         7.33         2.66         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       13.15        19.04        17.88        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       17.16        16.18         4.67        17.56        36.43        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        1.94         2.93        23.01        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 
       12.46        12.10        12.62        12.26        13.12        12.10 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AD 
       13.08         5.19        29.79        21.86        18.41       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       16.14        17.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6T 
       13.58         8.15        10.55       163.30        15.02        18.81 
TCGA-DK-AA6U TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       19.00        38.83        29.72         5.36         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
        0.56         0.66        26.96        26.24         4.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
       24.66        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SP 
       32.02        16.77        12.62        22.52        27.98        25.74 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       14.96        20.91        19.33         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        7.10        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25        22.88        61.94        15.95        26.93 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3F TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 
        7.23        20.12        29.36        15.91        14.07         8.94 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
       26.70         3.12        20.98        11.31        18.97         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH 
       20.05        15.78         4.73        14.27        21.34         8.48 
TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RH 
       36.49        19.40        38.60        64.01        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R 
       11.70        17.72         1.81        15.42        11.80        44.38 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.15        15.32        15.58        13.48        12.23        16.67 
TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       16.54        17.62        37.05        76.01        69.34        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SG 
       29.56        17.82         6.21         3.85         1.87        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        79.66        66.41         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-XF-AAN5 
       16.27         2.96         8.32         6.77        27.06        75.39 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-A9RN 
       21.86        28.41        13.41        64.08        47.84        20.22 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       59.38        60.16        56.35        19.40        54.21        29.49 
TCGA-ZF-AA5N 
        5.52 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.92             0.56 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          130.88           166.03 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           17.88            17.56 
[1] "0.9 - 130.9 (17.9)" "0.6 - 166.0 (17.6)"
[1] "hr=" "1.1"
D5V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PIK3CA MUTATED         0       28        33       25
  PIK3CA WILD-TYPE       2       94       102      109
D5V3, multiclass
           clus
vv          PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                0                2
  STAGE II              28               94
  STAGE III             33              102
  STAGE IV              25              109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  PIK3CA MUTATED         28  35  16
  PIK3CA WILD-TYPE       88 155  41
D5V4, multiclass
          clus
vv         PIK3CA MUTATED PIK3CA WILD-TYPE
  T0+T1+T2             28               88
  T3                   35              155
  T4                   16               41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PIK3CA MUTATED    52  12  12   0
  PIK3CA WILD-TYPE 173  34  63   8
D5V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             52              173
  N1             12               34
  N2             12               63
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    42   1
  PIK3CA WILD-TYPE 147  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     42    1
  PIK3CA WILD-TYPE  147   10
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             42              147
  1              1               10
[1] 2 2
[1] FALSE
D5V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    22  64
  PIK3CA WILD-TYPE  80 229
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     22   64
  PIK3CA WILD-TYPE   80  229
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             22               80
  MALE               64              229
[1] 2 2
[1] FALSE
D5V8, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    81   2
  PIK3CA WILD-TYPE 269  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     81    2
  PIK3CA WILD-TYPE  269   18
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              81              269
  YES              2               18
[1] 2 2
[1] FALSE
D5V9, continuous
D5V10, continuous
D5V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED       5                         3    76
  PIK3CA WILD-TYPE    34                        19   241
D5V12, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                  5               34
  BLACK OR AFRICAN AMERICAN              3               19
  WHITE                                 76              241
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     2  75
  PIK3CA WILD-TYPE   6 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      2   75
  PIK3CA WILD-TYPE    6  280
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  2                6
  NOT HISPANIC OR LATINO             75              280
[1] 2 2
[1] FALSE

Clustering(6) Variable = RHOB MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  RHOB MUTATED    13  13
  RHOB WILD-TYPE 204 162
  RHOB MUTATED RHOB WILD-TYPE 
            26            366 
  RHOB MUTATED RHOB WILD-TYPE 
            13            162 
$`RHOB MUTATED`
TCGA-BT-A20N TCGA-BT-A3PJ TCGA-DK-A3X1 TCGA-FD-A3SL TCGA-FD-A6TB TCGA-FJ-A3ZF 
       26.14        25.94        66.05        23.41        18.81        17.23 
TCGA-HQ-A5ND TCGA-K4-A4AC TCGA-XF-A9SK TCGA-ZF-A9R4 TCGA-4Z-AA7O TCGA-4Z-AA86 
        9.01         9.14        15.98        30.28        16.83        10.22 
TCGA-4Z-AA87 TCGA-DK-A3IL TCGA-E5-A2PC TCGA-E7-A5KF TCGA-E7-A97Q TCGA-G2-AA3F 
       47.80        13.58        43.59         0.66         8.09        29.36 
TCGA-KQ-A41R TCGA-UY-A78M TCGA-UY-A9PF TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-AA4U 
       44.38        22.68         3.85        22.36        31.20         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA52 
       60.16        35.41 

$`RHOB WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
       14.89         8.35        20.48         9.96        28.70         8.98 
TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        2.04        18.58        12.92         4.90        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       13.58         2.14        19.00        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       87.32         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
        9.67        17.98        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       15.68        50.70        36.66        38.24        52.01       165.73 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
      166.03        13.64        13.64        56.15        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       15.35        25.58         0.92         1.22        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
       60.66        24.30        17.98        29.16        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       12.85        27.35         3.62        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
        5.69         8.25        18.08        58.92         6.28        62.86 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.15        12.69        12.36         3.06         4.31         9.67 
TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM 
       31.07        11.08        33.01        17.62        70.32        21.40 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP 
       19.13        17.75        24.92        10.92        32.78        32.98 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       19.82        20.28        27.35         8.58        19.07        22.72 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
       25.02         3.45         2.76        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       35.97        46.98        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
       51.32         3.22        34.45        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.10        13.74        10.82        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       86.30        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       94.29         3.48        88.87        34.06        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       44.94        17.16        34.98        27.62        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       41.75        51.16        66.54         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50         5.06        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        8.25        17.16        16.18         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         1.94         2.93        23.01        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.00        12.10        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        1.84        21.86        66.41        18.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
        8.15        20.81        10.55       163.30        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3X6 
       18.81        19.00        15.35        12.03        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A677 
        5.36        22.16         2.24        16.70         0.56        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN 
       26.24         4.24        24.03        24.66        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       12.95        14.37        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
       20.91        19.33         5.36        27.45         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       13.35         2.27        10.85        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25        22.88        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 
       59.31         7.23        20.12        66.02         6.94        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91        14.07         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
       38.60        64.01        12.16        21.24         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S 
       17.72         1.81        15.42        16.27        11.80         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       15.32        15.58        13.48        12.23        16.67        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       38.99        17.62        37.05        76.01        69.34        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       29.56        17.82         6.21         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        79.66        66.41         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       16.27        92.98       110.60         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 
       56.48        27.06        75.39         0.66        11.97        25.41 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       35.84        21.86        28.41        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 
       47.84        20.22         2.89        59.38        67.20        56.35 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21        29.49         5.52        10.65 

  RHOB MUTATED RHOB WILD-TYPE 
          0.66           0.56 
  RHOB MUTATED RHOB WILD-TYPE 
         66.05         166.03 
  RHOB MUTATED RHOB WILD-TYPE 
         22.52          17.59 
[1] "0.7 - 66.0 (22.5)"  "0.6 - 166.0 (17.6)"
[1] "hr=" "1.1"
D6V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RHOB MUTATED         0        6        10       10
  RHOB WILD-TYPE       2      116       125      124
D6V3, multiclass
           clus
vv          RHOB MUTATED RHOB WILD-TYPE
  STAGE I              0              2
  STAGE II             6            116
  STAGE III           10            125
  STAGE IV            10            124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  RHOB MUTATED          8  13   4
  RHOB WILD-TYPE      108 177  53
D6V4, multiclass
          clus
vv         RHOB MUTATED RHOB WILD-TYPE
  T0+T1+T2            8            108
  T3                 13            177
  T4                  4             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RHOB MUTATED    11   5   4   1
  RHOB WILD-TYPE 214  41  71   7
D6V5, multiclass
    clus
vv   RHOB MUTATED RHOB WILD-TYPE
  N0           11            214
  N1            5             41
  N2            4             71
  N3            1              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"
D6V6, binary
                cls
clus               0   1
  RHOB MUTATED    13   1
  RHOB WILD-TYPE 176  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOB MUTATED     13    1
  RHOB WILD-TYPE  176   10
   clus
vv  RHOB MUTATED RHOB WILD-TYPE
  0           13            176
  1            1             10
[1] 2 2
[1] FALSE
D6V7, binary
                cls
clus               0   1
  RHOB MUTATED     7  19
  RHOB WILD-TYPE  95 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOB MUTATED      7   19
  RHOB WILD-TYPE   95  274
        clus
vv       RHOB MUTATED RHOB WILD-TYPE
  FEMALE            7             95
  MALE             19            274
[1] 2 2
[1] FALSE
D6V8, binary
                cls
clus               0   1
  RHOB MUTATED    22   1
  RHOB WILD-TYPE 328  19
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOB MUTATED     22    1
  RHOB WILD-TYPE  328   19
     clus
vv    RHOB MUTATED RHOB WILD-TYPE
  NO            22            328
  YES            1             19
[1] 2 2
[1] FALSE
D6V9, continuous
D6V10, continuous
D6V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RHOB MUTATED       2                         3    19
  RHOB WILD-TYPE    37                        19   298
D6V12, multiclass
                           clus
vv                          RHOB MUTATED RHOB WILD-TYPE
  ASIAN                                2             37
  BLACK OR AFRICAN AMERICAN            3             19
  WHITE                               19            298
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, binary
                cls
clus               0   1
  RHOB MUTATED     0  21
  RHOB WILD-TYPE   8 334
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOB MUTATED      0   21
  RHOB WILD-TYPE    8  334
                        clus
vv                       RHOB MUTATED RHOB WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           21            334
[1] 2 2
[1] FALSE

Clustering(7) Variable = KDM6A MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED    59  43
  KDM6A WILD-TYPE 158 132
  KDM6A MUTATED KDM6A WILD-TYPE 
            102             290 
  KDM6A MUTATED KDM6A WILD-TYPE 
             43             132 
$`KDM6A MUTATED`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A2LD 
       16.77        15.12        33.83        12.39        14.89        20.48 
TCGA-CU-A3KJ TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IS 
       18.48        19.00        16.70       130.88        87.32        50.27 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6W TCGA-DK-AA77 TCGA-E7-A7DU TCGA-FD-A3SJ 
       76.60        50.70        13.64        20.32         0.92        24.30 
TCGA-FD-A3SL TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A6TA 
       23.41        27.35         3.62         5.69        18.08        62.86 
TCGA-FD-A6TC TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3QF 
        6.15        33.01        70.32        10.92        32.98        20.28 
TCGA-GV-A6ZA TCGA-K4-A4AB TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-XF-A9SJ 
       22.72         2.76        52.73        50.56        35.97         3.22 
TCGA-XF-A9T0 TCGA-XF-AAN2 TCGA-ZF-A9R2 TCGA-ZF-A9RE TCGA-ZF-AA53 TCGA-2F-A9KP 
       26.27        61.45        21.11         3.48        57.90        11.97 
TCGA-4Z-AA7W TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-BT-A0S7 TCGA-BT-A2LB TCGA-BT-A3PH 
       27.62        51.16        66.54         6.58        16.18         4.67 
TCGA-CF-A1HS TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-DK-A1A3 TCGA-DK-A1A6 
       12.56        12.10        12.26        13.12        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-AA6P TCGA-DK-AA6X 
       18.41        17.62        15.62         7.79        15.02        15.35 
TCGA-E5-A2PC TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
       43.59        16.70         0.66        26.24         4.24        24.03 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3N5 
       13.68        14.07        12.95         8.09         8.94        22.52 
TCGA-FD-A5BV TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        5.36        10.65         8.94        15.95        26.93        59.31 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3RC TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42R 
       66.02         6.94        15.91        26.70         2.20        18.97 
TCGA-GU-AATQ TCGA-GV-A3QH TCGA-KQ-A41R TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HH 
        7.00         8.48        44.38        17.82         3.85         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-AAMG TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-ZF-A9R0 
       17.88        64.80       110.60         6.77        56.48        22.36 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-AA51 TCGA-ZF-AA56 
       31.20        35.84        13.41        58.72        56.35         8.52 

$`KDM6A WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A3PK 
      108.95        16.27        26.14         8.35        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ 
       15.12        13.58         2.14        46.68         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       21.30        23.21         9.67        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       53.29        67.36        15.68        36.66        38.24        52.01 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A4TZ 
      165.73       166.03        13.64        56.15        11.18        15.35 
TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SM 
       25.58         1.22        33.04         4.01        60.66        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A5BR TCGA-FD-A5BS 
       29.16        46.78        19.79        12.85        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TD 
       10.78         8.25        58.92         6.28        18.81        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.36         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       11.08        17.62        21.40        19.13        17.75        24.92 
TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND 
       32.78        19.82        27.35         8.58        19.07         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41Q TCGA-R3-A69X 
       25.02         3.45         9.14        27.68        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SK TCGA-XF-A9SM 
        1.84        33.14        86.83        51.32        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 
       14.93         4.21        12.76        11.90        21.04        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
        2.24        66.64         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63        71.57        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       30.94        86.30        18.58         3.88         9.63        13.64 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA5P 
       30.28        94.29        88.87        34.06        19.69        12.23 
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O 
       24.13        94.88       104.65         8.35        44.94        16.83 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA86 
       17.16        34.98        50.04         0.62        41.75        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A42B 
        5.06        14.96         5.06         8.25        17.16        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR 
       36.43        28.41         1.94         2.93        23.01        12.79 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.66        12.46        12.62        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1AD TCGA-DK-A1AE 
       13.08         5.19        29.79         1.84       112.44        16.14 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW 
       17.95       142.78         4.80        13.58         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA76 
       10.55       163.30        13.58        18.81        19.00        12.03 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE 
       38.83        29.72         5.36        22.16         2.24         0.56 
TCGA-E7-A677 TCGA-E7-A6MF TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 
       26.96        24.66        14.37        32.02        16.77        12.62 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       27.98         5.52        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF 
       19.33        27.45         2.70         7.10        13.35         2.27 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.85        12.66         3.25        22.88        61.94        48.00 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD 
        7.23        20.12        29.36        20.71        15.81        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q 
        8.94        13.91         2.10         3.12        20.98        11.31 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW 
        7.63        20.05        15.78         4.73        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.10        36.49         1.51        19.40        38.60        64.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       12.16        21.24         9.07        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       15.42        16.27        11.80         1.15        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       13.48        12.23        16.67        16.54        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       37.05        22.68        76.01        69.34        35.24        29.56 
TCGA-UY-A9PE TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
        6.21        48.62        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN4 
       28.24        16.27        92.98         2.96         8.32        27.06 
TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       75.39         0.66        11.97        25.41        21.86        28.41 
TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       64.08        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       60.16        67.20        35.41        19.40        54.21        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  KDM6A MUTATED KDM6A WILD-TYPE 
           0.66            0.56 
  KDM6A MUTATED KDM6A WILD-TYPE 
         130.88          166.03 
  KDM6A MUTATED KDM6A WILD-TYPE 
          17.98           17.49 
[1] "0.7 - 130.9 (18.0)" "0.6 - 166.0 (17.5)"
[1] "hr=" "1.1"
D7V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KDM6A MUTATED         0       33        30       40
  KDM6A WILD-TYPE       2       89       105       94
D7V3, multiclass
           clus
vv          KDM6A MUTATED KDM6A WILD-TYPE
  STAGE I               0               2
  STAGE II             33              89
  STAGE III            30             105
  STAGE IV             40              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  KDM6A MUTATED         34  48  14
  KDM6A WILD-TYPE       82 142  43
D7V4, multiclass
          clus
vv         KDM6A MUTATED KDM6A WILD-TYPE
  T0+T1+T2            34              82
  T3                  48             142
  T4                  14              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KDM6A MUTATED    53  12  23   4
  KDM6A WILD-TYPE 172  34  52   4
D7V5, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  N0            53             172
  N1            12              34
  N2            23              52
  N3             4               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                 cls
clus                0   1
  KDM6A MUTATED    59   4
  KDM6A WILD-TYPE 130   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     59    4
  KDM6A WILD-TYPE  130    7
   clus
vv  KDM6A MUTATED KDM6A WILD-TYPE
  0            59             130
  1             4               7
[1] 2 2
[1] FALSE
D7V7, binary
                 cls
clus                0   1
  KDM6A MUTATED    27  76
  KDM6A WILD-TYPE  75 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     27   76
  KDM6A WILD-TYPE   75  217
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE            27              75
  MALE              76             217
[1] 2 2
[1] FALSE
D7V8, binary
                 cls
clus                0   1
  KDM6A MUTATED    96   3
  KDM6A WILD-TYPE 254  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     96    3
  KDM6A WILD-TYPE  254   17
     clus
vv    KDM6A MUTATED KDM6A WILD-TYPE
  NO             96             254
  YES             3              17
[1] 2 2
[1] FALSE
D7V9, continuous
D7V10, continuous
D7V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED      11                         6    85
  KDM6A WILD-TYPE    28                        16   232
D7V12, multiclass
                           clus
vv                          KDM6A MUTATED KDM6A WILD-TYPE
  ASIAN                                11              28
  BLACK OR AFRICAN AMERICAN             6              16
  WHITE                                85             232
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, binary
                 cls
clus                0   1
  KDM6A MUTATED     1  93
  KDM6A WILD-TYPE   7 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      1   93
  KDM6A WILD-TYPE    7  262
                        clus
vv                       KDM6A MUTATED KDM6A WILD-TYPE
  HISPANIC OR LATINO                 1               7
  NOT HISPANIC OR LATINO            93             262
[1] 2 2
[1] FALSE

Clustering(8) Variable = CDKN2A MUTATION ANALYSIS
D8V1, survival
                  sevent
clus2                0   1
  CDKN2A MUTATED    14  12
  CDKN2A WILD-TYPE 203 163
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              26              366 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              12              163 
$`CDKN2A MUTATED`
TCGA-4Z-AA84 TCGA-DK-A3X1 TCGA-DK-A6B6 TCGA-DK-AA6S TCGA-FD-A6TI TCGA-G2-A2ES 
       15.12        66.05        36.66       166.03         9.67        33.01 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GV-A40E TCGA-K4-A54R TCGA-XF-A9SY TCGA-XF-AAN3 
       17.62        21.40         8.58        27.68        21.04        86.30 
TCGA-ZF-A9R4 TCGA-4Z-AA7R TCGA-DK-AA6Q TCGA-E7-A677 TCGA-E7-A7XN TCGA-FD-A5BV 
       30.28        17.16        13.58        26.96        14.07         5.36 
TCGA-G2-A2EO TCGA-GC-A6I1 TCGA-GD-A3OS TCGA-GU-A42Q TCGA-KQ-A41R TCGA-ZF-A9RD 
       59.31         8.94        20.98        11.31        44.38        13.41 
TCGA-ZF-AA4N TCGA-ZF-AA4W 
        2.89        60.16 

$`CDKN2A WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        16.77        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       23.21         9.67        17.98        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       67.36        15.68        50.70        38.24        52.01       165.73 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       13.64        13.64        56.15        11.18        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       25.58         0.92         1.22        33.04         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
       24.30        23.41        17.98        29.16        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       12.85        27.35         3.62        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
        5.69         8.25        18.08        58.92         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         3.06         4.31 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC 
       31.07        17.23        11.08        70.32        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       24.92        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
       27.35        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        2.76         9.14        52.73        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ 
       14.24         1.84        33.14        86.83        51.32         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
       15.98        34.45        14.93         4.21        12.76        11.90 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        66.64         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-XF-AAN8 
       98.99        44.32        30.94        61.45        18.58         3.88 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL 
        9.63        13.64        21.11        94.29         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       34.06        19.69        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S 
       94.88       104.65         8.35        44.94        16.83        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       10.22        47.80         2.50        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        2.66         6.74         6.58        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       17.88        19.50         5.06        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       17.16        16.18         4.67        17.56        36.43        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        1.94         2.93        23.01        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.10        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6T 
        8.15        20.81        10.55       163.30        15.02        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       19.00        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        22.16         2.24        16.70         0.56         0.66 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A85H 
       26.24         4.24        24.03        24.66        13.68        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       14.37         8.09        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       20.91        19.33        27.45         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.27        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
       22.88        61.94        48.00        15.95        26.93         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       20.12        66.02         6.94        29.36        20.71        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       15.91        14.07        13.91        26.70         2.10         3.12 
TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
        2.20        18.97         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        7.00        14.27        21.34        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       11.80         1.15        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        69.34        35.24        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        3.85         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 
      110.60         2.96         8.32         6.77        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       75.39         0.66        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       35.84        21.86        28.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       20.22         8.61        59.38        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21        29.49         5.52        10.65 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            2.89             0.56 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
          166.03           165.73 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           21.01            17.59 
[1] "2.9 - 166.0 (21.0)" "0.6 - 165.7 (17.6)"
[1] "hr=" "1.1"
D8V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CDKN2A MUTATED         0       12         7        7
  CDKN2A WILD-TYPE       2      110       128      127
D8V3, multiclass
           clus
vv          CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE I                0                2
  STAGE II              12              110
  STAGE III              7              128
  STAGE IV               7              127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  CDKN2A MUTATED          6  13   2
  CDKN2A WILD-TYPE      110 177  55
D8V4, multiclass
          clus
vv         CDKN2A MUTATED CDKN2A WILD-TYPE
  T0+T1+T2              6              110
  T3                   13              177
  T4                    2               55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CDKN2A MUTATED    14   2   4   0
  CDKN2A WILD-TYPE 211  44  71   8
D8V5, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  N0             14              211
  N1              2               44
  N2              4               71
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    11   1
  CDKN2A WILD-TYPE 178  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     11    1
  CDKN2A WILD-TYPE  178   10
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0             11              178
  1              1               10
[1] 2 2
[1] FALSE
D8V7, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     8  18
  CDKN2A WILD-TYPE  94 275
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      8   18
  CDKN2A WILD-TYPE   94  275
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE              8               94
  MALE               18              275
[1] 2 2
[1] FALSE
D8V8, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    25   1
  CDKN2A WILD-TYPE 325  19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     25    1
  CDKN2A WILD-TYPE  325   19
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO              25              325
  YES              1               19
[1] 2 2
[1] FALSE
D8V9, continuous
D8V10, continuous
D8V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED       3                         1    22
  CDKN2A WILD-TYPE    36                        21   295
D8V12, multiclass
                           clus
vv                          CDKN2A MUTATED CDKN2A WILD-TYPE
  ASIAN                                  3               36
  BLACK OR AFRICAN AMERICAN              1               21
  WHITE                                 22              295
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     0  24
  CDKN2A WILD-TYPE   8 331
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      0   24
  CDKN2A WILD-TYPE    8  331
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO             24              331
[1] 2 2
[1] FALSE

Clustering(9) Variable = ARID1A MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    51  45
  ARID1A WILD-TYPE 166 130
  ARID1A MUTATED ARID1A WILD-TYPE 
              96              296 
  ARID1A MUTATED ARID1A WILD-TYPE 
              45              130 
$`ARID1A MUTATED`
TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-CU-A0YO TCGA-CU-A3KJ 
       15.12        12.39        20.48        25.94         4.90        18.48 
TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B2 
       46.68         8.22        23.21        17.98        53.29        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA71 TCGA-E5-A4TZ TCGA-E7-A541 
       50.70       165.73        13.64        13.64        15.35        25.58 
TCGA-E7-A7DU TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TG 
        0.92        29.16        19.79        58.92         6.28         3.06 
TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-G2-AA3D TCGA-GU-A42P TCGA-GV-A3QK TCGA-GV-A6ZA 
        9.67        17.23        70.32        10.92        27.35        22.72 
TCGA-K4-A54R TCGA-KQ-A41Q TCGA-XF-A9SP TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T2 
       27.68        46.98        14.93        11.90        26.27        18.90 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAML TCGA-XF-AAN2 TCGA-YC-A8S6 TCGA-YF-AA3M 
       66.64        13.74         7.63        61.45         9.63        13.64 
TCGA-ZF-A9RC TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-5N-A9KI 
       94.29        24.13        11.97         8.35        16.83         2.50 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20Q TCGA-BT-A20R 
       40.08         7.33         6.74        13.15        19.50         5.06 
TCGA-BT-A3PH TCGA-CF-A1HR TCGA-CF-A3MG TCGA-CU-A5W6 TCGA-DK-A1AD TCGA-DK-A3IK 
        4.67        12.79        12.13         1.84       112.44         4.80 
TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA76 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A85H 
        8.15        15.02        12.03         2.24        16.70        12.95 
TCGA-FD-A3B3 TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A62O TCGA-FD-A6TK TCGA-FJ-A3Z9 
       32.02        25.74        22.98         7.10        10.85        12.66 
TCGA-FJ-A871 TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-AA3F TCGA-GC-A3RC TCGA-GD-A2C5 
        8.94        15.95        26.93        29.36        15.91        26.70 
TCGA-GU-A42R TCGA-GU-A766 TCGA-GV-A3JV TCGA-H4-A2HO TCGA-K4-A3WV TCGA-K4-A83P 
       18.97        15.78        14.27         1.51        21.24        16.27 
TCGA-LC-A66R TCGA-MV-A51V TCGA-SY-A9G5 TCGA-UY-A9PF TCGA-XF-A9SZ TCGA-XF-AAN0 
       15.32        13.48        38.99         3.85        28.24        56.48 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA5N 
       21.86        28.41        64.08        67.20        56.35         5.52 

$`ARID1A WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BT-A20N TCGA-BT-A20T 
      108.95        16.27        16.77        33.83        26.14        14.89 
TCGA-BT-A20W TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL 
        8.35         9.96        28.70         8.98         2.04        18.58 
TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       12.92        15.12        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV 
      130.88        87.32        17.72        50.27        21.30         9.67 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L 
       66.05        64.18        76.60        67.36        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6S TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A7DV 
       52.01       166.03        56.15        11.18        20.32         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       46.78        12.85        27.35         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TB 
       10.78         5.69         8.25        18.08        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A61P 
        6.15        12.69        12.36         4.31        31.07        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       33.01        17.62        21.40        19.13        17.75        24.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G 
       32.78        32.98        19.82        20.28         8.58        19.07 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41N 
        9.01        25.02         3.45         2.76         9.14        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       50.56        35.97        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SV 
       51.32         3.22        15.98        34.45         4.21        12.76 
TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       21.04         2.24         2.10        10.82        11.31        54.90 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 
       71.57        91.73        98.99        44.32        30.94        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RE TCGA-ZF-A9RL 
       18.58         3.88        21.11        30.28         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KQ TCGA-2F-A9KR 
       34.06        19.69        57.90        12.23        94.88       104.65 
TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       44.94        17.16        34.98        27.62        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM 
       41.75        51.16        66.54        10.22        47.80        17.42 
TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20U 
        2.66         6.58        19.04        12.16        17.88        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42B TCGA-BT-A42E 
        5.06         8.25        17.16        16.18        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C 
       28.41         1.94         2.93        23.01        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.59        13.08        12.16        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 
       11.87        13.08         5.19        29.79        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
       18.41        16.14        17.62        15.62        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q 
      142.78        13.58        20.81        10.55       163.30        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       18.81        19.00        15.35        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        5.36        22.16         0.56         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A97P 
        4.24        24.03        24.66        13.68        14.07        14.37 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.09        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
        5.52        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TF TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EC 
        2.70        13.35         2.27        10.65         3.25        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       61.94        48.00        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 
        6.94        20.71        15.81        14.07         8.94        13.91 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 
        2.10         3.12        20.98         2.20        11.31         7.63 
TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
       20.05         4.73         7.00        21.34        19.10         8.48 
TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A5RH 
       36.49        19.40        38.60        64.01        12.16         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R 
       11.70        17.72         1.81        15.42        11.80        44.38 
TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K 
        1.15        15.58        12.23        16.67        16.54        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       37.05        22.68        76.01        69.34        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       17.82         6.21         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-AAME 
       79.66        66.41         5.98        23.64        16.27        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-XF-AAN5 
      110.60         2.96         8.32         6.77        27.06        75.39 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       13.41        58.72        47.84        20.22         2.89         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       59.38        60.16        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-GU-AATO 
       29.49        10.65 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.92             0.56 
  ARID1A MUTATED ARID1A WILD-TYPE 
          165.73           166.03 
  ARID1A MUTATED ARID1A WILD-TYPE 
           15.93            17.85 
[1] "0.9 - 165.7 (15.9)" "0.6 - 166.0 (17.9)"
[1] "hr=" "1.1"
D9V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ARID1A MUTATED         1       28        31       36
  ARID1A WILD-TYPE       1       94       104       98
D9V3, multiclass
           clus
vv          ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                1                1
  STAGE II              28               94
  STAGE III             31              104
  STAGE IV              36               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  ARID1A MUTATED         25  49  16
  ARID1A WILD-TYPE       91 141  41
D9V4, multiclass
          clus
vv         ARID1A MUTATED ARID1A WILD-TYPE
  T0+T1+T2             25               91
  T3                   49              141
  T4                   16               41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ARID1A MUTATED    52  11  24   0
  ARID1A WILD-TYPE 173  35  51   8
D9V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  N0             52              173
  N1             11               35
  N2             24               51
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                  cls
clus                 0   1
  ARID1A MUTATED    49   2
  ARID1A WILD-TYPE 140   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     49    2
  ARID1A WILD-TYPE  140    9
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             49              140
  1              2                9
[1] 2 2
[1] FALSE
D9V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED    20  77
  ARID1A WILD-TYPE  82 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     20   77
  ARID1A WILD-TYPE   82  216
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE             20               82
  MALE               77              216
[1] 2 2
[1] FALSE
D9V8, binary
                  cls
clus                 0   1
  ARID1A MUTATED    89   3
  ARID1A WILD-TYPE 261  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     89    3
  ARID1A WILD-TYPE  261   17
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO              89              261
  YES              3               17
[1] 2 2
[1] FALSE
D9V9, continuous
D9V10, continuous
D9V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED       4                         1    91
  ARID1A WILD-TYPE    35                        21   226
D9V12, multiclass
                           clus
vv                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                  4               35
  BLACK OR AFRICAN AMERICAN              1               21
  WHITE                                 91              226
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, binary
                  cls
clus                 0   1
  ARID1A MUTATED     3  91
  ARID1A WILD-TYPE   5 264
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      3   91
  ARID1A WILD-TYPE    5  264
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  3                5
  NOT HISPANIC OR LATINO             91              264
[1] 2 2
[1] FALSE

Clustering(10) Variable = STAG2 MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2               0   1
  STAG2 MUTATED    38  18
  STAG2 WILD-TYPE 179 157
  STAG2 MUTATED STAG2 WILD-TYPE 
             56             336 
  STAG2 MUTATED STAG2 WILD-TYPE 
             18             157 
$`STAG2 MUTATED`
TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A3IS TCGA-DK-A3X2 
       15.12        33.83        13.58        19.00        50.27        17.98 
TCGA-DK-A6AW TCGA-DK-AA71 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3NA TCGA-FD-A3SL 
       53.29        13.64         0.92         1.22        60.66        23.41 
TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A5BX TCGA-FD-A6TA TCGA-G2-AA3D TCGA-KQ-A41O 
       17.98        46.78         5.69        62.86        70.32        50.56 
TCGA-R3-A69X TCGA-XF-A9ST TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-YC-A8S6 TCGA-ZF-A9RE 
       14.24         4.21        18.90         2.24         9.63         3.48 
TCGA-ZF-AA53 TCGA-4Z-AA7R TCGA-BL-A13J TCGA-BT-A42E TCGA-CF-A27C TCGA-CF-A3MI 
       57.90        17.16         2.66        36.43        13.97        12.16 
TCGA-CF-A47W TCGA-CF-A5U8 TCGA-DK-A1AF TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       12.10        13.12        17.62        43.59         5.36        22.16 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A97P 
       16.70         0.66        26.24         4.24        24.03        14.37 
TCGA-FD-A3B5 TCGA-FJ-A3ZE TCGA-GD-A6C6 TCGA-H4-A2HQ TCGA-K4-A83P TCGA-KQ-A41R 
        8.94        10.65         2.20        19.40        16.27        44.38 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-UY-A78M TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-AAN5 
       13.48        12.23        22.68        17.88        79.66        75.39 
TCGA-ZF-A9RD TCGA-ZF-A9RG 
       13.41        58.72 

$`STAG2 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
      108.95        16.27        16.77        12.39        26.14        14.89 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
        8.35        20.48        25.94         9.96        28.70         8.98 
TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        2.04        18.58        12.92         4.90        15.12        18.48 
TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN 
        2.14        16.70       130.88        46.68        87.32         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV 
       17.72        21.30        23.21         9.67        66.05        64.18 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA75 
       52.01       165.73       166.03        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ 
       20.32        15.35        25.58        33.04         4.01        24.30 
TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       29.16        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       53.88        10.78         8.25        18.08        58.92         6.28 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         3.06         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY 
        9.67        31.07        17.23        11.08        33.01        17.62 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 
       21.40        19.13        17.75        24.92        10.92        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       32.98        19.82        20.28        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       22.72         9.01        25.02         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-S5-A6DX TCGA-SY-A9G0 
       27.68        52.73        35.97        46.98         1.84        33.14 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       86.83        51.32         3.22        15.98        34.45        14.93 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-A9T6 
       12.76        11.90        21.04        26.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       13.74        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       18.58         3.88        13.64        21.11        30.28        94.29 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       88.87        34.06        19.69        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S 
       94.88       104.65         8.35        44.94        16.83        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       10.22        47.80         2.50        17.42        40.08         7.33 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 
       16.18         4.67        17.56        28.41         1.94         2.93 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       23.01        12.79        12.56        12.59        12.13        13.08 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5UA 
       10.95        12.66        12.46        12.62        12.26        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.10        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AG 
       21.86        66.41        18.41       112.44        16.14        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       17.95         7.79       142.78         4.80        13.58         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4XJ 
       19.00        15.35        12.03        38.83        29.72         2.24 
TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
        0.56        26.96        24.66        13.68        14.07        12.95 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.09        32.02        16.77        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
        5.52        25.74        22.98        14.96        20.91        19.33 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF 
        5.36        27.45         2.70         7.10        13.35         2.27 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
       10.85        12.66         8.94         3.25        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       48.00        15.95        26.93        59.31         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       66.02         6.94        29.36        20.71        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07         8.94        13.91        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
       20.98        11.31        18.97         7.63        20.05        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
        4.73         7.00        14.27        21.34        19.10         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
       36.49         1.51        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO 
        9.07        11.70        17.72         1.81        15.42        11.80 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
        1.15        15.32        15.58        16.67        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       17.62        37.05        76.01        69.34        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH 
       17.82         6.21         3.85         1.87        48.62        64.80 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 
      110.60         2.96         8.32         6.77        56.48        27.06 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       21.86        28.41        64.08        47.84        20.22         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21        29.49         5.52        10.65 

  STAG2 MUTATED STAG2 WILD-TYPE 
           0.66            0.56 
  STAG2 MUTATED STAG2 WILD-TYPE 
          79.66          166.03 
  STAG2 MUTATED STAG2 WILD-TYPE 
          16.93           17.72 
[1] "0.7 - 79.7 (16.9)"  "0.6 - 166.0 (17.7)"
[1] "hr=" "1.4"
D10V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  STAG2 MUTATED         0       19        12       25
  STAG2 WILD-TYPE       2      103       123      109
D10V3, multiclass
           clus
vv          STAG2 MUTATED STAG2 WILD-TYPE
  STAGE I               0               2
  STAGE II             19             103
  STAGE III            12             123
  STAGE IV             25             109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  STAG2 MUTATED         21  24   7
  STAG2 WILD-TYPE       95 166  50
D10V4, multiclass
          clus
vv         STAG2 MUTATED STAG2 WILD-TYPE
  T0+T1+T2            21              95
  T3                  24             166
  T4                   7              50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  STAG2 MUTATED    27   6  14   2
  STAG2 WILD-TYPE 198  40  61   6
D10V5, multiclass
    clus
vv   STAG2 MUTATED STAG2 WILD-TYPE
  N0            27             198
  N1             6              40
  N2            14              61
  N3             2               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                 cls
clus                0   1
  STAG2 MUTATED    29   5
  STAG2 WILD-TYPE 160   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED     29    5
  STAG2 WILD-TYPE  160    6
   clus
vv  STAG2 MUTATED STAG2 WILD-TYPE
  0            29             160
  1             5               6
[1] 2 2
[1] FALSE
D10V7, binary
                 cls
clus                0   1
  STAG2 MUTATED    12  44
  STAG2 WILD-TYPE  90 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED     12   44
  STAG2 WILD-TYPE   90  249
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  FEMALE            12              90
  MALE              44             249
[1] 2 2
[1] FALSE
D10V8, binary
                 cls
clus                0   1
  STAG2 MUTATED    48   4
  STAG2 WILD-TYPE 302  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED     48    4
  STAG2 WILD-TYPE  302   16
     clus
vv    STAG2 MUTATED STAG2 WILD-TYPE
  NO             48             302
  YES             4              16
[1] 2 2
[1] FALSE
D10V9, continuous
D10V10, continuous
D10V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STAG2 MUTATED      11                         3    41
  STAG2 WILD-TYPE    28                        19   276
D10V12, multiclass
                           clus
vv                          STAG2 MUTATED STAG2 WILD-TYPE
  ASIAN                                11              28
  BLACK OR AFRICAN AMERICAN             3              19
  WHITE                                41             276
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, binary
                 cls
clus                0   1
  STAG2 MUTATED     0  52
  STAG2 WILD-TYPE   8 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      0   52
  STAG2 WILD-TYPE    8  303
                        clus
vv                       STAG2 MUTATED STAG2 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            52             303
[1] 2 2
[1] FALSE

Clustering(11) Variable = ZFP36L1 MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  ZFP36L1 MUTATED    17   8
  ZFP36L1 WILD-TYPE 200 167
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
               25               367 
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
                8               167 
$`ZFP36L1 MUTATED`
TCGA-4Z-AA84 TCGA-CU-A72E TCGA-DK-A3X2 TCGA-DK-A6B6 TCGA-G2-A2ES TCGA-GC-A3WC 
       15.12        13.58        17.98        36.66        33.01        17.75 
TCGA-GU-AATP TCGA-GV-A3QF TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41P TCGA-XF-A9T6 
       32.98        20.28        27.68        52.73        35.97         2.10 
TCGA-XF-AAMR TCGA-BT-A20R TCGA-CF-A47S TCGA-DK-A1A3 TCGA-DK-AA6P TCGA-DK-AA6T 
       91.73         5.06        10.95        21.86        15.02        18.81 
TCGA-DK-AA6U TCGA-E7-A677 TCGA-FD-A43U TCGA-G2-AA3F TCGA-K4-A83P TCGA-XF-A9SU 
       19.00        26.96        20.91        29.36        16.27         5.98 
TCGA-ZF-AA5N 
        5.52 

$`ZFP36L1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        16.77        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       18.48         2.14        19.00        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       87.32         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
        9.67        66.05        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S 
       15.68        50.70        38.24        52.01       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       13.64        13.64        56.15        11.18        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       25.58         0.92         1.22        33.04         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
       24.30        23.41        17.98        29.16        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       12.85        27.35         3.62        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
        5.69         8.25        18.08        58.92         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         3.06         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3D 
        9.67        31.07        17.23        11.08        17.62        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ 
       21.40        19.13        24.92        10.92        32.78        19.82 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X 
        3.45         2.76         9.14        50.56        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK 
        1.84        33.14        86.83        51.32         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       34.45        14.93         4.21        12.76        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMF 
       26.27        18.90         2.24        66.64        13.74        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAMZ 
       11.31        54.90         7.63        71.57        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       30.94        61.45        86.30        18.58         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL 
       13.64        21.11        30.28        94.29         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       34.06        19.69        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       34.98        27.62        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       66.54        10.22        47.80         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       12.16        17.88        19.50        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       17.16        16.18         4.67        17.56        36.43        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        1.94         2.93        23.01        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47T TCGA-CF-A47V 
       12.59        12.13        13.08        12.16        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 
       11.87        13.08         5.19        29.79         1.84        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW 
        7.79       142.78         4.80        13.58         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       10.55       163.30        13.58        15.35        12.03        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         5.36        22.16         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        26.24         4.24        24.03        24.66 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       25.74        22.98        14.96        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.70         7.10        13.35         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65         8.94         3.25        22.88        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       15.95        26.93        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 
        6.94        20.71        15.81        15.91        14.07         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91        26.70         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31        18.97         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        7.00        14.27        21.34        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO 
        9.07        11.70        17.72         1.81        15.42        11.80 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       44.38         1.15        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        69.34        35.24        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        3.85         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
       66.41        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32         6.77        56.48        27.06        75.39 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       21.86        28.41        13.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       20.22         2.89         8.61        59.38        60.16        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        19.40         8.52        54.21        29.49 
TCGA-GU-AATO 
       10.65 

  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
             2.10              0.56 
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
            91.73            166.03 
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
            19.00             17.42 
[1] "2.1 - 91.7 (19.0)"  "0.6 - 166.0 (17.4)"
[1] "hr=" "1.5"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  ZFP36L1 MUTATED         0        8         4       13
  ZFP36L1 WILD-TYPE       2      114       131      121
D11V3, multiclass
           clus
vv          ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  STAGE I                 0                 2
  STAGE II                8               114
  STAGE III               4               131
  STAGE IV               13               121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  ZFP36L1 MUTATED          5  14   2
  ZFP36L1 WILD-TYPE      111 176  55
D11V4, multiclass
          clus
vv         ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  T0+T1+T2               5               111
  T3                    14               176
  T4                     2                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  ZFP36L1 MUTATED    11   4   7   1
  ZFP36L1 WILD-TYPE 214  42  68   7
D11V5, multiclass
    clus
vv   ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  N0              11               214
  N1               4                42
  N2               7                68
  N3               1                 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"
D11V6, binary
                   cls
clus                  0   1
  ZFP36L1 MUTATED    12   3
  ZFP36L1 WILD-TYPE 177   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED     12    3
  ZFP36L1 WILD-TYPE  177    8
   clus
vv  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  0              12               177
  1               3                 8
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  ZFP36L1 MUTATED     6  19
  ZFP36L1 WILD-TYPE  96 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED      6   19
  ZFP36L1 WILD-TYPE   96  274
        clus
vv       ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  FEMALE               6                96
  MALE                19               274
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  ZFP36L1 MUTATED    21   2
  ZFP36L1 WILD-TYPE 329  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED     21    2
  ZFP36L1 WILD-TYPE  329   18
     clus
vv    ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  NO               21               329
  YES               2                18
[1] 2 2
[1] FALSE
D11V9, continuous
D11V10, continuous
D11V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZFP36L1 MUTATED       2                         1    22
  ZFP36L1 WILD-TYPE    37                        21   295
D11V12, multiclass
                           clus
vv                          ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  ASIAN                                   2                37
  BLACK OR AFRICAN AMERICAN               1                21
  WHITE                                  22               295
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, binary
                   cls
clus                  0   1
  ZFP36L1 MUTATED     0  24
  ZFP36L1 WILD-TYPE   8 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED      0   24
  ZFP36L1 WILD-TYPE    8  331
                        clus
vv                       ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              24               331
[1] 2 2
[1] FALSE

Clustering(12) Variable = CDKN1A MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2                0   1
  CDKN1A MUTATED    22  13
  CDKN1A WILD-TYPE 195 162
  CDKN1A MUTATED CDKN1A WILD-TYPE 
              35              357 
  CDKN1A MUTATED CDKN1A WILD-TYPE 
              13              162 
$`CDKN1A MUTATED`
TCGA-BT-A20T TCGA-BT-A42C TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IN TCGA-FD-A3B7 
       14.89        28.70       130.88        46.68         8.22         4.01 
TCGA-FD-A3SM TCGA-FD-A5C1 TCGA-FD-A6TC TCGA-GV-A40E TCGA-KQ-A41Q TCGA-S5-A6DX 
       17.98        58.92         6.15         8.58        46.98         1.84 
TCGA-ZF-A9R2 TCGA-ZF-A9RL TCGA-2F-A9KQ TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-5N-A9KM 
       21.11        88.87        94.88        17.16        34.98        17.42 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.56        13.97        12.59        12.13        12.10        11.87 
TCGA-CU-A3QU TCGA-DK-A2I4 TCGA-E7-A5KF TCGA-FD-A3SO TCGA-G2-A3IB TCGA-GD-A3OQ 
        5.19       142.78         0.66         5.52         7.23         3.12 
TCGA-GV-A3JX TCGA-XF-A9SG TCGA-ZF-A9R1 TCGA-ZF-A9R7 TCGA-GU-AATO 
       19.10        48.62        25.41        21.86        10.65 

$`CDKN1A WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ 
       26.14         8.35        20.48        25.94         9.96         8.98 
TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        2.04        18.58        12.92         4.90        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2I6 TCGA-DK-A3IQ 
       13.58         2.14        19.00        16.70        87.32        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
       50.27        21.30        23.21         9.67        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        53.29        76.60        67.36        15.68        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       36.66        38.24        52.01       165.73       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 
       13.64        56.15        11.18        20.32        15.35        25.58 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        0.92         1.22        33.04        60.66        24.30        23.41 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       29.16        46.78        19.79        12.85        27.35         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
        6.28        62.86        18.81        12.69        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        4.31         9.67        31.07        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       17.62        70.32        21.40        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       10.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       19.07        22.72         9.01        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-R3-A69X 
        9.14        27.68        52.73        50.56        35.97        14.24 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
       33.14        86.83        51.32         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       14.93         4.21        12.76        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       18.90         2.24        66.64         2.10        13.74        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       11.31        54.90         7.63        71.57        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 
       44.32        30.94        61.45        86.30        18.58         3.88 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R 
        9.63        13.64        30.28        94.29         3.48        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR 
       19.69        57.90        12.23        24.13        11.97       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
        8.35        44.94        16.83        27.62        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
       41.75        51.16        66.54        10.22        47.80         2.50 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       19.04        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
        5.06         8.25        17.16        16.18         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR 
       36.43        28.41         1.94         2.93        23.01        12.79 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A9FM TCGA-CU-A3YL 
       12.62        12.26        13.12        12.00        13.08        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        1.84        21.86        66.41        18.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL 
       17.62        15.62        17.95         7.79         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
        8.15        20.81        10.55       163.30        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       18.81        19.00        15.35        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        22.16         2.24        16.70         0.56 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
       26.96        26.24         4.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FD-A43N 
        8.94        12.62        22.52        27.98        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       14.96        20.91        19.33         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        7.10        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        8.94         3.25        22.88        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       26.93        59.31        20.12        66.02         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 
       20.71        15.81        15.91        14.07         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
       26.70         2.10        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       21.34         8.48        36.49         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       64.01        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
        1.81        15.42        16.27        11.80        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       15.32        15.58        13.48        12.23        16.67        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       38.99        17.62        37.05        22.68        76.01        69.34 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       35.24        29.56        17.82         6.21         3.85         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       17.88        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW 
       28.24        16.27        92.98       110.60         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L 
        6.77        56.48        27.06        75.39         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       22.36        31.20        35.84        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       58.72        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        67.20        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       54.21        29.49         5.52 

  CDKN1A MUTATED CDKN1A WILD-TYPE 
            0.66             0.56 
  CDKN1A MUTATED CDKN1A WILD-TYPE 
          142.78           166.03 
  CDKN1A MUTATED CDKN1A WILD-TYPE 
           14.89            17.72 
[1] "0.7 - 142.8 (14.9)" "0.6 - 166.0 (17.7)"
[1] "hr=" "1.2"
D12V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CDKN1A MUTATED         0       11        14       10
  CDKN1A WILD-TYPE       2      111       121      124
D12V3, multiclass
           clus
vv          CDKN1A MUTATED CDKN1A WILD-TYPE
  STAGE I                0                2
  STAGE II              11              111
  STAGE III             14              121
  STAGE IV              10              124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  CDKN1A MUTATED          7  15   8
  CDKN1A WILD-TYPE      109 175  49
D12V4, multiclass
          clus
vv         CDKN1A MUTATED CDKN1A WILD-TYPE
  T0+T1+T2              7              109
  T3                   15              175
  T4                    8               49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CDKN1A MUTATED    22   5   4   0
  CDKN1A WILD-TYPE 203  41  71   8
D12V5, multiclass
    clus
vv   CDKN1A MUTATED CDKN1A WILD-TYPE
  N0             22              203
  N1              5               41
  N2              4               71
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                  cls
clus                 0   1
  CDKN1A MUTATED    20   1
  CDKN1A WILD-TYPE 169  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN1A MUTATED     20    1
  CDKN1A WILD-TYPE  169   10
   clus
vv  CDKN1A MUTATED CDKN1A WILD-TYPE
  0             20              169
  1              1               10
[1] 2 2
[1] FALSE
D12V7, binary
                  cls
clus                 0   1
  CDKN1A MUTATED     6  29
  CDKN1A WILD-TYPE  96 264
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN1A MUTATED      6   29
  CDKN1A WILD-TYPE   96  264
        clus
vv       CDKN1A MUTATED CDKN1A WILD-TYPE
  FEMALE              6               96
  MALE               29              264
[1] 2 2
[1] FALSE
D12V8, binary
                  cls
clus                 0   1
  CDKN1A MUTATED    30   2
  CDKN1A WILD-TYPE 320  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN1A MUTATED     30    2
  CDKN1A WILD-TYPE  320   18
     clus
vv    CDKN1A MUTATED CDKN1A WILD-TYPE
  NO              30              320
  YES              2               18
[1] 2 2
[1] FALSE
D12V9, continuous
D12V10, continuous
D12V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN1A MUTATED       7                         4    23
  CDKN1A WILD-TYPE    32                        18   294
D12V12, multiclass
                           clus
vv                          CDKN1A MUTATED CDKN1A WILD-TYPE
  ASIAN                                  7               32
  BLACK OR AFRICAN AMERICAN              4               18
  WHITE                                 23              294
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V13, binary
                  cls
clus                 0   1
  CDKN1A MUTATED     1  31
  CDKN1A WILD-TYPE   7 324
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN1A MUTATED      1   31
  CDKN1A WILD-TYPE    7  324
                        clus
vv                       CDKN1A MUTATED CDKN1A WILD-TYPE
  HISPANIC OR LATINO                  1                7
  NOT HISPANIC OR LATINO             31              324
[1] 2 2
[1] FALSE

Clustering(13) Variable = EP300 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  EP300 MUTATED    40  21
  EP300 WILD-TYPE 177 154
  EP300 MUTATED EP300 WILD-TYPE 
             61             331 
  EP300 MUTATED EP300 WILD-TYPE 
             21             154 
$`EP300 MUTATED`
TCGA-BT-A3PK TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A2I6 TCGA-DK-A6AW 
        9.96        15.12        18.48         2.14        87.32        53.29 
TCGA-DK-AA6M TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA77 TCGA-E7-A7DV TCGA-FD-A3SM 
       52.01        13.64        13.64        20.32         1.22        17.98 
TCGA-FD-A5C0 TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-GC-A3BM 
       18.08        12.36         3.06        17.23        11.08        21.40 
TCGA-GC-A3RB TCGA-GU-AATP TCGA-GV-A3JZ TCGA-K4-A54R TCGA-R3-A69X TCGA-XF-A9SM 
       19.13        32.98        19.82        27.68        14.24        34.45 
TCGA-XF-A9SY TCGA-XF-A9T5 TCGA-XF-AAN2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-2F-A9KR 
       21.04        66.64        61.45        30.28        94.29       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH 
        8.35        50.04        41.75         8.25        16.18         4.67 
TCGA-CF-A47Y TCGA-DK-A1A7 TCGA-DK-A2I4 TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-AA6U 
       12.26        18.41       142.78        20.81        10.55        19.00 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A7XN TCGA-E7-A97Q TCGA-FD-A3B8 TCGA-FD-A3SO 
       26.24         4.24        14.07         8.09        12.62         5.52 
TCGA-FD-A62S TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-GD-A3OQ TCGA-GV-A3JX TCGA-UY-A9PB 
       13.35        48.00        26.93         3.12        19.10        29.56 
TCGA-UY-A9PE TCGA-XF-A9SI TCGA-XF-A9SX TCGA-ZF-A9R5 TCGA-ZF-AA4V TCGA-ZF-AA51 
        6.21        79.66        23.64        35.84        59.38        56.35 
TCGA-ZF-AA58 
       54.21 

$`EP300 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C 
       26.14        14.89         8.35        20.48        25.94        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A72E 
        8.98         2.04        18.58        12.92         4.90        13.58 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ 
       19.00        16.70       130.88        46.68         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
       50.27        21.30        23.21         9.67        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       64.18        76.60        67.36        15.68        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A4TZ 
       38.24       165.73       166.03        56.15        11.18        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
       25.58         0.92        33.04         4.01        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       23.41        29.16        46.78        19.79        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
        3.62        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D 
        4.31         9.67        31.07        33.01        17.62        70.32 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3QF TCGA-GV-A3QK 
       17.75        24.92        10.92        32.78        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        8.58        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        2.76         9.14        52.73        50.56        35.97        46.98 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK 
        1.84        33.14        86.83        51.32         3.22        15.98 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T2 
       14.93         4.21        12.76        11.90        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.24         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
        7.63        71.57        91.73        98.99        44.32        30.94 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       86.30        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.48        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       24.13        11.97        94.88        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       34.98        27.62         0.62        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A42B 
       19.50         5.06        14.96         5.06        17.16        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR 
       36.43        28.41         1.94         2.93        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.56        13.97        12.59        12.13        13.08        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A5U8 
       10.95        12.66        12.46        12.10        12.62        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.00        12.10        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
        1.84        21.86        66.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       15.62        17.95         7.79         4.80        13.58         8.15 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA76 
      163.30        15.02        13.58        18.81        15.35        12.03 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        38.83        29.72         5.36        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A6ME TCGA-E7-A6MF 
       16.70         0.56         0.66        26.96        24.03        24.66 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       13.68        12.95        14.37        32.02        16.77         8.94 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       22.52        27.98        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TF 
       19.33         5.36        27.45         2.70         7.10         2.27 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC 
       10.85        12.66        10.65         8.94         3.25        22.88 
TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       61.94        15.95        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        29.36        20.71        15.81        15.91        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 
        8.94        13.91        26.70         2.10        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31        18.97         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
        7.00        14.27        21.34         8.48        36.49         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
       19.40        38.60        64.01        12.16        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70        17.72         1.81        15.42        16.27        11.80 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       44.38         1.15        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HH 
       76.01        69.34        35.24        17.82         3.85         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SZ 
       17.88        48.62        64.80        66.41         5.98        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       16.27        92.98       110.60         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
       56.48        27.06        75.39         0.66        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       25.41        31.20        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W 
       58.72        47.84        20.22         2.89         8.61        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       67.20        35.41        19.40         8.52        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  EP300 MUTATED EP300 WILD-TYPE 
           1.22            0.56 
  EP300 MUTATED EP300 WILD-TYPE 
         142.78          166.03 
  EP300 MUTATED EP300 WILD-TYPE 
          19.10           17.16 
[1] "1.2 - 142.8 (19.1)" "0.6 - 166.0 (17.2)"
[1] "hr=" "1.5"
D13V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  EP300 MUTATED         0       20        19       22
  EP300 WILD-TYPE       2      102       116      112
D13V3, multiclass
           clus
vv          EP300 MUTATED EP300 WILD-TYPE
  STAGE I               0               2
  STAGE II             20             102
  STAGE III            19             116
  STAGE IV             22             112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  EP300 MUTATED         21  30   6
  EP300 WILD-TYPE       95 160  51
D13V4, multiclass
          clus
vv         EP300 MUTATED EP300 WILD-TYPE
  T0+T1+T2            21              95
  T3                  30             160
  T4                   6              51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EP300 MUTATED    37   5  14   3
  EP300 WILD-TYPE 188  41  61   5
D13V5, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  N0            37             188
  N1             5              41
  N2            14              61
  N3             3               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                 cls
clus                0   1
  EP300 MUTATED    33   1
  EP300 WILD-TYPE 156  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     33    1
  EP300 WILD-TYPE  156   10
   clus
vv  EP300 MUTATED EP300 WILD-TYPE
  0            33             156
  1             1              10
[1] 2 2
[1] FALSE
D13V7, binary
                 cls
clus                0   1
  EP300 MUTATED    15  46
  EP300 WILD-TYPE  87 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     15   46
  EP300 WILD-TYPE   87  247
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  FEMALE            15              87
  MALE              46             247
[1] 2 2
[1] FALSE
D13V8, binary
                 cls
clus                0   1
  EP300 MUTATED    58   1
  EP300 WILD-TYPE 292  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     58    1
  EP300 WILD-TYPE  292   19
     clus
vv    EP300 MUTATED EP300 WILD-TYPE
  NO             58             292
  YES             1              19
[1] 2 2
[1] FALSE
D13V9, continuous
D13V10, continuous
D13V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EP300 MUTATED       4                         1    55
  EP300 WILD-TYPE    35                        21   262
D13V12, multiclass
                           clus
vv                          EP300 MUTATED EP300 WILD-TYPE
  ASIAN                                 4              35
  BLACK OR AFRICAN AMERICAN             1              21
  WHITE                                55             262
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V13, binary
                 cls
clus                0   1
  EP300 MUTATED     1  57
  EP300 WILD-TYPE   7 298
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      1   57
  EP300 WILD-TYPE    7  298
                        clus
vv                       EP300 MUTATED EP300 WILD-TYPE
  HISPANIC OR LATINO                 1               7
  NOT HISPANIC OR LATINO            57             298
[1] 2 2
[1] FALSE

Clustering(14) Variable = MLL2 MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  MLL2 MUTATED    66  48
  MLL2 WILD-TYPE 151 127
  MLL2 MUTATED MLL2 WILD-TYPE 
           114            278 
  MLL2 MUTATED MLL2 WILD-TYPE 
            48            127 
$`MLL2 MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A3PJ 
       16.27        16.77        15.12        12.39        26.14        25.94 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-DK-A1AC TCGA-DK-A3IT 
        9.96        28.70         2.04        18.58       130.88        21.30 
TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B6 TCGA-DK-AA6M 
       23.21        66.05        64.18        53.29        36.66        52.01 
TCGA-DK-AA6S TCGA-DK-AA71 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A5BX TCGA-FD-A62P 
      166.03        13.64        23.41        17.98         5.69         6.28 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB 
        6.15        12.36         4.31        17.62        21.40        19.13 
TCGA-GC-A3WC TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND 
       17.75        32.78        32.98         8.58        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A54R TCGA-S5-A6DX TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK 
       25.02        27.68         1.84        51.32         3.22        15.98 
TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMJ TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       18.90        66.64        13.74        54.90        30.28        94.29 
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA81 
       24.13       104.65        16.83        17.16         0.62        41.75 
TCGA-BT-A0YX TCGA-BT-A20X TCGA-BT-A42B TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A47T 
       13.15         8.25        17.56         2.93        23.01        12.66 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A3IM 
       29.79         1.84       112.44        16.14        17.95         8.15 
TCGA-DK-A3WW TCGA-DK-AA6U TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A678 TCGA-E7-A6ME 
       20.81        19.00        38.83         5.36        26.24        24.03 
TCGA-FD-A3B5 TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FD-A5BU TCGA-G2-A2EF TCGA-G2-A2EL 
        8.94        27.98        25.74        19.33        61.94        26.93 
TCGA-G2-A3IB TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A6I1 
        7.23        66.02        29.36        20.71        14.07         8.94 
TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A767 
       13.91         2.10         2.20         7.63        20.05         4.73 
TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-KQ-A41R 
       36.49        19.40        11.70        17.72        15.42        44.38 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-UY-A78M TCGA-UY-A9PE TCGA-XF-A9SG 
       13.48        12.23        16.54        22.68         6.21        48.62 
TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-YC-A9TC 
       79.66        23.64       110.60         2.96        56.48         0.66 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-AA4N TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-GU-AATO 
       31.20        35.84         2.89        19.40        54.21        10.65 

$`MLL2 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-C4-A0EZ 
      108.95        33.83        14.89         8.35        20.48         8.98 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 
       12.92         4.90        15.12        18.48        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ 
       19.00        16.70        46.68        87.32         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       50.27         9.67        17.98        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA75 
       50.70        38.24       165.73        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
        4.01        60.66        24.30        29.16        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       12.85        27.35         3.62        26.73        53.88        10.78 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
        8.25        18.08        58.92        62.86        18.81        12.69 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        3.06         9.67        31.07        17.23        11.08        33.01 
TCGA-G2-AA3D TCGA-GC-A3YS TCGA-GU-A42P TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       70.32        24.92        10.92        19.82        20.28        27.35 
TCGA-GV-A40G TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41N TCGA-KQ-A41O 
       19.07         3.45         2.76         9.14        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A9SM 
       35.97        46.98        14.24        33.14        86.83        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       14.93         4.21        12.76        11.90        21.04        26.27 
TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ 
        2.24         2.10        10.82        11.31         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RE 
       18.58         3.88         9.63        13.64        21.11         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KP 
       88.87        34.06        19.69        57.90        12.23        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       94.88         8.35        44.94        34.98        27.62        50.04 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM 
       51.16        66.54        10.22        47.80         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J 
       40.08         7.33         2.66         6.74         6.58        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50         5.06        14.96         5.06 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       17.16        16.18         4.67        36.43        28.41         1.94 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       12.79        12.56        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       12.16        10.95        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU 
       13.12        12.00        12.10        11.87        13.08         5.19 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
       21.86        66.41        18.41        17.62        15.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P 
      142.78         4.80        13.58        10.55       163.30        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 
       13.58        18.81        15.35        12.03        43.59        29.72 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
       22.16         2.24        16.70         0.56         0.66        26.96 
TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        4.24        24.66        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SO 
        8.09        32.02        16.77        12.62        22.52         5.52 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       22.98        14.96        20.91         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        7.10        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
        8.94         3.25        22.88        48.00        15.95        59.31 
TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GD-A2C5 TCGA-GD-A3OQ 
       20.12         6.94        15.81        15.91        26.70         3.12 
TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JV 
       20.98        11.31        18.97        15.78         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF 
       21.34        19.10         8.48         1.51        38.60        64.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO 
       12.16        21.24         9.07         1.81        16.27        11.80 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K 
        1.15        15.32        15.58        16.67        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       37.05        76.01        69.34        35.24        29.56        17.82 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU 
        3.85         1.87        17.88        64.80        66.41         5.98 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN4 
       28.24        16.27        92.98         8.32         6.77        27.06 
TCGA-XF-AAN5 TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       75.39        11.97        22.36        25.41        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4U 
       13.41        64.08        58.72        47.84        20.22         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 
       59.38        60.16        67.20        56.35        35.41         8.52 
TCGA-ZF-AA5H TCGA-ZF-AA5N 
       29.49         5.52 

  MLL2 MUTATED MLL2 WILD-TYPE 
          0.62           0.56 
  MLL2 MUTATED MLL2 WILD-TYPE 
        166.03         165.73 
  MLL2 MUTATED MLL2 WILD-TYPE 
        19.065         16.685 
[1] "0.6 - 166.0 (19.1)" "0.6 - 165.7 (16.7)"
[1] "hr=" "1.2"
D14V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MLL2 MUTATED         0       40        40       34
  MLL2 WILD-TYPE       2       82        95      100
D14V3, multiclass
           clus
vv          MLL2 MUTATED MLL2 WILD-TYPE
  STAGE I              0              2
  STAGE II            40             82
  STAGE III           40             95
  STAGE IV            34            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  MLL2 MUTATED         34  53  15
  MLL2 WILD-TYPE       82 137  42
D14V4, multiclass
          clus
vv         MLL2 MUTATED MLL2 WILD-TYPE
  T0+T1+T2           34             82
  T3                 53            137
  T4                 15             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MLL2 MUTATED    71  10  21   0
  MLL2 WILD-TYPE 154  36  54   8
D14V5, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  N0           71            154
  N1           10             36
  N2           21             54
  N3            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                cls
clus               0   1
  MLL2 MUTATED    54   5
  MLL2 WILD-TYPE 135   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     54    5
  MLL2 WILD-TYPE  135    6
   clus
vv  MLL2 MUTATED MLL2 WILD-TYPE
  0           54            135
  1            5              6
[1] 2 2
[1] FALSE
D14V7, binary
                cls
clus               0   1
  MLL2 MUTATED    28  86
  MLL2 WILD-TYPE  74 207
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     28   86
  MLL2 WILD-TYPE   74  207
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  FEMALE           28             74
  MALE             86            207
[1] 2 2
[1] FALSE
D14V8, binary
                cls
clus               0   1
  MLL2 MUTATED   100   5
  MLL2 WILD-TYPE 250  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED    100    5
  MLL2 WILD-TYPE  250   15
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO           100            250
  YES            5             15
[1] 2 2
[1] FALSE
D14V9, continuous
D14V10, continuous
D14V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL2 MUTATED       9                         9    88
  MLL2 WILD-TYPE    30                        13   229
D14V12, multiclass
                           clus
vv                          MLL2 MUTATED MLL2 WILD-TYPE
  ASIAN                                9             30
  BLACK OR AFRICAN AMERICAN            9             13
  WHITE                               88            229
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V13, binary
                cls
clus               0   1
  MLL2 MUTATED     2  97
  MLL2 WILD-TYPE   6 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      2   97
  MLL2 WILD-TYPE    6  258
                        clus
vv                       MLL2 MUTATED MLL2 WILD-TYPE
  HISPANIC OR LATINO                2              6
  NOT HISPANIC OR LATINO           97            258
[1] 2 2
[1] FALSE

Clustering(15) Variable = FGFR3 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  FGFR3 MUTATED    35  20
  FGFR3 WILD-TYPE 182 155
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             55             337 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             20             155 
$`FGFR3 MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BT-A20T TCGA-BT-A42C TCGA-CU-A72E TCGA-DK-A3IS 
      108.95        33.83        14.89        28.70        13.58        50.27 
TCGA-DK-A6B0 TCGA-DK-AA71 TCGA-DK-AA77 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3SM 
       76.60        13.64        20.32         0.92         1.22        17.98 
TCGA-FD-A43X TCGA-FJ-A3ZF TCGA-GC-A3BM TCGA-GU-A763 TCGA-UY-A78N TCGA-XF-A9SJ 
        3.62        17.23        21.40        32.78        86.83         3.22 
TCGA-XF-A9SV TCGA-XF-AAN1 TCGA-ZF-A9R2 TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-2F-A9KQ 
       12.76        30.94        21.11         3.48        88.87        94.88 
TCGA-2F-A9KR TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-BT-A0S7 TCGA-CF-A27C 
      104.65        50.04        41.75        66.54         6.58        13.97 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.46        12.10        12.26        13.12        12.10        11.87 
TCGA-CF-A9FM TCGA-DK-A1AG TCGA-DK-AA6P TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 
       13.08        15.62        15.02        43.59        29.72         5.36 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 TCGA-FJ-A3ZE TCGA-G2-A2EO TCGA-GU-A42R 
       16.70         0.66        26.24        10.65        59.31        18.97 
TCGA-GU-AATQ TCGA-H4-A2HQ TCGA-XF-A8HI TCGA-XF-A9SL TCGA-ZF-A9R5 TCGA-ZF-A9RG 
        7.00        19.40        17.88        66.41        35.84        58.72 
TCGA-ZF-AA4U 
        8.61 

$`FGFR3 WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W 
       16.27        16.77        15.12        12.39        26.14         8.35 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL 
       20.48        25.94         9.96         8.98         2.04        18.58 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AA 
       12.92         4.90        15.12        18.48         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ 
       16.70       130.88        46.68        87.32         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       21.30        23.21         9.67        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       53.29        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA75 
       52.01       165.73       166.03        13.64        56.15        11.18 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
       15.35        25.58        33.04         4.01        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       23.41        29.16        46.78        19.79        12.85        27.35 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FT-A61P 
       12.36         3.06         4.31         9.67        31.07        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       33.01        17.62        70.32        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       10.92        32.98        19.82        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       19.07        22.72         9.01        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        9.14        27.68        52.73        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A9SK TCGA-XF-A9SM 
       14.24         1.84        33.14        51.32        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
       14.93         4.21        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
        2.24        66.64         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63        71.57        91.73        98.99        44.32 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       61.45        86.30        18.58         3.88         9.63        13.64 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
       30.28        94.29        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       24.13        11.97         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-4Z-AA87 
       34.98        27.62         0.62        51.16        10.22        47.80 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
        2.50        17.42        40.08         7.33         2.66         6.74 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       14.96         5.06         8.25        17.16        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       17.56        36.43        28.41         1.94         2.93        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.79        12.56        12.59        12.13        13.08        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47X TCGA-CF-A5UA TCGA-CU-A3QU TCGA-CU-A3YL 
       10.95        12.66        12.62        12.00         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        1.84        21.86        66.41        18.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       17.62        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T 
        8.15        20.81        10.55       163.30        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       19.00        15.35        12.03        38.83        22.16         2.24 
TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
        0.56        26.96         4.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.70         7.10        13.35         2.27        10.85        12.66 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        8.94         3.25        22.88        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       26.93         7.23        20.12        66.02         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 
       20.71        15.81        15.91        14.07         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       26.70         2.10         3.12        20.98         2.20        11.31 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW 
        7.63        20.05        15.78         4.73        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.10         8.48        36.49         1.51        38.60        64.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       12.16        21.24         9.07        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       15.42        16.27        11.80        44.38         1.15        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       15.58        13.48        12.23        16.67        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       17.62        37.05        22.68        76.01        69.34        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SG 
       29.56        17.82         6.21         3.85         1.87        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       64.80        79.66         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RM 
       31.20        21.86        28.41        13.41        64.08        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       20.22         2.89        59.38        60.16        67.20        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        19.40         8.52        54.21        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  FGFR3 MUTATED FGFR3 WILD-TYPE 
           0.66            0.56 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
         108.95          166.03 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
          17.88           17.62 
[1] "0.7 - 109.0 (17.9)" "0.6 - 166.0 (17.6)"
[1] "hr=" "1.4"
D15V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  FGFR3 MUTATED         1       26        15       14
  FGFR3 WILD-TYPE       1       96       120      120
D15V3, multiclass
           clus
vv          FGFR3 MUTATED FGFR3 WILD-TYPE
  STAGE I               1               1
  STAGE II             26              96
  STAGE III            15             120
  STAGE IV             14             120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  FGFR3 MUTATED         25  15   8
  FGFR3 WILD-TYPE       91 175  49
D15V4, multiclass
          clus
vv         FGFR3 MUTATED FGFR3 WILD-TYPE
  T0+T1+T2            25              91
  T3                  15             175
  T4                   8              49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  FGFR3 MUTATED    38   3   7   2
  FGFR3 WILD-TYPE 187  43  68   6
D15V5, multiclass
    clus
vv   FGFR3 MUTATED FGFR3 WILD-TYPE
  N0            38             187
  N1             3              43
  N2             7              68
  N3             2               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                 cls
clus                0   1
  FGFR3 MUTATED    38   4
  FGFR3 WILD-TYPE 151   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED     38    4
  FGFR3 WILD-TYPE  151    7
   clus
vv  FGFR3 MUTATED FGFR3 WILD-TYPE
  0            38             151
  1             4               7
[1] 2 2
[1] FALSE
D15V7, binary
                 cls
clus                0   1
  FGFR3 MUTATED     8  48
  FGFR3 WILD-TYPE  94 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED      8   48
  FGFR3 WILD-TYPE   94  245
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  FEMALE             8              94
  MALE              48             245
[1] 2 2
[1] FALSE
D15V8, binary
                 cls
clus                0   1
  FGFR3 MUTATED    50   5
  FGFR3 WILD-TYPE 300  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED     50    5
  FGFR3 WILD-TYPE  300   15
     clus
vv    FGFR3 MUTATED FGFR3 WILD-TYPE
  NO             50             300
  YES             5              15
[1] 2 2
[1] FALSE
D15V9, continuous
D15V10, continuous
D15V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FGFR3 MUTATED      11                         1    42
  FGFR3 WILD-TYPE    28                        21   275
D15V12, multiclass
                           clus
vv                          FGFR3 MUTATED FGFR3 WILD-TYPE
  ASIAN                                11              28
  BLACK OR AFRICAN AMERICAN             1              21
  WHITE                                42             275
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, binary
                 cls
clus                0   1
  FGFR3 MUTATED     0  51
  FGFR3 WILD-TYPE   8 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED      0   51
  FGFR3 WILD-TYPE    8  304
                        clus
vv                       FGFR3 MUTATED FGFR3 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            51             304
[1] 2 2
[1] FALSE

Clustering(16) Variable = ERCC2 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  ERCC2 MUTATED    26  12
  ERCC2 WILD-TYPE 191 163
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             38             354 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             12             163 
$`ERCC2 MUTATED`
TCGA-4Z-AA84 TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CU-A0YR TCGA-DK-A1AC TCGA-DK-A2I6 
       15.12        25.94         9.96        15.12       130.88        87.32 
TCGA-DK-AA75 TCGA-FD-A3SN TCGA-FT-A61P TCGA-G2-A2ES TCGA-KQ-A41N TCGA-UY-A78N 
       11.18        29.16        11.08        33.01        52.73        86.83 
TCGA-XF-A9SJ TCGA-XF-A9ST TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-ZF-A9RC TCGA-4Z-AA87 
        3.22         4.21        26.27         2.24        94.29        47.80 
TCGA-BT-A20O TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-E5-A2PC TCGA-E7-A5KE TCGA-E7-A677 
       12.16        21.86        18.41        43.59         0.56        26.96 
TCGA-E7-A85H TCGA-E7-A97P TCGA-FD-A3N5 TCGA-FT-A3EE TCGA-GC-A3RC TCGA-GD-A3OQ 
       12.95        14.37        22.52         3.25        15.91         3.12 
TCGA-H4-A2HO TCGA-KQ-A41R TCGA-MV-A51V TCGA-UY-A9PF TCGA-XF-AAMG TCGA-ZF-A9RG 
        1.51        44.38        13.48         3.85       110.60        58.72 
TCGA-ZF-AA4V TCGA-ZF-AA51 
       59.38        56.35 

$`ERCC2 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        16.77        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 
       14.89         8.35        20.48        28.70         8.98         2.04 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 
       18.58        12.92         4.90        18.48        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
       19.00        16.70        46.68         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       21.30        23.21         9.67        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       53.29        76.60        67.36        15.68        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       38.24        52.01       165.73       166.03        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       56.15        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3VY 
        3.06         4.31         9.67        31.07        17.23        17.62 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
       70.32        21.40        19.13        17.75        24.92        10.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       32.78        32.98        19.82        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       19.07        22.72         9.01        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
        9.14        27.68        50.56        35.97        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
        1.84        33.14        51.32        15.98        34.45        14.93 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 
       12.76        11.90        21.04        18.90        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       13.74        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.48        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       16.83        17.16        34.98        27.62        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-5N-A9KM 
       41.75        51.16        66.54        10.22         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       19.04        17.88        19.50         5.06        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        8.25        17.16        16.18         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         1.94         2.93        23.01        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.00        12.10        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
        1.84        66.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       17.95         7.79       142.78         4.80        13.58         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       19.00        15.35        12.03        38.83        29.72         5.36 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MD 
       22.16         2.24        16.70         0.66        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A97Q TCGA-FD-A3B3 
       24.03        24.66        13.68        14.07         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
       16.77         8.94        12.62        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.70         7.10        13.35         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       10.65         8.94        22.88        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       26.93        59.31         7.23        20.12        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 
       29.36        20.71        15.81        14.07         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
       26.70         2.10        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A2OE 
       21.34        19.10         8.48        36.49        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       64.01        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R 
        1.81        15.42        16.27        11.80         1.15        15.32 
TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       15.58        12.23        16.67        16.54        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       37.05        22.68        76.01        69.34        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       17.82         6.21         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       79.66        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 
       92.98         2.96         8.32         6.77        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       75.39         0.66        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RM 
       35.84        21.86        28.41        13.41        64.08        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 
       20.22         2.89         8.61        60.16        67.20        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21        29.49         5.52        10.65 

  ERCC2 MUTATED ERCC2 WILD-TYPE 
           0.56            0.62 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
         130.88          166.03 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
         20.135          17.620 
[1] "0.6 - 130.9 (20.1)" "0.6 - 166.0 (17.6)"
[1] "hr=" "1.7"
D16V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ERCC2 MUTATED         0        9        17       12
  ERCC2 WILD-TYPE       2      113       118      122
D16V3, multiclass
           clus
vv          ERCC2 MUTATED ERCC2 WILD-TYPE
  STAGE I               0               2
  STAGE II              9             113
  STAGE III            17             118
  STAGE IV             12             122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  ERCC2 MUTATED         12  21   5
  ERCC2 WILD-TYPE      104 169  52
D16V4, multiclass
          clus
vv         ERCC2 MUTATED ERCC2 WILD-TYPE
  T0+T1+T2            12             104
  T3                  21             169
  T4                   5              52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ERCC2 MUTATED    24   4   8   0
  ERCC2 WILD-TYPE 201  42  67   8
D16V5, multiclass
    clus
vv   ERCC2 MUTATED ERCC2 WILD-TYPE
  N0            24             201
  N1             4              42
  N2             8              67
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                 cls
clus                0   1
  ERCC2 MUTATED    18   1
  ERCC2 WILD-TYPE 171  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC2 MUTATED     18    1
  ERCC2 WILD-TYPE  171   10
   clus
vv  ERCC2 MUTATED ERCC2 WILD-TYPE
  0            18             171
  1             1              10
[1] 2 2
[1] FALSE
D16V7, binary
                 cls
clus                0   1
  ERCC2 MUTATED     8  30
  ERCC2 WILD-TYPE  94 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC2 MUTATED      8   30
  ERCC2 WILD-TYPE   94  263
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  FEMALE             8              94
  MALE              30             263
[1] 2 2
[1] FALSE
D16V8, binary
                 cls
clus                0   1
  ERCC2 MUTATED    34   0
  ERCC2 WILD-TYPE 316  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC2 MUTATED     34    0
  ERCC2 WILD-TYPE  316   20
     clus
vv    ERCC2 MUTATED ERCC2 WILD-TYPE
  NO             34             316
  YES             0              20
[1] 2 2
[1] FALSE
D16V9, continuous
D16V10, continuous
D16V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERCC2 MUTATED       4                         3    31
  ERCC2 WILD-TYPE    35                        19   286
D16V12, multiclass
                           clus
vv                          ERCC2 MUTATED ERCC2 WILD-TYPE
  ASIAN                                 4              35
  BLACK OR AFRICAN AMERICAN             3              19
  WHITE                                31             286
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, binary
                 cls
clus                0   1
  ERCC2 MUTATED     2  33
  ERCC2 WILD-TYPE   6 322
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC2 MUTATED      2   33
  ERCC2 WILD-TYPE    6  322
                        clus
vv                       ERCC2 MUTATED ERCC2 WILD-TYPE
  HISPANIC OR LATINO                 2               6
  NOT HISPANIC OR LATINO            33             322
[1] 2 2
[1] FALSE

Clustering(17) Variable = CREBBP MUTATION ANALYSIS
D17V1, survival
                  sevent
clus2                0   1
  CREBBP MUTATED    28  19
  CREBBP WILD-TYPE 189 156
  CREBBP MUTATED CREBBP WILD-TYPE 
              47              345 
  CREBBP MUTATED CREBBP WILD-TYPE 
              19              156 
$`CREBBP MUTATED`
TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A3PJ TCGA-CF-A9FL TCGA-DK-A3X2 TCGA-DK-A6AW 
       12.39        14.89        25.94        18.58        17.98        53.29 
TCGA-DK-A6B0 TCGA-DK-AA6R TCGA-E5-A4TZ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FT-A61P 
       76.60       165.73        15.35        23.41        17.98        11.08 
TCGA-KQ-A41O TCGA-XF-A9T3 TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-4Z-AA81 TCGA-4Z-AA86 
       50.56         2.24        88.87        34.06        41.75        10.22 
TCGA-BT-A20O TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-CF-A47X TCGA-CU-A3YL TCGA-DK-A1A3 
       12.16         1.94         2.93        12.62        29.79        21.86 
TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-AA6U TCGA-E7-A519 TCGA-E7-A6ME TCGA-E7-A7PW 
      112.44        17.95        19.00        16.70        24.03        13.68 
TCGA-FD-A3N5 TCGA-FD-A3SP TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EL TCGA-G2-A2EO 
       22.52        25.74        12.66         8.94        26.93        59.31 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GV-A3JX TCGA-K4-A5RH TCGA-K4-AAQO TCGA-PQ-A6FI 
       15.91        14.07        19.10         9.07        11.80        12.23 
TCGA-XF-AAMT TCGA-XF-AAN5 TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N 
        2.96        75.39        58.72        20.22         2.89 

$`CREBBP WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BT-A20N 
      108.95        16.27        16.77        15.12        33.83        26.14 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 
        8.35        20.48         9.96        28.70         8.98         2.04 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 
       12.92         4.90        15.12        18.48        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN 
       19.00        16.70       130.88        46.68        87.32         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 
       17.72        50.27        21.30        23.21         9.67        66.05 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       64.18        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
       52.01       166.03        13.64        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       20.32        25.58         0.92         1.22        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       60.66        24.30        29.16        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       27.35         3.62        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
        8.25        18.08        58.92         6.28        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.15        12.69        12.36         3.06         4.31         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM 
       31.07        17.23        33.01        17.62        70.32        21.40 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP 
       19.13        17.75        24.92        10.92        32.78        32.98 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       19.82        20.28        27.35         8.58        19.07        22.72 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        9.01        25.02         3.45         2.76         9.14        27.68 
TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       52.73        35.97        46.98        14.24         1.84        33.14 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       86.83        51.32         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
        4.21        12.76        11.90        21.04        26.27        18.90 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
        7.63        71.57        91.73        98.99        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       61.45        86.30        18.58         3.88         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4T TCGA-ZF-AA53 
       21.11        30.28        94.29         3.48        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM 
        0.62        51.16        66.54        47.80         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       19.04        17.88        19.50         5.06        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        8.25        17.16        16.18         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
       28.41        23.01        12.79        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.10        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AE 
       13.08         5.19         1.84        66.41        18.41        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       17.62        15.62         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
        8.15        20.81        10.55       163.30        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       18.81        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        5.36        22.16         2.24         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
       26.24         4.24        24.66        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 
        8.09        32.02        16.77         8.94        12.62        27.98 
TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
        5.52        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       10.65         3.25        22.88        61.94        48.00        15.95 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
        7.23        20.12        66.02         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       15.81         8.94        13.91        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
       20.98         2.20        11.31        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH 
       15.78         4.73         7.00        14.27        21.34         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
       36.49         1.51        19.40        38.60        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
       21.24        11.70        17.72         1.81        15.42        16.27 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN 
       44.38         1.15        15.32        15.58        13.48        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.54        38.99        17.62        37.05        22.68        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34        35.24        29.56        17.82         6.21         3.85 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-YC-A9TC TCGA-YF-AA3L 
        8.32         6.77        56.48        27.06         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       13.41        64.08        47.84         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       67.20        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

  CREBBP MUTATED CREBBP WILD-TYPE 
            1.94             0.56 
  CREBBP MUTATED CREBBP WILD-TYPE 
          165.73           166.03 
  CREBBP MUTATED CREBBP WILD-TYPE 
           17.98            17.56 
[1] "1.9 - 165.7 (18.0)" "0.6 - 166.0 (17.6)"
[1] "hr=" "1.2"
D17V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CREBBP MUTATED         0       15        17       15
  CREBBP WILD-TYPE       2      107       118      119
D17V3, multiclass
           clus
vv          CREBBP MUTATED CREBBP WILD-TYPE
  STAGE I                0                2
  STAGE II              15              107
  STAGE III             17              118
  STAGE IV              15              119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  CREBBP MUTATED         11  27   5
  CREBBP WILD-TYPE      105 163  52
D17V4, multiclass
          clus
vv         CREBBP MUTATED CREBBP WILD-TYPE
  T0+T1+T2             11              105
  T3                   27              163
  T4                    5               52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CREBBP MUTATED    26   5   9   1
  CREBBP WILD-TYPE 199  41  66   7
D17V5, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  N0             26              199
  N1              5               41
  N2              9               66
  N3              1                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"
D17V6, binary
                  cls
clus                 0   1
  CREBBP MUTATED    27   2
  CREBBP WILD-TYPE 162   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     27    2
  CREBBP WILD-TYPE  162    9
   clus
vv  CREBBP MUTATED CREBBP WILD-TYPE
  0             27              162
  1              2                9
[1] 2 2
[1] FALSE
D17V7, binary
                  cls
clus                 0   1
  CREBBP MUTATED     8  40
  CREBBP WILD-TYPE  94 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED      8   40
  CREBBP WILD-TYPE   94  253
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  FEMALE              8               94
  MALE               40              253
[1] 2 2
[1] FALSE
D17V8, binary
                  cls
clus                 0   1
  CREBBP MUTATED    42   1
  CREBBP WILD-TYPE 308  19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     42    1
  CREBBP WILD-TYPE  308   19
     clus
vv    CREBBP MUTATED CREBBP WILD-TYPE
  NO              42              308
  YES              1               19
[1] 2 2
[1] FALSE
D17V9, continuous
D17V10, continuous
D17V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CREBBP MUTATED       4                         2    39
  CREBBP WILD-TYPE    35                        20   278
D17V12, multiclass
                           clus
vv                          CREBBP MUTATED CREBBP WILD-TYPE
  ASIAN                                  4               35
  BLACK OR AFRICAN AMERICAN              2               20
  WHITE                                 39              278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V13, binary
                  cls
clus                 0   1
  CREBBP MUTATED     0  42
  CREBBP WILD-TYPE   8 313
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED      0   42
  CREBBP WILD-TYPE    8  313
                        clus
vv                       CREBBP MUTATED CREBBP WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO             42              313
[1] 2 2
[1] FALSE

Clustering(18) Variable = HRAS MUTATION ANALYSIS
D18V1, survival
                sevent
clus2              0   1
  HRAS MUTATED     8   9
  HRAS WILD-TYPE 209 166
  HRAS MUTATED HRAS WILD-TYPE 
            17            375 
  HRAS MUTATED HRAS WILD-TYPE 
             9            166 
$`HRAS MUTATED`
TCGA-DK-A1AC TCGA-YC-A8S6 TCGA-2F-A9KO TCGA-BT-A2LB TCGA-BT-A3PH TCGA-CF-A3MI 
      130.88         9.63        24.13        16.18         4.67        12.16 
TCGA-CF-A47T TCGA-E7-A677 TCGA-E7-A6MF TCGA-E7-A97P TCGA-FT-A3EE TCGA-G2-A2EJ 
       12.66        26.96        24.66        14.37         3.25        48.00 
TCGA-GD-A3OQ TCGA-XF-A9T4 TCGA-XF-AAMW TCGA-ZF-AA58 TCGA-ZF-AA5N 
        3.12        16.27         8.32        54.21         5.52 

$`HRAS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       29.16        46.78        19.79        12.85        27.35         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.36         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       11.08        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       17.75        24.92        10.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       20.28        27.35         8.58        19.07        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
       25.02         3.45         2.76         9.14        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       50.56        35.97        46.98        14.24         1.84        33.14 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       86.83        51.32         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
        4.21        12.76        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
        2.24        66.64         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63        71.57        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YF-AA3M 
       30.94        61.45        86.30        18.58         3.88        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
       21.11        30.28        94.29         3.48        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       19.69        57.90        12.23        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       50.04         0.62        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       17.56        36.43        28.41         1.94         2.93        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       12.79        12.56        13.97        12.59        12.13        13.08 
TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       10.95        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.00        12.10        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        1.84        21.86        66.41        18.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P 
       13.58         8.15        20.81        10.55       163.30        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       13.58        18.81        19.00        15.35        12.03        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         5.36        22.16         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7PW 
        0.56         0.66        26.24         4.24        24.03        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       14.07        12.95         8.09        32.02        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       12.62        22.52        27.98         5.52        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       14.96        20.91        19.33         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        7.10        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        8.94        22.88        61.94        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
        7.23        20.12        66.02         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91        14.07         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.10        20.98         2.20        11.31        18.97         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05        15.78         4.73         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       19.10         8.48        36.49         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       64.01        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
        1.81        15.42        16.27        11.80        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       15.32        15.58        13.48        12.23        16.67        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       38.99        17.62        37.05        22.68        76.01        69.34 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       35.24        29.56        17.82         6.21         3.85         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
       17.88        48.62        64.80        79.66        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMX 
       23.64        28.24        92.98       110.60         2.96         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
       56.48        27.06        75.39         0.66        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       25.41        31.20        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       64.08        58.72        47.84        20.22         2.89         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 
       59.38        60.16        67.20        56.35        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-GU-AATO 
        8.52        29.49        10.65 

  HRAS MUTATED HRAS WILD-TYPE 
          3.12           0.56 
  HRAS MUTATED HRAS WILD-TYPE 
        130.88         166.03 
  HRAS MUTATED HRAS WILD-TYPE 
         14.37          17.72 
[1] "3.1 - 130.9 (14.4)" "0.6 - 166.0 (17.7)"
[1] "hr=" "1.4"
D18V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  HRAS MUTATED         0        7         3        7
  HRAS WILD-TYPE       2      115       132      127
D18V3, multiclass
           clus
vv          HRAS MUTATED HRAS WILD-TYPE
  STAGE I              0              2
  STAGE II             7            115
  STAGE III            3            132
  STAGE IV             7            127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  HRAS MUTATED          9   5   2
  HRAS WILD-TYPE      107 185  55
D18V4, multiclass
          clus
vv         HRAS MUTATED HRAS WILD-TYPE
  T0+T1+T2            9            107
  T3                  5            185
  T4                  2             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  HRAS MUTATED     9   3   2   0
  HRAS WILD-TYPE 216  43  73   8
D18V5, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  N0            9            216
  N1            3             43
  N2            2             73
  N3            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                cls
clus               0   1
  HRAS MUTATED     9   1
  HRAS WILD-TYPE 180  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      9    1
  HRAS WILD-TYPE  180   10
   clus
vv  HRAS MUTATED HRAS WILD-TYPE
  0            9            180
  1            1             10
[1] 2 2
[1] FALSE
D18V7, binary
                cls
clus               0   1
  HRAS MUTATED     7  10
  HRAS WILD-TYPE  95 283
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      7   10
  HRAS WILD-TYPE   95  283
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  FEMALE            7             95
  MALE             10            283
[1] 2 2
[1] FALSE
D18V8, binary
                cls
clus               0   1
  HRAS MUTATED    14   1
  HRAS WILD-TYPE 336  19
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED     14    1
  HRAS WILD-TYPE  336   19
     clus
vv    HRAS MUTATED HRAS WILD-TYPE
  NO            14            336
  YES            1             19
[1] 2 2
[1] FALSE
D18V9, continuous
D18V10, continuous
D18V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HRAS MUTATED       5                         0    12
  HRAS WILD-TYPE    34                        22   305
D18V12, multiclass
                           clus
vv                          HRAS MUTATED HRAS WILD-TYPE
  ASIAN                                5             34
  BLACK OR AFRICAN AMERICAN            0             22
  WHITE                               12            305
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, binary
                cls
clus               0   1
  HRAS MUTATED     0  16
  HRAS WILD-TYPE   8 339
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0   16
  HRAS WILD-TYPE    8  339
                        clus
vv                       HRAS MUTATED HRAS WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           16            339
[1] 2 2
[1] FALSE

Clustering(19) Variable = FOXA1 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  FOXA1 MUTATED     8   6
  FOXA1 WILD-TYPE 209 169
  FOXA1 MUTATED FOXA1 WILD-TYPE 
             14             378 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
              6             169 
$`FOXA1 MUTATED`
TCGA-BT-A2LD TCGA-FD-A3SL TCGA-FD-A3SM TCGA-GV-A3QK TCGA-XF-AAMF TCGA-BT-A2LB 
       20.48        23.41        17.98        27.35        10.82        16.18 
TCGA-E5-A2PC TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A43N TCGA-FD-A62O TCGA-G2-AA3F 
       43.59        26.96        26.24        22.98         7.10        29.36 
TCGA-HQ-A2OE TCGA-SY-A9G5 
       38.60        38.99 

$`FOXA1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       26.14        14.89         8.35        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SQ 
       33.04         4.01        60.66        24.30        29.16        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       19.79        12.85        27.35         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       10.78         5.69         8.25        18.08        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
       62.86        18.81         6.15        12.69        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        4.31         9.67        31.07        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       17.62        70.32        21.40        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E 
       10.92        32.78        32.98        19.82        20.28         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       19.07        22.72         9.01        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        9.14        27.68        52.73        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ 
       14.24         1.84        33.14        86.83        51.32         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
       15.98        34.45        14.93         4.21        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       13.74        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       98.99        44.32        30.94        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
        3.88         9.63        13.64        21.11        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.48        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       16.83        17.16        34.98        27.62        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
       41.75        51.16        66.54        10.22        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       17.42        40.08         7.33         2.66         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B 
       14.96         5.06         8.25        17.16         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR 
       36.43        28.41         1.94         2.93        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.56        13.97        12.59        12.13        13.08        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU 
       13.12        12.00        12.10        11.87        13.08         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       29.79         1.84        21.86        66.41        18.41       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       15.02        13.58        18.81        19.00        15.35        12.03 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         5.36        22.16         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
        0.56         0.66         4.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       14.96        20.91        19.33         5.36        27.45         2.70 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       13.35         2.27        10.85        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25        22.88        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 
       59.31         7.23        20.12        66.02         6.94        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91        14.07         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       64.01        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
        1.81        15.42        16.27        11.80        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       15.32        15.58        13.48        12.23        16.67        16.54 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       17.62        37.05        22.68        76.01        69.34        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         6.21         3.85         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       48.62        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW 
       28.24        16.27        92.98       110.60         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L 
        6.77        56.48        27.06        75.39         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       13.41        64.08        58.72        47.84        20.22         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21        29.49         5.52        10.65 

  FOXA1 MUTATED FOXA1 WILD-TYPE 
           7.10            0.56 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
          43.59          166.03 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
         24.825          17.325 
[1] "7.1 - 43.6 (24.8)"  "0.6 - 166.0 (17.3)"
[1] "hr=" "1.2"
D19V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  FOXA1 MUTATED         0        1         4        8
  FOXA1 WILD-TYPE       2      121       131      126
D19V3, multiclass
           clus
vv          FOXA1 MUTATED FOXA1 WILD-TYPE
  STAGE I               0               2
  STAGE II              1             121
  STAGE III             4             131
  STAGE IV              8             126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  FOXA1 MUTATED          3   7   4
  FOXA1 WILD-TYPE      113 183  53
D19V4, multiclass
          clus
vv         FOXA1 MUTATED FOXA1 WILD-TYPE
  T0+T1+T2             3             113
  T3                   7             183
  T4                   4              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  FOXA1 MUTATED     5   3   6   0
  FOXA1 WILD-TYPE 220  43  69   8
D19V5, multiclass
    clus
vv   FOXA1 MUTATED FOXA1 WILD-TYPE
  N0             5             220
  N1             3              43
  N2             6              69
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                 cls
clus                0   1
  FOXA1 MUTATED     7   2
  FOXA1 WILD-TYPE 182   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA1 MUTATED      7    2
  FOXA1 WILD-TYPE  182    9
   clus
vv  FOXA1 MUTATED FOXA1 WILD-TYPE
  0             7             182
  1             2               9
[1] 2 2
[1] FALSE
D19V7, binary
                 cls
clus                0   1
  FOXA1 MUTATED     4  10
  FOXA1 WILD-TYPE  98 283
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA1 MUTATED      4   10
  FOXA1 WILD-TYPE   98  283
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  FEMALE             4              98
  MALE              10             283
[1] 2 2
[1] FALSE
D19V8, binary
                 cls
clus                0   1
  FOXA1 MUTATED    13   1
  FOXA1 WILD-TYPE 337  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA1 MUTATED     13    1
  FOXA1 WILD-TYPE  337   19
     clus
vv    FOXA1 MUTATED FOXA1 WILD-TYPE
  NO             13             337
  YES             1              19
[1] 2 2
[1] FALSE
D19V9, continuous
D19V10, continuous
D19V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FOXA1 MUTATED       2                         0    11
  FOXA1 WILD-TYPE    37                        22   306
D19V12, multiclass
                           clus
vv                          FOXA1 MUTATED FOXA1 WILD-TYPE
  ASIAN                                 2              37
  BLACK OR AFRICAN AMERICAN             0              22
  WHITE                                11             306
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, binary
                 cls
clus                0   1
  FOXA1 MUTATED     0  13
  FOXA1 WILD-TYPE   8 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA1 MUTATED      0   13
  FOXA1 WILD-TYPE    8  342
                        clus
vv                       FOXA1 MUTATED FOXA1 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            13             342
[1] 2 2
[1] FALSE

Clustering(20) Variable = KRAS MUTATION ANALYSIS
D20V1, survival
                sevent
clus2              0   1
  KRAS MUTATED     3  10
  KRAS WILD-TYPE 214 165
  KRAS MUTATED KRAS WILD-TYPE 
            13            379 
  KRAS MUTATED KRAS WILD-TYPE 
            10            165 
$`KRAS MUTATED`
TCGA-FD-A5BX TCGA-XF-AAMH TCGA-XF-AAN7 TCGA-ZF-A9R4 TCGA-4Z-AA81 TCGA-CF-A47X 
        5.69        11.31        18.58        30.28        41.75        12.62 
TCGA-CF-A5UA TCGA-E7-A4XJ TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-AA3C TCGA-XF-A9SU 
       12.00         2.24        12.66         8.94         6.94         5.98 
TCGA-ZF-AA54 
       19.40 

$`KRAS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      130.88        46.68        87.32         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       21.30        23.21         9.67        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       53.29        76.60        67.36        15.68        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       38.24        52.01       165.73       166.03        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU 
       56.15        11.18        20.32        15.35        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        1.22        33.04         4.01        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       17.98        29.16        46.78        19.79        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BY TCGA-FD-A5C0 
        3.62        26.73        53.88        10.78         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.36         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       11.08        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       17.75        24.92        10.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       20.28        27.35         8.58        19.07        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
       25.02         3.45         2.76         9.14        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       50.56        35.97        46.98        14.24         1.84        33.14 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       86.83        51.32         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
        4.21        12.76        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMJ 
        2.24        66.64         2.10        13.74        10.82        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
        7.63        71.57        91.73        98.99        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       61.45        86.30         3.88         9.63        13.64        21.11 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       94.29         3.48        88.87        34.06        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
        0.62        51.16        66.54        10.22        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       17.42        40.08         7.33         2.66         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       14.96         5.06         8.25        17.16        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       17.56        36.43        28.41         1.94         2.93        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       12.79        12.56        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
       12.16        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       13.12        12.10        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        1.84        21.86        66.41        18.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P 
       13.58         8.15        20.81        10.55       163.30        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       13.58        18.81        19.00        15.35        12.03        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A519 TCGA-E7-A5KE 
       38.83        29.72         5.36        22.16        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       10.65         3.25        22.88        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F 
       26.93        59.31         7.23        20.12        66.02        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 
       20.71        15.81        15.91        14.07         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       26.70         2.10         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       18.97         7.63        20.05        15.78         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
       14.27        21.34        19.10         8.48        36.49         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
       19.40        38.60        64.01        12.16        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70        17.72         1.81        15.42        16.27        11.80 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       44.38         1.15        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        69.34        35.24        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        3.85         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
       66.41        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32         6.77        56.48        27.06        75.39 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       21.86        28.41        13.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       20.22         2.89         8.61        59.38        60.16        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       56.35        35.41         8.52        54.21        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  KRAS MUTATED KRAS WILD-TYPE 
          2.24           0.56 
  KRAS MUTATED KRAS WILD-TYPE 
         41.75         166.03 
  KRAS MUTATED KRAS WILD-TYPE 
         12.00          17.72 
[1] "2.2 - 41.8 (12.0)"  "0.6 - 166.0 (17.7)"
[1] "hr=" "2.9"
D20V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  KRAS MUTATED         0        5         2        5
  KRAS WILD-TYPE       2      117       133      129
D20V3, multiclass
           clus
vv          KRAS MUTATED KRAS WILD-TYPE
  STAGE I              0              2
  STAGE II             5            117
  STAGE III            2            133
  STAGE IV             5            129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  KRAS MUTATED          5   7   0
  KRAS WILD-TYPE      111 183  57
D20V4, multiclass
          clus
vv         KRAS MUTATED KRAS WILD-TYPE
  T0+T1+T2            5            111
  T3                  7            183
  T4                  0             57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  KRAS MUTATED     5   5   0   0
  KRAS WILD-TYPE 220  41  75   8
D20V5, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  N0            5            220
  N1            5             41
  N2            0             75
  N3            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                cls
clus               0   1
  KRAS MUTATED     7   0
  KRAS WILD-TYPE 182  11
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      7    0
  KRAS WILD-TYPE  182   11
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0            7            182
  1            0             11
[1] 2 2
[1] FALSE
D20V7, binary
                cls
clus               0   1
  KRAS MUTATED     1  12
  KRAS WILD-TYPE 101 281
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      1   12
  KRAS WILD-TYPE  101  281
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE            1            101
  MALE             12            281
[1] 2 2
[1] FALSE
D20V8, binary
                cls
clus               0   1
  KRAS MUTATED    11   1
  KRAS WILD-TYPE 339  19
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     11    1
  KRAS WILD-TYPE  339   19
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO            11            339
  YES            1             19
[1] 2 2
[1] FALSE
D20V9, continuous
D20V10, continuous
D20V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       3                         0    10
  KRAS WILD-TYPE    36                        22   307
D20V12, multiclass
                           clus
vv                          KRAS MUTATED KRAS WILD-TYPE
  ASIAN                                3             36
  BLACK OR AFRICAN AMERICAN            0             22
  WHITE                               10            307
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, binary
                cls
clus               0   1
  KRAS MUTATED     0  12
  KRAS WILD-TYPE   8 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0   12
  KRAS WILD-TYPE    8  343
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           12            343
[1] 2 2
[1] FALSE

Clustering(21) Variable = RHOA MUTATION ANALYSIS
D21V1, survival
                sevent
clus2              0   1
  RHOA MUTATED    10   8
  RHOA WILD-TYPE 207 167
  RHOA MUTATED RHOA WILD-TYPE 
            18            374 
  RHOA MUTATED RHOA WILD-TYPE 
             8            167 
$`RHOA MUTATED`
TCGA-BT-A2LD TCGA-FD-A62P TCGA-FD-A6TI TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-DK-A2I1 
       20.48         6.28         9.67        50.04         0.62        17.95 
TCGA-DK-AA6U TCGA-FD-A3SO TCGA-FD-A62N TCGA-FD-A62O TCGA-G2-A2EK TCGA-GU-A767 
       19.00         5.52         2.70         7.10        15.95         4.73 
TCGA-H4-A2HQ TCGA-KQ-A41S TCGA-UY-A78O TCGA-UY-A8OB TCGA-ZF-A9RM TCGA-ZF-AA5N 
       19.40         1.15        76.01        69.34        47.84         5.52 

$`RHOA WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       26.14        14.89         8.35        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       29.16        46.78        19.79        12.85        27.35         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       58.92        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        3.06         4.31        31.07        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       17.62        70.32        21.40        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       10.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        8.58        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       46.98        14.24         1.84        33.14        86.83        51.32 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
        3.22        15.98        34.45        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.10        13.74        10.82        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       86.30        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       30.28        94.29         3.48        88.87        34.06        19.69 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       57.90        12.23        24.13        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
       41.75        51.16        66.54        10.22        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       17.42        40.08         7.33         2.66         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       14.96         5.06         8.25        17.16        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       17.56        36.43        28.41         1.94         2.93        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       12.79        12.56        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       12.16        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.19        29.79         1.84        21.86        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 
      112.44        16.14        17.62        15.62         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       15.02        13.58        18.81        15.35        12.03        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         5.36        22.16         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
        0.56         0.66        26.96        26.24         4.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
       24.66        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       27.45        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL 
        8.94         3.25        22.88        61.94        48.00        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       59.31         7.23        20.12        66.02         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 
       20.71        15.81        15.91        14.07         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       26.70         2.10         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JV 
       18.97         7.63        20.05        15.78         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE 
       21.34        19.10         8.48        36.49         1.51        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       64.01        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LC-A66R 
        1.81        15.42        16.27        11.80        44.38        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       15.58        13.48        12.23        16.67        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       17.62        37.05        22.68        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        6.21         3.85         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       79.66        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       58.72        20.22         2.89         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       67.20        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-GU-AATO 
       29.49        10.65 

  RHOA MUTATED RHOA WILD-TYPE 
          0.62           0.56 
  RHOA MUTATED RHOA WILD-TYPE 
         76.01         166.03 
  RHOA MUTATED RHOA WILD-TYPE 
         12.81          17.67 
[1] "0.6 - 76.0 (12.8)"  "0.6 - 166.0 (17.7)"
[1] "hr=" "1.3"
D21V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RHOA MUTATED         0        8         2        8
  RHOA WILD-TYPE       2      114       133      126
D21V3, multiclass
           clus
vv          RHOA MUTATED RHOA WILD-TYPE
  STAGE I              0              2
  STAGE II             8            114
  STAGE III            2            133
  STAGE IV             8            126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  RHOA MUTATED          7   6   2
  RHOA WILD-TYPE      109 184  55
D21V4, multiclass
          clus
vv         RHOA MUTATED RHOA WILD-TYPE
  T0+T1+T2            7            109
  T3                  6            184
  T4                  2             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RHOA MUTATED     9   4   2   0
  RHOA WILD-TYPE 216  42  73   8
D21V5, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  N0            9            216
  N1            4             42
  N2            2             73
  N3            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                cls
clus               0   1
  RHOA MUTATED     6   2
  RHOA WILD-TYPE 183   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      6    2
  RHOA WILD-TYPE  183    9
   clus
vv  RHOA MUTATED RHOA WILD-TYPE
  0            6            183
  1            2              9
[1] 2 2
[1] FALSE
D21V7, binary
                cls
clus               0   1
  RHOA MUTATED     6  12
  RHOA WILD-TYPE  96 281
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      6   12
  RHOA WILD-TYPE   96  281
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  FEMALE            6             96
  MALE             12            281
[1] 2 2
[1] FALSE
D21V8, binary
                cls
clus               0   1
  RHOA MUTATED    17   0
  RHOA WILD-TYPE 333  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED     17    0
  RHOA WILD-TYPE  333   20
     clus
vv    RHOA MUTATED RHOA WILD-TYPE
  NO            17            333
  YES            0             20
[1] 2 2
[1] FALSE
D21V9, continuous
[1] "Remove cluster labels:" "RHOA MUTATED"          
clus
  RHOA MUTATED RHOA WILD-TYPE 
             2            128 
    TCGA-2F-A9KT     TCGA-DK-A2HX     TCGA-DK-A3IN     TCGA-DK-A3IV 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-DK-A3X2     TCGA-DK-A6B2     TCGA-DK-A6B5     TCGA-DK-A6B6 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-DK-AA6M     TCGA-DK-AA6R     TCGA-DK-AA6S     TCGA-DK-AA6W 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-DK-AA75     TCGA-E5-A4TZ     TCGA-E7-A541     TCGA-E7-A7DU 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-E7-A7DV     TCGA-FT-A61P     TCGA-G2-A2ES     TCGA-G2-A3VY 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-GC-A3BM     TCGA-GC-A3YS     TCGA-GV-A3JZ     TCGA-GV-A3QF 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-GV-A3QK     TCGA-GV-A40E     TCGA-GV-A40G     TCGA-GV-A6ZA 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-KQ-A41N     TCGA-SY-A9G0     TCGA-UY-A78N     TCGA-XF-A9SJ 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-A9SK     TCGA-XF-A9SM     TCGA-XF-A9SP     TCGA-XF-A9ST 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-A9SV     TCGA-XF-A9SW     TCGA-XF-A9SY     TCGA-XF-A9T0 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-A9T2     TCGA-XF-A9T3     TCGA-XF-A9T5     TCGA-XF-A9T6 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-A9T8     TCGA-XF-AAMF     TCGA-XF-AAMH     TCGA-XF-AAMJ 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-AAML     TCGA-XF-AAMQ     TCGA-XF-AAMR     TCGA-XF-AAMY 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-AAMZ     TCGA-XF-AAN1     TCGA-XF-AAN2     TCGA-XF-AAN3 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-AAN7     TCGA-XF-AAN8     TCGA-YF-AA3M     TCGA-2F-A9KO 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-2F-A9KP     TCGA-2F-A9KQ     TCGA-2F-A9KR     TCGA-2F-A9KW 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-CF-A1HS     TCGA-CF-A27C     TCGA-CF-A3MF     TCGA-CF-A3MG 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-CF-A3MH     TCGA-CF-A3MI     TCGA-CF-A47S     TCGA-CF-A47T 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-CF-A47V     TCGA-CF-A47W     TCGA-CF-A47X     TCGA-CF-A47Y 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-CF-A5U8     TCGA-CF-A5UA     TCGA-CF-A7I0     TCGA-DK-A3WX 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-DK-AA6P     TCGA-DK-AA76     TCGA-E5-A2PC     TCGA-E5-A4U1 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-E7-A519     TCGA-E7-A6MD     TCGA-G2-A2EC     TCGA-G2-A2EF 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-G2-A2EJ     TCGA-G2-A2EL     TCGA-G2-A2EO     TCGA-G2-A3IB 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-G2-A3IE     TCGA-GC-A3I6     TCGA-GC-A3OO     TCGA-GC-A3RC 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-GC-A3RD     TCGA-GC-A6I1     TCGA-GC-A6I3     TCGA-GD-A3OS 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-GD-A6C6     TCGA-GV-A3JV     TCGA-GV-A3JW     TCGA-GV-A3JX 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-GV-A3QH     TCGA-GV-A3QI     TCGA-SY-A9G5     TCGA-UY-A78L 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-UY-A78M     TCGA-XF-A8HH     TCGA-XF-A8HI     TCGA-XF-A9SG 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-A9SH     TCGA-XF-A9SI     TCGA-XF-A9SL     TCGA-XF-A9SU 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-A9SX     TCGA-XF-A9SZ     TCGA-XF-A9T4     TCGA-XF-AAME 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-AAMG     TCGA-XF-AAMT     TCGA-XF-AAMW     TCGA-XF-AAMX 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-AAN0     TCGA-XF-AAN4     TCGA-XF-AAN5     TCGA-YF-AA3L 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
D21V10, continuous
D21V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RHOA MUTATED       1                         1    16
  RHOA WILD-TYPE    38                        21   301
D21V12, multiclass
                           clus
vv                          RHOA MUTATED RHOA WILD-TYPE
  ASIAN                                1             38
  BLACK OR AFRICAN AMERICAN            1             21
  WHITE                               16            301
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, binary
                cls
clus               0   1
  RHOA MUTATED     1  14
  RHOA WILD-TYPE   7 341
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      1   14
  RHOA WILD-TYPE    7  341
                        clus
vv                       RHOA MUTATED RHOA WILD-TYPE
  HISPANIC OR LATINO                1              7
  NOT HISPANIC OR LATINO           14            341
[1] 2 2
[1] FALSE

Clustering(22) Variable = KIAA1267 MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  KIAA1267 MUTATED    15   9
  KIAA1267 WILD-TYPE 202 166
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                24                368 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                 9                166 
$`KIAA1267 MUTATED`
TCGA-DK-A6AW TCGA-FD-A3SL TCGA-FD-A6TB TCGA-G2-A3VY TCGA-GC-A3RB TCGA-K4-A3WS 
       53.29        23.41        18.81        17.62        19.13        25.02 
TCGA-XF-A9SJ TCGA-XF-A9T0 TCGA-XF-AAMZ TCGA-XF-AAN7 TCGA-ZF-A9RL TCGA-2F-A9KR 
        3.22        26.27        44.32        18.58        88.87       104.65 
TCGA-4Z-AA7W TCGA-BT-A20Q TCGA-CF-A47T TCGA-CF-A47X TCGA-DK-AA6P TCGA-E7-A5KF 
       27.62        19.50        12.66        12.62        15.02         0.66 
TCGA-G2-A2EO TCGA-G2-AA3F TCGA-GU-A42Q TCGA-XF-AAMG TCGA-ZF-A9R5 TCGA-ZF-AA4W 
       59.31        29.36        11.31       110.60        35.84        60.16 

$`KIAA1267 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      130.88        46.68        87.32         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       21.30        23.21         9.67        66.05        17.98        64.18 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN 
       33.04         4.01        60.66        24.30        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
        6.28        62.86         6.15        12.69        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        4.31         9.67        31.07        17.23        11.08        33.01 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 
       70.32        21.40        17.75        24.92        10.92        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       32.98        19.82        20.28        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       22.72         9.01         3.45         2.76         9.14        27.68 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX 
       52.73        50.56        35.97        46.98        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       33.14        86.83        51.32        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 
        4.21        12.76        11.90        21.04        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 
        7.63        71.57        91.73        98.99        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       86.30         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
       94.29         3.48        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O 
       24.13        11.97        94.88         8.35        44.94        16.83 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       17.16        34.98        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       66.54        10.22        47.80         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       12.16        17.88         5.06        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       17.16        16.18         4.67        17.56        36.43        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        1.94         2.93        23.01        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47V 
       12.59        12.13        13.08        12.16        10.95        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.10        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       13.08         5.19        29.79         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW 
        7.79       142.78         4.80        13.58         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
       10.55       163.30        13.58        18.81        19.00        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       12.03        43.59        38.83        29.72         5.36        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
        2.24        16.70         0.56        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
       24.03        24.66        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       27.98         5.52        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       19.33         5.36        27.45         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.27        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
       22.88        61.94        48.00        15.95        26.93         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       20.12        66.02         6.94        20.71        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07         8.94        13.91        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
       20.98         2.20        18.97         7.63        20.05        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
        4.73         7.00        14.27        21.34        19.10         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
       36.49         1.51        19.40        38.60        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       21.24         9.07        11.70        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       16.27        11.80        44.38         1.15        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       13.48        12.23        16.67        16.54        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       37.05        22.68        76.01        69.34        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         6.21         3.85         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        79.66        66.41         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       16.27        92.98         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       31.20        21.86        28.41        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X 
       47.84        20.22         2.89         8.61        59.38        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        19.40         8.52        54.21        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
              0.66               0.56 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
            110.60             166.03 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
            24.215             17.160 
[1] "0.7 - 110.6 (24.2)" "0.6 - 166.0 (17.2)"
[1] "hr=" "1.6"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  KIAA1267 MUTATED         0        8        10        6
  KIAA1267 WILD-TYPE       2      114       125      128
D22V3, multiclass
           clus
vv          KIAA1267 MUTATED KIAA1267 WILD-TYPE
  STAGE I                  0                  2
  STAGE II                 8                114
  STAGE III               10                125
  STAGE IV                 6                128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  KIAA1267 MUTATED          5  14   2
  KIAA1267 WILD-TYPE      111 176  55
D22V4, multiclass
          clus
vv         KIAA1267 MUTATED KIAA1267 WILD-TYPE
  T0+T1+T2                5                111
  T3                     14                176
  T4                      2                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA1267 MUTATED    16   2   4   0
  KIAA1267 WILD-TYPE 209  44  71   8
D22V5, multiclass
    clus
vv   KIAA1267 MUTATED KIAA1267 WILD-TYPE
  N0               16                209
  N1                2                 44
  N2                4                 71
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED    13   1
  KIAA1267 WILD-TYPE 176  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED     13    1
  KIAA1267 WILD-TYPE  176   10
   clus
vv  KIAA1267 MUTATED KIAA1267 WILD-TYPE
  0               13                176
  1                1                 10
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED     4  20
  KIAA1267 WILD-TYPE  98 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED      4   20
  KIAA1267 WILD-TYPE   98  273
        clus
vv       KIAA1267 MUTATED KIAA1267 WILD-TYPE
  FEMALE                4                 98
  MALE                 20                273
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED    21   2
  KIAA1267 WILD-TYPE 329  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED     21    2
  KIAA1267 WILD-TYPE  329   18
     clus
vv    KIAA1267 MUTATED KIAA1267 WILD-TYPE
  NO                21                329
  YES                2                 18
[1] 2 2
[1] FALSE
D22V9, continuous
D22V10, continuous
D22V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1267 MUTATED       4                         0    19
  KIAA1267 WILD-TYPE    35                        22   298
D22V12, multiclass
                           clus
vv                          KIAA1267 MUTATED KIAA1267 WILD-TYPE
  ASIAN                                    4                 35
  BLACK OR AFRICAN AMERICAN                0                 22
  WHITE                                   19                298
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V13, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED     1  21
  KIAA1267 WILD-TYPE   7 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED      1   21
  KIAA1267 WILD-TYPE    7  334
                        clus
vv                       KIAA1267 MUTATED KIAA1267 WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               21                334
[1] 2 2
[1] FALSE

Clustering(23) Variable = MLL MUTATION ANALYSIS
D23V1, survival
               sevent
clus2             0   1
  MLL MUTATED    26  18
  MLL WILD-TYPE 191 157
  MLL MUTATED MLL WILD-TYPE 
           44           348 
  MLL MUTATED MLL WILD-TYPE 
           18           157 
$`MLL MUTATED`
TCGA-BT-A20N TCGA-CU-A0YO TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3X1 TCGA-DK-A6B2 
       26.14         4.90       130.88        87.32        66.05        15.68 
TCGA-FD-A3B6 TCGA-FD-A3SJ TCGA-FD-A6TG TCGA-FD-A6TH TCGA-G2-A3VY TCGA-GC-A3WC 
       33.04        24.30         3.06         4.31        17.62        17.75 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-XF-A9SM TCGA-XF-A9T8 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
        2.76         9.14        34.45        13.74        30.28        94.29 
TCGA-4Z-AA7W TCGA-5N-A9KI TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20Q 
       27.62         2.50         6.74        13.15        19.04        19.50 
TCGA-BT-A2LB TCGA-C4-A0F1 TCGA-CF-A1HR TCGA-E7-A7XN TCGA-FD-A3N5 TCGA-GC-A3RC 
       16.18         2.93        12.79        14.07        22.52        15.91 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GU-A766 TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB 
        8.94        13.91        15.78         9.07        17.72        15.42 
TCGA-MV-A51V TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HI 
       13.48        38.99        76.01        17.82         3.85        17.88 
TCGA-ZF-A9RF TCGA-GU-AATO 
       64.08        10.65 

$`MLL WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ 
        8.98         2.04        18.58        12.92        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A3IN 
       13.58         2.14        19.00        16.70        46.68         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 
       17.72        50.27        21.30        23.21         9.67        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 
       64.18        53.29        76.60        67.36        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       38.24        52.01       165.73       166.03        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU 
       56.15        11.18        20.32        15.35        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        1.22         4.01        60.66        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-AA3D 
        9.67        31.07        17.23        11.08        33.01        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP 
       21.40        19.13        24.92        10.92        32.78        32.98 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       19.82        20.28        27.35         8.58        19.07        22.72 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        9.01        25.02         3.45        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       35.97        46.98        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
       51.32         3.22        15.98        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
        2.10        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RE 
       18.58         3.88         9.63        13.64        21.11         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO 
       88.87        34.06        19.69        57.90        12.23        24.13 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O 
       11.97        94.88       104.65         8.35        44.94        16.83 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       17.16        34.98        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       66.54        10.22        47.80        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20U 
        2.66         6.58        12.16        17.88         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        5.06         8.25        17.16         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
       28.41         1.94        23.01        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.87        13.08         5.19        29.79         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       66.41        18.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       17.95         7.79       142.78         4.80        13.58         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       19.00        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        22.16         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
       26.96        26.24         4.24        24.03        24.66        13.68 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       12.62        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
       20.91        19.33         5.36        27.45         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       13.35         2.27        10.85        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25        22.88        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       59.31         7.23        20.12        66.02         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       20.71        15.81        14.07        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
       20.98         2.20        11.31        18.97         7.63        20.05 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
        4.73         7.00        14.27        21.34        19.10         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
       36.49         1.51        19.40        38.60        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       21.24        11.70         1.81        16.27        11.80        44.38 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
        1.15        15.32        15.58        12.23        16.67        16.54 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       17.62        37.05        22.68        69.34        35.24        29.56 
TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        6.21         1.87        48.62        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32         6.77        56.48        27.06        75.39 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       21.86        28.41        13.41        58.72        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
        2.89         8.61        59.38        60.16        67.20        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        19.40         8.52        54.21        29.49         5.52 

  MLL MUTATED MLL WILD-TYPE 
         2.50          0.56 
  MLL MUTATED MLL WILD-TYPE 
       130.88        166.03 
  MLL MUTATED MLL WILD-TYPE 
       16.045        17.800 
[1] "2.5 - 130.9 (16.0)" "0.6 - 166.0 (17.8)"
[1] "hr=" "1"  
D23V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  MLL MUTATED         0       13        19       12
  MLL WILD-TYPE       2      109       116      122
D23V3, multiclass
           clus
vv          MLL MUTATED MLL WILD-TYPE
  STAGE I             0             2
  STAGE II           13           109
  STAGE III          19           116
  STAGE IV           12           122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1+T2  T3  T4
  MLL MUTATED         15  24   4
  MLL WILD-TYPE      101 166  53
D23V4, multiclass
          clus
vv         MLL MUTATED MLL WILD-TYPE
  T0+T1+T2          15           101
  T3                24           166
  T4                 4            53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  MLL MUTATED    28   4   8   0
  MLL WILD-TYPE 197  42  67   8
D23V5, multiclass
    clus
vv   MLL MUTATED MLL WILD-TYPE
  N0          28           197
  N1           4            42
  N2           8            67
  N3           0             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
               cls
clus              0   1
  MLL MUTATED    17   0
  MLL WILD-TYPE 172  11
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED     17    0
  MLL WILD-TYPE  172   11
   clus
vv  MLL MUTATED MLL WILD-TYPE
  0          17           172
  1           0            11
[1] 2 2
[1] FALSE
D23V7, binary
               cls
clus              0   1
  MLL MUTATED     9  35
  MLL WILD-TYPE  93 258
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED      9   35
  MLL WILD-TYPE   93  258
        clus
vv       MLL MUTATED MLL WILD-TYPE
  FEMALE           9            93
  MALE            35           258
[1] 2 2
[1] FALSE
D23V8, binary
               cls
clus              0   1
  MLL MUTATED    40   1
  MLL WILD-TYPE 310  19
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED     40    1
  MLL WILD-TYPE  310   19
     clus
vv    MLL MUTATED MLL WILD-TYPE
  NO           40           310
  YES           1            19
[1] 2 2
[1] FALSE
D23V9, continuous
D23V10, continuous
D23V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL MUTATED       3                         2    37
  MLL WILD-TYPE    36                        20   280
D23V12, multiclass
                           clus
vv                          MLL MUTATED MLL WILD-TYPE
  ASIAN                               3            36
  BLACK OR AFRICAN AMERICAN           2            20
  WHITE                              37           280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, binary
               cls
clus              0   1
  MLL MUTATED     0  40
  MLL WILD-TYPE   8 315
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED      0   40
  MLL WILD-TYPE    8  315
                        clus
vv                       MLL MUTATED MLL WILD-TYPE
  HISPANIC OR LATINO               0             8
  NOT HISPANIC OR LATINO          40           315
[1] 2 2
[1] FALSE

Clustering(24) Variable = FAT1 MUTATION ANALYSIS
D24V1, survival
                sevent
clus2              0   1
  FAT1 MUTATED    26  24
  FAT1 WILD-TYPE 191 151
  FAT1 MUTATED FAT1 WILD-TYPE 
            50            342 
  FAT1 MUTATED FAT1 WILD-TYPE 
            24            151 
$`FAT1 MUTATED`
TCGA-BT-A3PK TCGA-DK-A3IQ TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-DK-AA6S TCGA-E5-A4TZ 
        9.96        17.72        64.18        36.66       166.03        15.35 
TCGA-GC-A3WC TCGA-GU-AATP TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A54R TCGA-XF-A9T8 
       17.75        32.98        22.72        25.02        27.68        13.74 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA53 
        7.63        71.57        94.29        88.87        19.69        57.90 
TCGA-2F-A9KO TCGA-BL-A13I TCGA-BT-A20O TCGA-BT-A20U TCGA-BT-A2LB TCGA-BT-A42B 
       24.13         7.33        12.16        14.96        16.18        17.56 
TCGA-CF-A27C TCGA-CU-A3YL TCGA-DK-A1AG TCGA-DK-AA6Q TCGA-E5-A4U1 TCGA-E7-A4IJ 
       13.97        29.79        15.62        13.58        38.83        22.16 
TCGA-FD-A3B4 TCGA-FD-A6TK TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-AA3B TCGA-GC-A6I1 
       16.77        10.85        48.00        59.31        66.02         8.94 
TCGA-GU-A762 TCGA-GV-A3QI TCGA-HQ-A2OF TCGA-S5-AA26 TCGA-XF-A9SG TCGA-XF-A9SX 
        7.63        36.49        64.01        16.54        48.62        23.64 
TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9RN 
       92.98         2.96        75.39         0.66        11.97        20.22 
TCGA-ZF-AA4W TCGA-ZF-AA5N 
       60.16         5.52 

$`FAT1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C 
       26.14        14.89         8.35        20.48        25.94        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       46.68        87.32         8.22        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
        9.67        66.05        17.98        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W 
       15.68        50.70        38.24        52.01       165.73        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU 
       13.64        56.15        11.18        20.32        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        1.22        33.04         4.01        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       17.98        29.16        46.78        19.79        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
        3.62        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
       18.08        58.92         6.28        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
       12.69        12.36         3.06         4.31         9.67        31.07 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM 
       17.23        11.08        33.01        17.62        70.32        21.40 
TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QF 
       19.13        24.92        10.92        32.78        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AB 
       27.35         8.58        19.07         9.01         3.45         2.76 
TCGA-K4-A4AC TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
        9.14        52.73        50.56        35.97        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK 
        1.84        33.14        86.83        51.32         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       34.45        14.93         4.21        12.76        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMF 
       26.27        18.90         2.24        66.64         2.10        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
       11.31        54.90        91.73        98.99        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       61.45        86.30        18.58         3.88         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA5P TCGA-2F-A9KP 
       21.11        30.28         3.48        34.06        12.23        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       34.98        27.62        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       66.54        10.22        47.80         2.50        17.42        40.08 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20P 
        2.66         6.74         6.58        13.15        19.04        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH 
       19.50         5.06         5.06         8.25        17.16         4.67 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR 
       36.43        28.41         1.94         2.93        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       12.56        12.59        12.13        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A5W6 
       12.00        12.10        11.87        13.08         5.19         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       17.95         7.79       142.78         4.80        13.58         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U 
       20.81        10.55       163.30        15.02        18.81        19.00 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       15.35        12.03        43.59        29.72         5.36         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
       24.03        24.66        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.09        32.02         8.94        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
        5.52        25.74        22.98        14.96        20.91        19.33 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF 
        5.36        27.45         2.70         7.10        13.35         2.27 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
       12.66        10.65         8.94         3.25        22.88        61.94 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F 
       15.95        26.93         7.23        20.12         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 
       20.71        15.81        15.91        14.07        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05        15.78         4.73         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE 
       19.10         8.48         1.51        19.40        38.60        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       21.24         9.07        11.70        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       16.27        11.80        44.38         1.15        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       13.48        12.23        16.67        38.99        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       22.68        76.01        69.34        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
        6.21         3.85         1.87        17.88        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAMG TCGA-XF-AAMW 
       66.41         5.98        28.24        16.27       110.60         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
        6.77        56.48        27.06        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       35.84        21.86        28.41        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 
       47.84         2.89         8.61        59.38        67.20        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-GU-AATO 
       35.41        19.40         8.52        54.21        29.49        10.65 

  FAT1 MUTATED FAT1 WILD-TYPE 
          0.66           0.56 
  FAT1 MUTATED FAT1 WILD-TYPE 
        166.03         165.73 
  FAT1 MUTATED FAT1 WILD-TYPE 
        21.190         17.195 
[1] "0.7 - 166.0 (21.2)" "0.6 - 165.7 (17.2)"
[1] "hr=" "1.1"
D24V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  FAT1 MUTATED         0       17        22       11
  FAT1 WILD-TYPE       2      105       113      123
D24V3, multiclass
           clus
vv          FAT1 MUTATED FAT1 WILD-TYPE
  STAGE I              0              2
  STAGE II            17            105
  STAGE III           22            113
  STAGE IV            11            123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  FAT1 MUTATED         16  25   5
  FAT1 WILD-TYPE      100 165  52
D24V4, multiclass
          clus
vv         FAT1 MUTATED FAT1 WILD-TYPE
  T0+T1+T2           16            100
  T3                 25            165
  T4                  5             52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  FAT1 MUTATED    34   3   6   0
  FAT1 WILD-TYPE 191  43  69   8
D24V5, multiclass
    clus
vv   FAT1 MUTATED FAT1 WILD-TYPE
  N0           34            191
  N1            3             43
  N2            6             69
  N3            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                cls
clus               0   1
  FAT1 MUTATED    19   2
  FAT1 WILD-TYPE 170   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED     19    2
  FAT1 WILD-TYPE  170    9
   clus
vv  FAT1 MUTATED FAT1 WILD-TYPE
  0           19            170
  1            2              9
[1] 2 2
[1] FALSE
D24V7, binary
                cls
clus               0   1
  FAT1 MUTATED    19  31
  FAT1 WILD-TYPE  83 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED     19   31
  FAT1 WILD-TYPE   83  262
        clus
vv       FAT1 MUTATED FAT1 WILD-TYPE
  FEMALE           19             83
  MALE             31            262
[1] 2 2
[1] FALSE
D24V8, binary
                cls
clus               0   1
  FAT1 MUTATED    45   3
  FAT1 WILD-TYPE 305  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED     45    3
  FAT1 WILD-TYPE  305   17
     clus
vv    FAT1 MUTATED FAT1 WILD-TYPE
  NO            45            305
  YES            3             17
[1] 2 2
[1] FALSE
D24V9, continuous
D24V10, continuous
D24V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAT1 MUTATED       3                         2    41
  FAT1 WILD-TYPE    36                        20   276
D24V12, multiclass
                           clus
vv                          FAT1 MUTATED FAT1 WILD-TYPE
  ASIAN                                3             36
  BLACK OR AFRICAN AMERICAN            2             20
  WHITE                               41            276
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, binary
                cls
clus               0   1
  FAT1 MUTATED     2  47
  FAT1 WILD-TYPE   6 308
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED      2   47
  FAT1 WILD-TYPE    6  308
                        clus
vv                       FAT1 MUTATED FAT1 WILD-TYPE
  HISPANIC OR LATINO                2              6
  NOT HISPANIC OR LATINO           47            308
[1] 2 2
[1] FALSE

Clustering(25) Variable = KLF5 MUTATION ANALYSIS
D25V1, survival
                sevent
clus2              0   1
  KLF5 MUTATED    14   8
  KLF5 WILD-TYPE 203 167
  KLF5 MUTATED KLF5 WILD-TYPE 
            22            370 
  KLF5 MUTATED KLF5 WILD-TYPE 
             8            167 
$`KLF5 MUTATED`
TCGA-BT-A42C TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A6B0 TCGA-DK-AA71 TCGA-FD-A3SS 
       28.70        23.21        66.05        76.60        13.64        12.85 
TCGA-GC-A3WC TCGA-GV-A3QK TCGA-KQ-A41N TCGA-S5-A6DX TCGA-XF-A9SY TCGA-XF-A9T3 
       17.75        27.35        52.73         1.84        21.04         2.24 
TCGA-XF-AAMH TCGA-4Z-AA87 TCGA-BL-A3JM TCGA-BT-A0YX TCGA-C4-A0F6 TCGA-E7-A3Y1 
       11.31        47.80         6.74        13.15        23.01         5.36 
TCGA-FJ-A3Z9 TCGA-K4-A83P TCGA-SY-A9G5 TCGA-ZF-A9R9 
       12.66        16.27        38.99        28.41 

$`KLF5 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-DK-A6B2 
        9.67        17.98        64.18        53.29        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S 
       50.70        36.66        38.24        52.01       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 
       13.64        56.15        11.18        20.32        15.35        25.58 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
        0.92         1.22        33.04         4.01        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P 
       23.41        17.98        29.16        46.78        19.79        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
        3.62        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
       18.08        58.92         6.28        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
       12.69        12.36         3.06         4.31         9.67        31.07 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM 
       17.23        11.08        33.01        17.62        70.32        21.40 
TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       19.13        24.92        10.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       20.28         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41P 
        3.45         2.76         9.14        27.68        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ 
       46.98        14.24        33.14        86.83        51.32         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
       15.98        34.45        14.93         4.21        12.76        11.90 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       26.27        18.90        66.64         2.10        13.74        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63        71.57        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       30.94        61.45        86.30        18.58         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL 
       13.64        21.11        30.28        94.29         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       34.06        19.69        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       34.98        27.62        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       66.54        10.22         2.50        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        2.66         6.58        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 
        4.67        17.56        36.43        28.41         1.94         2.93 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       12.79        12.56        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       12.16        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.19        29.79         1.84        21.86        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX 
      142.78         4.80        13.58         8.15        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
      163.30        15.02        13.58        18.81        19.00        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       12.03        43.59        38.83        29.72        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
       24.03        24.66        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       27.98         5.52        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       19.33         5.36        27.45         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC 
        2.27        10.85        10.65         8.94         3.25        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       61.94        48.00        15.95        26.93        59.31         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       20.12        66.02         6.94        29.36        20.71        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07         8.94        13.91        26.70         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        3.12        20.98         2.20        11.31        18.97         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05        15.78         4.73         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       19.10         8.48        36.49         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       64.01        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
        1.81        15.42        11.80        44.38         1.15        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K 
       15.58        13.48        12.23        16.67        16.54        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       37.05        22.68        76.01        69.34        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         6.21         3.85         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        79.66        66.41         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       16.27        92.98       110.60         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
       56.48        27.06        75.39         0.66        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       25.41        31.20        35.84        21.86        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       58.72        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        67.20        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  KLF5 MUTATED KLF5 WILD-TYPE 
          1.84           0.56 
  KLF5 MUTATED KLF5 WILD-TYPE 
         76.60         166.03 
  KLF5 MUTATED KLF5 WILD-TYPE 
        19.395         17.620 
[1] "1.8 - 76.6 (19.4)"  "0.6 - 166.0 (17.6)"
[1] "hr=" "1.3"
D25V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  KLF5 MUTATED         0        6         8        8
  KLF5 WILD-TYPE       2      116       127      126
D25V3, multiclass
           clus
vv          KLF5 MUTATED KLF5 WILD-TYPE
  STAGE I              0              2
  STAGE II             6            116
  STAGE III            8            127
  STAGE IV             8            126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  KLF5 MUTATED          4  10   6
  KLF5 WILD-TYPE      112 180  51
D25V4, multiclass
          clus
vv         KLF5 MUTATED KLF5 WILD-TYPE
  T0+T1+T2            4            112
  T3                 10            180
  T4                  6             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  KLF5 MUTATED    15   2   5   1
  KLF5 WILD-TYPE 210  44  70   7
D25V5, multiclass
    clus
vv   KLF5 MUTATED KLF5 WILD-TYPE
  N0           15            210
  N1            2             44
  N2            5             70
  N3            1              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"
D25V6, binary
                cls
clus               0   1
  KLF5 MUTATED    14   0
  KLF5 WILD-TYPE 175  11
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED     14    0
  KLF5 WILD-TYPE  175   11
   clus
vv  KLF5 MUTATED KLF5 WILD-TYPE
  0           14            175
  1            0             11
[1] 2 2
[1] FALSE
D25V7, binary
                cls
clus               0   1
  KLF5 MUTATED     8  15
  KLF5 WILD-TYPE  94 278
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED      8   15
  KLF5 WILD-TYPE   94  278
        clus
vv       KLF5 MUTATED KLF5 WILD-TYPE
  FEMALE            8             94
  MALE             15            278
[1] 2 2
[1] FALSE
D25V8, binary
                cls
clus               0   1
  KLF5 MUTATED    19   2
  KLF5 WILD-TYPE 331  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED     19    2
  KLF5 WILD-TYPE  331   18
     clus
vv    KLF5 MUTATED KLF5 WILD-TYPE
  NO            19            331
  YES            2             18
[1] 2 2
[1] FALSE
D25V9, continuous
D25V10, continuous
D25V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLF5 MUTATED       0                         2    20
  KLF5 WILD-TYPE    39                        20   297
D25V12, multiclass
                           clus
vv                          KLF5 MUTATED KLF5 WILD-TYPE
  ASIAN                                0             39
  BLACK OR AFRICAN AMERICAN            2             20
  WHITE                               20            297
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, binary
                cls
clus               0   1
  KLF5 MUTATED     0  21
  KLF5 WILD-TYPE   8 334
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED      0   21
  KLF5 WILD-TYPE    8  334
                        clus
vv                       KLF5 MUTATED KLF5 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           21            334
[1] 2 2
[1] FALSE

Clustering(26) Variable = PTEN MUTATION ANALYSIS
D26V1, survival
                sevent
clus2              0   1
  PTEN MUTATED     9   5
  PTEN WILD-TYPE 208 170
  PTEN MUTATED PTEN WILD-TYPE 
            14            378 
  PTEN MUTATED PTEN WILD-TYPE 
             5            170 
$`PTEN MUTATED`
TCGA-BL-A5ZZ TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GV-A40E 
       12.39        87.32         8.22        17.62        70.32         8.58 
TCGA-XF-AAMF TCGA-DK-A3WW TCGA-FJ-A871 TCGA-G2-A2EL TCGA-KQ-A41R TCGA-LT-A5Z6 
       10.82        20.81         8.94        26.93        44.38        15.58 
TCGA-UY-A78L TCGA-UY-A9PE 
       37.05         6.21 

$`PTEN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BT-A20N 
      108.95        16.27        16.77        15.12        33.83        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       46.68        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       66.05        17.98        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       15.68        50.70        36.66        38.24        52.01       165.73 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
      166.03        13.64        13.64        56.15        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       15.35        25.58         0.92         1.22        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
       60.66        24.30        23.41        17.98        29.16        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       19.79        12.85        27.35         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       10.78         5.69         8.25        18.08        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
       62.86        18.81         6.15        12.69        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        4.31         9.67        31.07        17.23        11.08        33.01 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 
       21.40        19.13        17.75        24.92        10.92        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA 
       32.98        19.82        20.28        27.35        19.07        22.72 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        9.01        25.02         3.45         2.76         9.14        27.68 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX 
       52.73        50.56        35.97        46.98        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
       33.14        86.83        51.32         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       14.93         4.21        12.76        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMH 
       18.90         2.24        66.64         2.10        13.74        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63        71.57        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       30.94        61.45        86.30        18.58         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL 
       13.64        21.11        30.28        94.29         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       34.06        19.69        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       34.98        27.62        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       66.54        10.22        47.80         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50         5.06        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        8.25        17.16        16.18         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         1.94         2.93        23.01        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.00        12.10        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        1.84        21.86        66.41        18.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
       13.58         8.15        10.55       163.30        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       18.81        19.00        15.35        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        22.16         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       12.66        10.65         3.25        22.88        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       15.95        59.31         7.23        20.12        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 
       29.36        20.71        15.81        15.91        14.07         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91        26.70         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31        18.97         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        7.00        14.27        21.34        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80         1.15        15.32        13.48        12.23        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       16.54        38.99        17.62        22.68        76.01        69.34 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       35.24        29.56        17.82         3.85         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       48.62        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW 
       28.24        16.27        92.98       110.60         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L 
        6.77        56.48        27.06        75.39         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       13.41        64.08        58.72        47.84        20.22         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21        29.49         5.52        10.65 

  PTEN MUTATED PTEN WILD-TYPE 
          6.21           0.56 
  PTEN MUTATED PTEN WILD-TYPE 
         87.32         166.03 
  PTEN MUTATED PTEN WILD-TYPE 
         16.60          17.67 
[1] "6.2 - 87.3 (16.6)"  "0.6 - 166.0 (17.7)"
[1] "hr=" "1.3"
D26V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PTEN MUTATED         0        5         4        5
  PTEN WILD-TYPE       2      117       131      129
D26V3, multiclass
           clus
vv          PTEN MUTATED PTEN WILD-TYPE
  STAGE I              0              2
  STAGE II             5            117
  STAGE III            4            131
  STAGE IV             5            129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  PTEN MUTATED          3   3   3
  PTEN WILD-TYPE      113 187  54
D26V4, multiclass
          clus
vv         PTEN MUTATED PTEN WILD-TYPE
  T0+T1+T2            3            113
  T3                  3            187
  T4                  3             54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PTEN MUTATED     5   2   3   0
  PTEN WILD-TYPE 220  44  72   8
D26V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0            5            220
  N1            2             44
  N2            3             72
  N3            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                cls
clus               0   1
  PTEN MUTATED     5   0
  PTEN WILD-TYPE 184  11
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      5    0
  PTEN WILD-TYPE  184   11
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            5            184
  1            0             11
[1] 2 2
[1] FALSE
D26V7, binary
                cls
clus               0   1
  PTEN MUTATED     2  12
  PTEN WILD-TYPE 100 281
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      2   12
  PTEN WILD-TYPE  100  281
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            2            100
  MALE             12            281
[1] 2 2
[1] FALSE
D26V8, binary
                cls
clus               0   1
  PTEN MUTATED    14   0
  PTEN WILD-TYPE 336  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     14    0
  PTEN WILD-TYPE  336   20
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO            14            336
  YES            0             20
[1] 2 2
[1] FALSE
D26V9, continuous
D26V10, continuous
D26V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       1                         0    13
  PTEN WILD-TYPE    38                        22   304
D26V12, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                1             38
  BLACK OR AFRICAN AMERICAN            0             22
  WHITE                               13            304
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, binary
                cls
clus               0   1
  PTEN MUTATED     0  14
  PTEN WILD-TYPE   8 341
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0   14
  PTEN WILD-TYPE    8  341
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           14            341
[1] 2 2
[1] FALSE

Clustering(27) Variable = C3ORF70 MUTATION ANALYSIS
D27V1, survival
                   sevent
clus2                 0   1
  C3ORF70 MUTATED    12   5
  C3ORF70 WILD-TYPE 205 170
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
               17               375 
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
                5               170 
$`C3ORF70 MUTATED`
TCGA-DK-A3IS TCGA-DK-A6AW TCGA-FD-A6TB TCGA-XF-AAML TCGA-ZF-A9RC TCGA-4Z-AA81 
       50.27        53.29        18.81         7.63        94.29        41.75 
TCGA-BT-A0YX TCGA-DK-A1AD TCGA-DK-A2I4 TCGA-G2-A2EO TCGA-GU-A42Q TCGA-H4-A2HQ 
       13.15       112.44       142.78        59.31        11.31        19.40 
TCGA-K4-A5RJ TCGA-PQ-A6FI TCGA-UY-A9PF TCGA-XF-AAN5 TCGA-ZF-A9R7 
       17.72        12.23         3.85        75.39        21.86 

$`C3ORF70 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
      130.88        46.68        87.32         8.22        17.72        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 
       23.21         9.67        66.05        17.98        64.18        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       67.36        15.68        50.70        36.66        38.24        52.01 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
      165.73       166.03        13.64        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
        6.28        62.86         6.15        12.69        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        4.31         9.67        31.07        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       17.62        70.32        21.40        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       10.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        8.58        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       46.98        14.24         1.84        33.14        86.83        51.32 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
        3.22        15.98        34.45        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ 
        2.10        13.74        10.82        11.31        54.90        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.48        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       16.83        17.16        34.98        27.62        50.04         0.62 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM 
       51.16        66.54        10.22        47.80         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J 
       40.08         7.33         2.66         6.74         6.58        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50         5.06        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        8.25        17.16        16.18         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         1.94         2.93        23.01        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.00        12.10        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF 
        1.84        21.86        66.41        18.41        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       15.62        17.95         7.79         4.80        13.58         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       19.00        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        22.16         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
       26.96        26.24         4.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.70         7.10        13.35         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65         8.94         3.25        22.88        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       15.95        26.93         7.23        20.12        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 
       29.36        20.71        15.81        15.91        14.07         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91        26.70         2.10         3.12        20.98         2.20 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       18.97         7.63        20.05        15.78         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
       14.27        21.34        19.10         8.48        36.49         1.51 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
       38.60        64.01        12.16        21.24         9.07        11.70 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
        1.81        15.42        16.27        11.80        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       15.32        15.58        13.48        16.67        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       17.62        37.05        22.68        76.01        69.34        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       29.56        17.82         6.21         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        79.66        66.41         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       16.27        92.98       110.60         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       56.48        27.06         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       31.20        35.84        28.41        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       47.84        20.22         2.89         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       67.20        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
             3.85              0.56 
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
           142.78            166.03 
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
            21.86             17.42 
[1] "3.9 - 142.8 (21.9)" "0.6 - 166.0 (17.4)"
[1] "hr=" "2.2"
D27V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  C3ORF70 MUTATED         0        7         7        3
  C3ORF70 WILD-TYPE       2      115       128      131
D27V3, multiclass
           clus
vv          C3ORF70 MUTATED C3ORF70 WILD-TYPE
  STAGE I                 0                 2
  STAGE II                7               115
  STAGE III               7               128
  STAGE IV                3               131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  C3ORF70 MUTATED          6   9   0
  C3ORF70 WILD-TYPE      110 181  57
D27V4, multiclass
          clus
vv         C3ORF70 MUTATED C3ORF70 WILD-TYPE
  T0+T1+T2               6               110
  T3                     9               181
  T4                     0                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C3ORF70 MUTATED    13   0   2   0
  C3ORF70 WILD-TYPE 212  46  73   8
D27V5, multiclass
    clus
vv   C3ORF70 MUTATED C3ORF70 WILD-TYPE
  N0              13               212
  N1               0                46
  N2               2                73
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                   cls
clus                  0   1
  C3ORF70 MUTATED     9   1
  C3ORF70 WILD-TYPE 180  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF70 MUTATED      9    1
  C3ORF70 WILD-TYPE  180   10
   clus
vv  C3ORF70 MUTATED C3ORF70 WILD-TYPE
  0               9               180
  1               1                10
[1] 2 2
[1] FALSE
D27V7, binary
                   cls
clus                  0   1
  C3ORF70 MUTATED     4  13
  C3ORF70 WILD-TYPE  98 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF70 MUTATED      4   13
  C3ORF70 WILD-TYPE   98  280
        clus
vv       C3ORF70 MUTATED C3ORF70 WILD-TYPE
  FEMALE               4                98
  MALE                13               280
[1] 2 2
[1] FALSE
D27V8, binary
                   cls
clus                  0   1
  C3ORF70 MUTATED    16   0
  C3ORF70 WILD-TYPE 334  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF70 MUTATED     16    0
  C3ORF70 WILD-TYPE  334   20
     clus
vv    C3ORF70 MUTATED C3ORF70 WILD-TYPE
  NO               16               334
  YES               0                20
[1] 2 2
[1] FALSE
D27V9, continuous
D27V10, continuous
D27V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C3ORF70 MUTATED       0                         1    16
  C3ORF70 WILD-TYPE    39                        21   301
D27V12, multiclass
                           clus
vv                          C3ORF70 MUTATED C3ORF70 WILD-TYPE
  ASIAN                                   0                39
  BLACK OR AFRICAN AMERICAN               1                21
  WHITE                                  16               301
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V13, binary
                   cls
clus                  0   1
  C3ORF70 MUTATED     0  15
  C3ORF70 WILD-TYPE   8 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF70 MUTATED      0   15
  C3ORF70 WILD-TYPE    8  340
                        clus
vv                       C3ORF70 MUTATED C3ORF70 WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              15               340
[1] 2 2
[1] FALSE

Clustering(28) Variable = PSIP1 MUTATION ANALYSIS
D28V1, survival
                 sevent
clus2               0   1
  PSIP1 MUTATED    11   9
  PSIP1 WILD-TYPE 206 166
  PSIP1 MUTATED PSIP1 WILD-TYPE 
             20             372 
  PSIP1 MUTATED PSIP1 WILD-TYPE 
              9             166 
$`PSIP1 MUTATED`
TCGA-2F-A9KT TCGA-DK-A3IS TCGA-DK-A6AW TCGA-DK-AA6W TCGA-DK-AA75 TCGA-FD-A3SS 
      108.95        50.27        53.29        13.64        11.18        12.85 
TCGA-FD-A5BR TCGA-FD-A6TC TCGA-G2-A3VY TCGA-XF-A9SV TCGA-XF-AAML TCGA-4Z-AA80 
       26.73         6.15        17.62        12.76         7.63         0.62 
TCGA-BT-A2LB TCGA-CF-A27C TCGA-DK-A1AG TCGA-E5-A4U1 TCGA-E7-A5KF TCGA-FD-A3SO 
       16.18        13.97        15.62        38.83         0.66         5.52 
TCGA-MV-A51V TCGA-UY-A78M 
       13.48        22.68 

$`PSIP1 WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
       16.27        16.77        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
       46.68        87.32         8.22        17.72        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 
        9.67        66.05        17.98        64.18        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       15.68        50.70        36.66        38.24        52.01       165.73 
TCGA-DK-AA6S TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 
      166.03        13.64        56.15        20.32        15.35        25.58 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
        0.92         1.22        33.04         4.01        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P 
       23.41        17.98        29.16        46.78        19.79        27.35 
TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
        3.62        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE 
       58.92         6.28        62.86        18.81        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       33.01        70.32        21.40        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       10.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        8.58        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       46.98        14.24         1.84        33.14        86.83        51.32 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW 
        3.22        15.98        34.45        14.93         4.21        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR 
       13.74        10.82        11.31        54.90        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       98.99        44.32        30.94        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
        3.88         9.63        13.64        21.11        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.48        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 
       16.83        17.16        34.98        27.62        50.04        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM 
       51.16        66.54        10.22        47.80         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       19.04        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        5.06         8.25        17.16         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         1.94         2.93        23.01        12.79        12.56 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.10        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       17.95         7.79       142.78         4.80        13.58         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 
       19.00        15.35        12.03        43.59        29.72         5.36 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 
       22.16         2.24        16.70         0.56        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
        4.24        24.03        24.66        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       14.37         8.09        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       22.52        27.98        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       19.33         5.36        27.45         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.27        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
        7.23        20.12        66.02         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91        14.07         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
       38.60        64.01        12.16        21.24         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       17.72         1.81        15.42        16.27        11.80        44.38 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
        1.15        15.32        15.58        12.23        16.67        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       38.99        17.62        37.05        76.01        69.34        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         6.21         3.85         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       48.62        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW 
       28.24        16.27        92.98       110.60         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L 
        6.77        56.48        27.06        75.39         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       13.41        64.08        58.72        47.84        20.22         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21        29.49         5.52        10.65 

  PSIP1 MUTATED PSIP1 WILD-TYPE 
           0.62            0.56 
  PSIP1 MUTATED PSIP1 WILD-TYPE 
         108.95          166.03 
  PSIP1 MUTATED PSIP1 WILD-TYPE 
         13.805          17.785 
[1] "0.6 - 109.0 (13.8)" "0.6 - 166.0 (17.8)"
[1] "hr=" "1.2"
D28V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PSIP1 MUTATED         0       10         6        4
  PSIP1 WILD-TYPE       2      112       129      130
D28V3, multiclass
           clus
vv          PSIP1 MUTATED PSIP1 WILD-TYPE
  STAGE I               0               2
  STAGE II             10             112
  STAGE III             6             129
  STAGE IV              4             130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  PSIP1 MUTATED         10   6   3
  PSIP1 WILD-TYPE      106 184  54
D28V4, multiclass
          clus
vv         PSIP1 MUTATED PSIP1 WILD-TYPE
  T0+T1+T2            10             106
  T3                   6             184
  T4                   3              54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PSIP1 MUTATED    15   1   2   1
  PSIP1 WILD-TYPE 210  45  73   7
D28V5, multiclass
    clus
vv   PSIP1 MUTATED PSIP1 WILD-TYPE
  N0            15             210
  N1             1              45
  N2             2              73
  N3             1               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"
D28V6, binary
                 cls
clus                0   1
  PSIP1 MUTATED    12   1
  PSIP1 WILD-TYPE 177  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSIP1 MUTATED     12    1
  PSIP1 WILD-TYPE  177   10
   clus
vv  PSIP1 MUTATED PSIP1 WILD-TYPE
  0            12             177
  1             1              10
[1] 2 2
[1] FALSE
D28V7, binary
                 cls
clus                0   1
  PSIP1 MUTATED     3  17
  PSIP1 WILD-TYPE  99 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSIP1 MUTATED      3   17
  PSIP1 WILD-TYPE   99  276
        clus
vv       PSIP1 MUTATED PSIP1 WILD-TYPE
  FEMALE             3              99
  MALE              17             276
[1] 2 2
[1] FALSE
D28V8, binary
                 cls
clus                0   1
  PSIP1 MUTATED    16   2
  PSIP1 WILD-TYPE 334  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSIP1 MUTATED     16    2
  PSIP1 WILD-TYPE  334   18
     clus
vv    PSIP1 MUTATED PSIP1 WILD-TYPE
  NO             16             334
  YES             2              18
[1] 2 2
[1] FALSE
D28V9, continuous
D28V10, continuous
D28V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PSIP1 MUTATED       4                         0    15
  PSIP1 WILD-TYPE    35                        22   302
D28V12, multiclass
                           clus
vv                          PSIP1 MUTATED PSIP1 WILD-TYPE
  ASIAN                                 4              35
  BLACK OR AFRICAN AMERICAN             0              22
  WHITE                                15             302
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, binary
                 cls
clus                0   1
  PSIP1 MUTATED     0  19
  PSIP1 WILD-TYPE   8 336
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSIP1 MUTATED      0   19
  PSIP1 WILD-TYPE    8  336
                        clus
vv                       PSIP1 MUTATED PSIP1 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            19             336
[1] 2 2
[1] FALSE

Clustering(29) Variable = MLL3 MUTATION ANALYSIS
D29V1, survival
                sevent
clus2              0   1
  MLL3 MUTATED    41  33
  MLL3 WILD-TYPE 176 142
  MLL3 MUTATED MLL3 WILD-TYPE 
            74            318 
  MLL3 MUTATED MLL3 WILD-TYPE 
            33            142 
$`MLL3 MUTATED`
TCGA-2F-A9KT TCGA-BT-A20T TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CF-A9FL 
      108.95        14.89        25.94         9.96         8.98        18.58 
TCGA-DK-A2HX TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A6AW TCGA-DK-A6B2 TCGA-DK-A6B6 
       46.68        50.27        21.30        53.29        15.68        36.66 
TCGA-DK-AA6L TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-FD-A3NA TCGA-FD-A3SJ 
       38.24        11.18        20.32        15.35        60.66        24.30 
TCGA-FD-A3SM TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A5BX TCGA-G2-A2ES TCGA-G2-A3VY 
       17.98        12.85        27.35         5.69        33.01        17.62 
TCGA-GC-A3BM TCGA-GU-AATP TCGA-HQ-A5ND TCGA-KQ-A41N TCGA-UY-A9PH TCGA-XF-A9T5 
       21.40        32.98         9.01        52.73        51.32        66.64 
TCGA-XF-A9T8 TCGA-YC-A8S6 TCGA-2F-A9KO TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA83 
       13.74         9.63        24.13        17.16         0.62        66.54 
TCGA-5N-A9KI TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20X TCGA-BT-A3PH 
        2.50         7.33         2.66        19.04         8.25         4.67 
TCGA-C4-A0F1 TCGA-CF-A3MF TCGA-CF-A3MI TCGA-CF-A47W TCGA-CF-A47Y TCGA-DK-A1AE 
        2.93        12.59        12.16        12.10        12.26        16.14 
TCGA-DK-A3WW TCGA-DK-AA6X TCGA-E7-A3Y1 TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A7XN 
       20.81        15.35         5.36        16.70         0.66        14.07 
TCGA-FD-A3B5 TCGA-FD-A3N6 TCGA-FD-A6TK TCGA-FJ-A871 TCGA-G2-A3IE TCGA-G2-AA3B 
        8.94        27.98        10.85         8.94        20.12        66.02 
TCGA-GC-A3I6 TCGA-GU-A767 TCGA-GV-A3JX TCGA-H4-A2HQ TCGA-K4-A5RH TCGA-K4-A6FZ 
       20.71         4.73        19.10        19.40         9.07         1.81 
TCGA-KQ-A41R TCGA-MV-A51V TCGA-UY-A9PF TCGA-XF-AAMT TCGA-YC-A9TC TCGA-ZF-AA4V 
       44.38        13.48         3.85         2.96         0.66        59.38 
TCGA-ZF-AA51 TCGA-GU-AATO 
       56.35        10.65 

$`MLL3 WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
       16.27        16.77        15.12        33.83        12.39        26.14 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A42C TCGA-C4-A0F7 TCGA-CU-A0YN TCGA-CU-A0YO 
        8.35        20.48        28.70         2.04        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3IV 
      130.88        87.32         8.22        17.72        23.21         9.67 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 
       66.05        17.98        64.18        76.60        67.36        50.70 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SL 
       25.58         0.92         1.22        33.04         4.01        23.41 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       29.16        46.78        19.79         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
       10.78         8.25        18.08        58.92         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         3.06         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-AA3D TCGA-GC-A3RB 
        9.67        31.07        17.23        11.08        70.32        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QF 
       17.75        24.92        10.92        32.78        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A3WU 
       27.35         8.58        19.07        22.72        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        2.76         9.14        27.68        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A9SJ TCGA-XF-A9SK 
       14.24         1.84        33.14        86.83         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       34.45        14.93         4.21        12.76        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH 
       26.27        18.90         2.24         2.10        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63        71.57        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YF-AA3M 
       30.94        61.45        86.30        18.58         3.88        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
       21.11        30.28        94.29         3.48        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       19.69        57.90        12.23        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
        8.35        44.94        16.83        34.98        27.62        50.04 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A0C8 
       41.75        51.16        10.22        47.80        17.42        40.08 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74         6.58        13.15        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42B 
        5.06        14.96         5.06        17.16        16.18        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       36.43        28.41         1.94        23.01        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       13.97        12.13        13.08        10.95        12.66        12.46 
TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.62        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.19        29.79         1.84        21.86        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
      112.44        17.62        15.62        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P 
        4.80        13.58         8.15        10.55       163.30        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       13.58        18.81        19.00        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 
       29.72        22.16         2.24         0.56        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P 
        4.24        24.03        24.66        13.68        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SO 
        8.09        32.02        16.77        12.62        22.52         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FJ-A3Z9 
       27.45         2.70         7.10        13.35         2.27        12.66 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       10.65         3.25        22.88        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO 
       26.93        59.31         7.23         6.94        29.36        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07         8.94        13.91        26.70         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        3.12        20.98         2.20        11.31        18.97         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH 
       20.05        15.78         7.00        14.27        21.34         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
       36.49         1.51        38.60        64.01        12.16        21.24 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S 
       11.70        17.72        15.42        16.27        11.80         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       15.32        15.58        12.23        16.67        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       17.62        37.05        22.68        76.01        69.34        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       29.56        17.82         6.21         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        79.66        66.41         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       16.27        92.98       110.60         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       27.06        75.39        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       35.84        21.86        28.41        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X 
       47.84        20.22         2.89         8.61        60.16        67.20 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        19.40         8.52        54.21        29.49         5.52 

  MLL3 MUTATED MLL3 WILD-TYPE 
          0.62           0.56 
  MLL3 MUTATED MLL3 WILD-TYPE 
        108.95         166.03 
  MLL3 MUTATED MLL3 WILD-TYPE 
        15.910         17.785 
[1] "0.6 - 109.0 (15.9)" "0.6 - 166.0 (17.8)"
[1] "hr=" "1.1"
D29V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MLL3 MUTATED         0       28        21       25
  MLL3 WILD-TYPE       2       94       114      109
D29V3, multiclass
           clus
vv          MLL3 MUTATED MLL3 WILD-TYPE
  STAGE I              0              2
  STAGE II            28             94
  STAGE III           21            114
  STAGE IV            25            109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  MLL3 MUTATED         25  35   7
  MLL3 WILD-TYPE       91 155  50
D29V4, multiclass
          clus
vv         MLL3 MUTATED MLL3 WILD-TYPE
  T0+T1+T2           25             91
  T3                 35            155
  T4                  7             50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MLL3 MUTATED    43   9  12   1
  MLL3 WILD-TYPE 182  37  63   7
D29V5, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  N0           43            182
  N1            9             37
  N2           12             63
  N3            1              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"
D29V6, binary
                cls
clus               0   1
  MLL3 MUTATED    39   4
  MLL3 WILD-TYPE 150   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     39    4
  MLL3 WILD-TYPE  150    7
   clus
vv  MLL3 MUTATED MLL3 WILD-TYPE
  0           39            150
  1            4              7
[1] 2 2
[1] FALSE
D29V7, binary
                cls
clus               0   1
  MLL3 MUTATED    12  62
  MLL3 WILD-TYPE  90 231
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     12   62
  MLL3 WILD-TYPE   90  231
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  FEMALE           12             90
  MALE             62            231
[1] 2 2
[1] FALSE
D29V8, binary
                cls
clus               0   1
  MLL3 MUTATED    67   3
  MLL3 WILD-TYPE 283  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     67    3
  MLL3 WILD-TYPE  283   17
     clus
vv    MLL3 MUTATED MLL3 WILD-TYPE
  NO            67            283
  YES            3             17
[1] 2 2
[1] FALSE
D29V9, continuous
D29V10, continuous
D29V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL3 MUTATED       8                         6    57
  MLL3 WILD-TYPE    31                        16   260
D29V12, multiclass
                           clus
vv                          MLL3 MUTATED MLL3 WILD-TYPE
  ASIAN                                8             31
  BLACK OR AFRICAN AMERICAN            6             16
  WHITE                               57            260
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V13, binary
                cls
clus               0   1
  MLL3 MUTATED     0  68
  MLL3 WILD-TYPE   8 287
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      0   68
  MLL3 WILD-TYPE    8  287
                        clus
vv                       MLL3 MUTATED MLL3 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           68            287
[1] 2 2
[1] FALSE

Clustering(30) Variable = ASXL2 MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2               0   1
  ASXL2 MUTATED    22  14
  ASXL2 WILD-TYPE 195 161
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             36             356 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             14             161 
$`ASXL2 MUTATED`
TCGA-BT-A20N TCGA-BT-A20T TCGA-DK-A1AC TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-E5-A4TZ 
       26.14        14.89       130.88        53.29        67.36        15.35 
TCGA-E7-A7DU TCGA-FD-A3SS TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TC TCGA-GV-A3JZ 
        0.92        12.85        18.08         6.28         6.15        19.82 
TCGA-XF-A9T6 TCGA-XF-AAN7 TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-4Z-AA7W TCGA-BT-A0YX 
        2.10        18.58        94.29        88.87        27.62        13.15 
TCGA-CF-A1HR TCGA-CF-A9FF TCGA-CU-A5W6 TCGA-E7-A3X6 TCGA-E7-A6MD TCGA-E7-A7XN 
       12.79        11.87         1.84        29.72         4.24        14.07 
TCGA-FD-A5BU TCGA-G2-AA3B TCGA-GD-A2C5 TCGA-GU-A764 TCGA-S5-AA26 TCGA-SY-A9G5 
       19.33        66.02        26.70        20.05        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A9PE TCGA-XF-AAMX TCGA-ZF-A9RG TCGA-ZF-AA54 TCGA-ZF-AA5N 
       17.62         6.21         6.77        58.72        19.40         5.52 

$`ASXL2 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
        8.35        20.48        25.94         9.96        28.70         8.98 
TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        2.04        18.58        12.92         4.90        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I6 
       13.58         2.14        19.00        16.70        46.68        87.32 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 
       66.05        17.98        64.18        76.60        15.68        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       36.66        38.24        52.01       165.73       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DV 
       13.64        56.15        11.18        20.32        25.58         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       29.16        46.78        19.79        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A6TA 
       53.88        10.78         5.69         8.25        58.92        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       18.81        12.69        12.36         3.06         4.31         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D 
       31.07        17.23        11.08        33.01        17.62        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 
       21.40        19.13        17.75        24.92        10.92        32.78 
TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       32.98        20.28        27.35         8.58        19.07        22.72 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        9.01        25.02         3.45         2.76         9.14        27.68 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX 
       52.73        50.56        35.97        46.98        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
       33.14        86.83        51.32         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       14.93         4.21        12.76        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
       18.90         2.24        66.64        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63        71.57        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       30.94        61.45        86.30         3.88         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       21.11        30.28         3.48        34.06        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 
       44.94        16.83        17.16        34.98        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
       41.75        51.16        66.54        10.22        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       17.42        40.08         7.33         2.66         6.74         6.58 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       19.04        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
        5.06         8.25        17.16        16.18         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HS 
       36.43        28.41         1.94         2.93        23.01        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 
       12.00        12.10        13.08         5.19        29.79        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       66.41        18.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       17.95         7.79       142.78         4.80        13.58         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3Y1 
       19.00        15.35        12.03        43.59        38.83         5.36 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
       22.16         2.24        16.70         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P 
       26.24        24.03        24.66        13.68        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       27.98         5.52        25.74        22.98        14.96        20.91 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF 
        5.36        27.45         2.70         7.10        13.35         2.27 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC 
       10.85        12.66        10.65         8.94         3.25        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       61.94        48.00        15.95        26.93        59.31         7.23 
TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       20.12         6.94        29.36        20.71        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       14.07         8.94        13.91         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 
        2.20        11.31        18.97         7.63        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        7.00        14.27        21.34        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       11.80        44.38         1.15        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       12.23        16.67        37.05        22.68        76.01        69.34 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       35.24        29.56        17.82         3.85         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       48.62        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW 
       28.24        16.27        92.98       110.60         2.96         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
       56.48        27.06        75.39         0.66        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       25.41        31.20        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       64.08        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA58 
       60.16        67.20        56.35        35.41         8.52        54.21 
TCGA-ZF-AA5H TCGA-GU-AATO 
       29.49        10.65 

  ASXL2 MUTATED ASXL2 WILD-TYPE 
           0.92            0.56 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
         130.88          166.03 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
          17.85           17.62 
[1] "0.9 - 130.9 (17.9)" "0.6 - 166.0 (17.6)"
[1] "hr=" "1.2"
D30V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ASXL2 MUTATED         0       10        15       11
  ASXL2 WILD-TYPE       2      112       120      123
D30V3, multiclass
           clus
vv          ASXL2 MUTATED ASXL2 WILD-TYPE
  STAGE I               0               2
  STAGE II             10             112
  STAGE III            15             120
  STAGE IV             11             123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  ASXL2 MUTATED         11  16   7
  ASXL2 WILD-TYPE      105 174  50
D30V4, multiclass
          clus
vv         ASXL2 MUTATED ASXL2 WILD-TYPE
  T0+T1+T2            11             105
  T3                  16             174
  T4                   7              50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ASXL2 MUTATED    22   3   5   2
  ASXL2 WILD-TYPE 203  43  70   6
D30V5, multiclass
    clus
vv   ASXL2 MUTATED ASXL2 WILD-TYPE
  N0            22             203
  N1             3              43
  N2             5              70
  N3             2               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                 cls
clus                0   1
  ASXL2 MUTATED    15   1
  ASXL2 WILD-TYPE 174  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED     15    1
  ASXL2 WILD-TYPE  174   10
   clus
vv  ASXL2 MUTATED ASXL2 WILD-TYPE
  0            15             174
  1             1              10
[1] 2 2
[1] FALSE
D30V7, binary
                 cls
clus                0   1
  ASXL2 MUTATED     9  27
  ASXL2 WILD-TYPE  93 266
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED      9   27
  ASXL2 WILD-TYPE   93  266
        clus
vv       ASXL2 MUTATED ASXL2 WILD-TYPE
  FEMALE             9              93
  MALE              27             266
[1] 2 2
[1] FALSE
D30V8, binary
                 cls
clus                0   1
  ASXL2 MUTATED    31   0
  ASXL2 WILD-TYPE 319  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED     31    0
  ASXL2 WILD-TYPE  319   20
     clus
vv    ASXL2 MUTATED ASXL2 WILD-TYPE
  NO             31             319
  YES             0              20
[1] 2 2
[1] FALSE
D30V9, continuous
D30V10, continuous
D30V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASXL2 MUTATED       3                         3    29
  ASXL2 WILD-TYPE    36                        19   288
D30V12, multiclass
                           clus
vv                          ASXL2 MUTATED ASXL2 WILD-TYPE
  ASIAN                                 3              36
  BLACK OR AFRICAN AMERICAN             3              19
  WHITE                                29             288
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V13, binary
                 cls
clus                0   1
  ASXL2 MUTATED     0  33
  ASXL2 WILD-TYPE   8 322
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED      0   33
  ASXL2 WILD-TYPE    8  322
                        clus
vv                       ASXL2 MUTATED ASXL2 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            33             322
[1] 2 2
[1] FALSE

Clustering(31) Variable = ZBTB7B MUTATION ANALYSIS
D31V1, survival
                  sevent
clus2                0   1
  ZBTB7B MUTATED     8   2
  ZBTB7B WILD-TYPE 209 173
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
              10              382 
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
               2              173 
$`ZBTB7B MUTATED`
TCGA-4Z-AA89 TCGA-FD-A3B7 TCGA-GV-A40E TCGA-KQ-A41N TCGA-DK-A2I4 TCGA-GD-A3OP 
       33.83         4.01         8.58        52.73       142.78         2.10 
TCGA-S5-AA26 TCGA-UY-A9PF TCGA-XF-AAN5 TCGA-ZF-AA51 
       16.54         3.85        75.39        56.35 

$`ZBTB7B WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        16.77        15.12        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       33.04        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       33.01        17.62        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       24.92        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
       27.35        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        2.76         9.14        27.68        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ 
       14.24         1.84        33.14        86.83        51.32         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
       15.98        34.45        14.93         4.21        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       13.74        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       94.29         3.48        88.87        34.06        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
        0.62        41.75        51.16        66.54        10.22        47.80 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
        2.50        17.42        40.08         7.33         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 
        4.67        17.56        36.43        28.41         1.94         2.93 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       23.01        12.79        12.56        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       13.08         5.19        29.79         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX 
        7.79         4.80        13.58         8.15        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
      163.30        15.02        13.58        18.81        19.00        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       12.03        43.59        38.83        29.72         5.36        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70         0.56         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
        4.24        24.03        24.66        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       14.37         8.09        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
       20.91        19.33         5.36        27.45         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       13.35         2.27        10.85        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25        22.88        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       59.31         7.23        20.12        66.02         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 
       20.71        15.81        15.91        14.07         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
       26.70         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
       38.60        64.01        12.16        21.24         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       17.72         1.81        15.42        16.27        11.80        44.38 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.15        15.32        15.58        13.48        12.23        16.67 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       38.99        17.62        37.05        22.68        76.01        69.34 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI 
       35.24        29.56        17.82         6.21         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       48.62        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW 
       28.24        16.27        92.98       110.60         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
        6.77        56.48        27.06         0.66        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       25.41        31.20        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       64.08        58.72        47.84        20.22         2.89         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       59.38        60.16        67.20        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
            2.10             0.56 
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
          142.78           166.03 
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
          25.185           17.620 
[1] "2.1 - 142.8 (25.2)" "0.6 - 166.0 (17.6)"
[1] "hr=" "2.7"
D31V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZBTB7B MUTATED         0        3         5        3
  ZBTB7B WILD-TYPE       2      119       130      131
D31V3, multiclass
           clus
vv          ZBTB7B MUTATED ZBTB7B WILD-TYPE
  STAGE I                0                2
  STAGE II               3              119
  STAGE III              5              130
  STAGE IV               3              131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  ZBTB7B MUTATED          2   6   2
  ZBTB7B WILD-TYPE      114 184  55
D31V4, multiclass
          clus
vv         ZBTB7B MUTATED ZBTB7B WILD-TYPE
  T0+T1+T2              2              114
  T3                    6              184
  T4                    2               55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZBTB7B MUTATED     7   0   2   0
  ZBTB7B WILD-TYPE 218  46  73   8
D31V5, multiclass
    clus
vv   ZBTB7B MUTATED ZBTB7B WILD-TYPE
  N0              7              218
  N1              0               46
  N2              2               73
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                  cls
clus                 0   1
  ZBTB7B MUTATED     4   0
  ZBTB7B WILD-TYPE 185  11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7B MUTATED      4    0
  ZBTB7B WILD-TYPE  185   11
   clus
vv  ZBTB7B MUTATED ZBTB7B WILD-TYPE
  0              4              185
  1              0               11
[1] 2 2
[1] FALSE
D31V7, binary
                  cls
clus                 0   1
  ZBTB7B MUTATED     4   7
  ZBTB7B WILD-TYPE  98 286
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7B MUTATED      4    7
  ZBTB7B WILD-TYPE   98  286
        clus
vv       ZBTB7B MUTATED ZBTB7B WILD-TYPE
  FEMALE              4               98
  MALE                7              286
[1] 2 2
[1] FALSE
D31V8, binary
                  cls
clus                 0   1
  ZBTB7B MUTATED    10   0
  ZBTB7B WILD-TYPE 340  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7B MUTATED     10    0
  ZBTB7B WILD-TYPE  340   20
     clus
vv    ZBTB7B MUTATED ZBTB7B WILD-TYPE
  NO              10              340
  YES              0               20
[1] 2 2
[1] FALSE
D31V9, continuous
D31V10, continuous
D31V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZBTB7B MUTATED       0                         3     8
  ZBTB7B WILD-TYPE    39                        19   309
D31V12, multiclass
                           clus
vv                          ZBTB7B MUTATED ZBTB7B WILD-TYPE
  ASIAN                                  0               39
  BLACK OR AFRICAN AMERICAN              3               19
  WHITE                                  8              309
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, binary
                  cls
clus                 0   1
  ZBTB7B MUTATED     0  10
  ZBTB7B WILD-TYPE   8 345
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7B MUTATED      0   10
  ZBTB7B WILD-TYPE    8  345
                        clus
vv                       ZBTB7B MUTATED ZBTB7B WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO             10              345
[1] 2 2
[1] FALSE

Clustering(32) Variable = RXRA MUTATION ANALYSIS
D32V1, survival
                sevent
clus2              0   1
  RXRA MUTATED    13  11
  RXRA WILD-TYPE 204 164
  RXRA MUTATED RXRA WILD-TYPE 
            24            368 
  RXRA MUTATED RXRA WILD-TYPE 
            11            164 
$`RXRA MUTATED`
TCGA-DK-A1AC TCGA-DK-A3IQ TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3SN TCGA-FD-A5BX 
      130.88        17.72        15.35        25.58        29.16         5.69 
TCGA-FJ-A3ZF TCGA-GV-A40G TCGA-XF-AAMH TCGA-ZF-AA53 TCGA-2F-A9KQ TCGA-4Z-AA80 
       17.23        19.07        11.31        57.90        94.88         0.62 
TCGA-4Z-AA82 TCGA-BT-A3PH TCGA-CF-A47X TCGA-DK-A1AF TCGA-DK-A3IL TCGA-DK-AA76 
       51.16         4.67        12.62        17.62        13.58        12.03 
TCGA-FD-A3B5 TCGA-G2-A2EF TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-KQ-A41R TCGA-UY-A9PF 
        8.94        61.94         8.48        19.40        44.38         3.85 

$`RXRA WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       46.68        87.32         8.22        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        66.05        17.98        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       67.36        15.68        50.70        36.66        38.24        52.01 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
      165.73       166.03        13.64        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       20.32         0.92         1.22        33.04         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       24.30        23.41        17.98        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BY 
       27.35         3.62        26.73        53.88        10.78         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
       18.08        58.92         6.28        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
       12.69        12.36         3.06         4.31         9.67        31.07 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       11.08        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       17.75        24.92        10.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       20.28        27.35         8.58        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        3.45         2.76         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       35.97        46.98        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       51.32         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML 
       66.64         2.10        13.74        10.82        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       86.30        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       30.28        94.29         3.48        88.87        34.06        19.69 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       12.23        24.13        11.97       104.65         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 
       16.83        17.16        34.98        27.62        50.04        41.75 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       66.54        10.22        47.80         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50         5.06        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
        8.25        17.16        16.18        17.56        36.43        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        1.94         2.93        23.01        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.46        12.10        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.87        13.08         5.19        29.79         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2I1 
       66.41        18.41       112.44        16.14        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX 
        7.79       142.78         4.80         8.15        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
      163.30        15.02        13.58        18.81        19.00        15.35 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        38.83        29.72         5.36        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
       24.03        24.66        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.09        32.02        16.77        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
        5.52        25.74        22.98        14.96        20.91        19.33 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF 
        5.36        27.45         2.70         7.10        13.35         2.27 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC 
       10.85        12.66        10.65         8.94         3.25        22.88 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       48.00        15.95        26.93        59.31         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       66.02         6.94        29.36        20.71        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07         8.94        13.91        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
       20.98         2.20        11.31        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       15.78         4.73         7.00        14.27        21.34        19.10 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
       36.49         1.51        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       11.80         1.15        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        69.34        35.24        29.56        17.82         6.21 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32         6.77        56.48        27.06        75.39 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       21.86        28.41        13.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       20.22         2.89         8.61        59.38        60.16        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        19.40         8.52        54.21        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  RXRA MUTATED RXRA WILD-TYPE 
          0.62           0.56 
  RXRA MUTATED RXRA WILD-TYPE 
        130.88         166.03 
  RXRA MUTATED RXRA WILD-TYPE 
        17.425         17.670 
[1] "0.6 - 130.9 (17.4)" "0.6 - 166.0 (17.7)"
[1] "hr=" "1"  
D32V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RXRA MUTATED         0        9         5       10
  RXRA WILD-TYPE       2      113       130      124
D32V3, multiclass
           clus
vv          RXRA MUTATED RXRA WILD-TYPE
  STAGE I              0              2
  STAGE II             9            113
  STAGE III            5            130
  STAGE IV            10            124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  RXRA MUTATED          8  10   1
  RXRA WILD-TYPE      108 180  56
D32V4, multiclass
          clus
vv         RXRA MUTATED RXRA WILD-TYPE
  T0+T1+T2            8            108
  T3                 10            180
  T4                  1             56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RXRA MUTATED    12   4   5   0
  RXRA WILD-TYPE 213  42  70   8
D32V5, multiclass
    clus
vv   RXRA MUTATED RXRA WILD-TYPE
  N0           12            213
  N1            4             42
  N2            5             70
  N3            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                cls
clus               0   1
  RXRA MUTATED    12   1
  RXRA WILD-TYPE 177  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRA MUTATED     12    1
  RXRA WILD-TYPE  177   10
   clus
vv  RXRA MUTATED RXRA WILD-TYPE
  0           12            177
  1            1             10
[1] 2 2
[1] FALSE
D32V7, binary
                cls
clus               0   1
  RXRA MUTATED     5  19
  RXRA WILD-TYPE  97 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRA MUTATED      5   19
  RXRA WILD-TYPE   97  274
        clus
vv       RXRA MUTATED RXRA WILD-TYPE
  FEMALE            5             97
  MALE             19            274
[1] 2 2
[1] FALSE
D32V8, binary
                cls
clus               0   1
  RXRA MUTATED    22   1
  RXRA WILD-TYPE 328  19
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRA MUTATED     22    1
  RXRA WILD-TYPE  328   19
     clus
vv    RXRA MUTATED RXRA WILD-TYPE
  NO            22            328
  YES            1             19
[1] 2 2
[1] FALSE
D32V9, continuous
D32V10, continuous
D32V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RXRA MUTATED       1                         3    20
  RXRA WILD-TYPE    38                        19   297
D32V12, multiclass
                           clus
vv                          RXRA MUTATED RXRA WILD-TYPE
  ASIAN                                1             38
  BLACK OR AFRICAN AMERICAN            3             19
  WHITE                               20            297
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V13, binary
                cls
clus               0   1
  RXRA MUTATED     1  20
  RXRA WILD-TYPE   7 335
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRA MUTATED      1   20
  RXRA WILD-TYPE    7  335
                        clus
vv                       RXRA MUTATED RXRA WILD-TYPE
  HISPANIC OR LATINO                1              7
  NOT HISPANIC OR LATINO           20            335
[1] 2 2
[1] FALSE

Clustering(33) Variable = FBXW7 MUTATION ANALYSIS
D33V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED    15  15
  FBXW7 WILD-TYPE 202 160
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             30             362 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             15             160 
$`FBXW7 MUTATED`
TCGA-CU-A0YR TCGA-DK-A1AC TCGA-DK-A3IN TCGA-DK-A6AW TCGA-DK-AA6S TCGA-DK-AA75 
       15.12       130.88         8.22        53.29       166.03        11.18 
TCGA-FD-A6TA TCGA-G2-A2ES TCGA-K4-A3WU TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-AAN1 
       62.86        33.01         3.45        18.90        66.64        30.94 
TCGA-XF-AAN2 TCGA-4Z-AA7O TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20O TCGA-C4-A0F0 
       61.45        16.83         7.33        13.15        12.16         1.94 
TCGA-C4-A0F1 TCGA-DK-A2I2 TCGA-DK-A3WX TCGA-E7-A5KE TCGA-FD-A6TF TCGA-GC-A3RD 
        2.93         7.79        10.55         0.56         2.27        14.07 
TCGA-GU-A42Q TCGA-LT-A5Z6 TCGA-PQ-A6FN TCGA-UY-A9PF TCGA-YC-A9TC TCGA-ZF-A9R7 
       11.31        15.58        16.67         3.85         0.66        21.86 

$`FBXW7 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX 
       18.48        13.58         2.14        19.00        16.70        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       87.32        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       66.05        17.98        64.18        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W 
       50.70        36.66        38.24        52.01       165.73        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU 
       13.64        56.15        20.32        15.35        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        1.22        33.04         4.01        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       17.98        29.16        46.78        19.79        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
        3.62        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       18.08        58.92         6.28        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.36         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       11.08        17.62        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       24.92        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       46.98        14.24         1.84        33.14        86.83        51.32 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
        3.22        15.98        34.45        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 
       11.90        21.04        26.27         2.24         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       98.99        44.32        86.30        18.58         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL 
       13.64        21.11        30.28        94.29         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       34.06        19.69        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA7S 
       94.88       104.65         8.35        44.94        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J 
       10.22        47.80         2.50        17.42        40.08         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
        6.74         6.58        19.04        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       14.96         5.06         8.25        17.16        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       17.56        36.43        28.41        23.01        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.00        12.10        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        1.84        21.86        66.41        18.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       17.62        15.62        17.95       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
        8.15        20.81       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       19.00        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 
        5.36        22.16         2.24        16.70         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN 
       26.24         4.24        24.03        24.66        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       12.62        22.52        27.98         5.52        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       14.96        20.91        19.33         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        7.10        13.35        10.85        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25        22.88        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       59.31         7.23        20.12        66.02         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       20.71        15.81        15.91         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-A762 
        2.10         3.12        20.98         2.20        18.97         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05        15.78         4.73         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       19.10         8.48        36.49         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       64.01        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
        1.81        15.42        16.27        11.80        44.38         1.15 
TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       15.32        13.48        12.23        16.54        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       37.05        22.68        76.01        69.34        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       17.82         6.21         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       79.66        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       27.06        75.39        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       35.84        28.41        13.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       20.22         2.89         8.61        59.38        60.16        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        19.40         8.52        54.21        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           0.56            0.62 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         166.03          165.73 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          13.61           17.85 
[1] "0.6 - 166.0 (13.6)" "0.6 - 165.7 (17.9)"
[1] "hr=" "1.3"
D33V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  FBXW7 MUTATED         0        8        15        7
  FBXW7 WILD-TYPE       2      114       120      127
D33V3, multiclass
           clus
vv          FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I               0               2
  STAGE II              8             114
  STAGE III            15             120
  STAGE IV              7             127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  FBXW7 MUTATED          6  18   3
  FBXW7 WILD-TYPE      110 172  54
D33V4, multiclass
          clus
vv         FBXW7 MUTATED FBXW7 WILD-TYPE
  T0+T1+T2             6             110
  T3                  18             172
  T4                   3              54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  FBXW7 MUTATED    21   1   4   1
  FBXW7 WILD-TYPE 204  45  71   7
D33V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0            21             204
  N1             1              45
  N2             4              71
  N3             1               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"
D33V6, binary
                 cls
clus                0   1
  FBXW7 MUTATED    19   2
  FBXW7 WILD-TYPE 170   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     19    2
  FBXW7 WILD-TYPE  170    9
   clus
vv  FBXW7 MUTATED FBXW7 WILD-TYPE
  0            19             170
  1             2               9
[1] 2 2
[1] FALSE
D33V7, binary
                 cls
clus                0   1
  FBXW7 MUTATED    11  19
  FBXW7 WILD-TYPE  91 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     11   19
  FBXW7 WILD-TYPE   91  274
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE            11              91
  MALE              19             274
[1] 2 2
[1] FALSE
D33V8, binary
                 cls
clus                0   1
  FBXW7 MUTATED    26   2
  FBXW7 WILD-TYPE 324  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     26    2
  FBXW7 WILD-TYPE  324   18
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO             26             324
  YES             2              18
[1] 2 2
[1] FALSE
D33V9, continuous
D33V10, continuous
D33V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FBXW7 MUTATED       1                         1    25
  FBXW7 WILD-TYPE    38                        21   292
D33V12, multiclass
                           clus
vv                          FBXW7 MUTATED FBXW7 WILD-TYPE
  ASIAN                                 1              38
  BLACK OR AFRICAN AMERICAN             1              21
  WHITE                                25             292
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V13, binary
                 cls
clus                0   1
  FBXW7 MUTATED     0  26
  FBXW7 WILD-TYPE   8 329
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      0   26
  FBXW7 WILD-TYPE    8  329
                        clus
vv                       FBXW7 MUTATED FBXW7 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            26             329
[1] 2 2
[1] FALSE

Clustering(34) Variable = RBM10 MUTATION ANALYSIS
D34V1, survival
                 sevent
clus2               0   1
  RBM10 MUTATED    12  10
  RBM10 WILD-TYPE 205 165
  RBM10 MUTATED RBM10 WILD-TYPE 
             22             370 
  RBM10 MUTATED RBM10 WILD-TYPE 
             10             165 
$`RBM10 MUTATED`
TCGA-2F-A9KT TCGA-CU-A72E TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A6AW TCGA-E5-A4TZ 
      108.95        13.58        46.68         8.22        53.29        15.35 
TCGA-FD-A3NA TCGA-FD-A6TA TCGA-GU-A42P TCGA-K4-A4AB TCGA-ZF-AA53 TCGA-BL-A13J 
       60.66        62.86        10.92         2.76        57.90         2.66 
TCGA-BT-A20V TCGA-C4-A0F1 TCGA-DK-AA76 TCGA-E7-A5KE TCGA-FD-A62O TCGA-FD-A6TK 
        5.06         2.93        12.03         0.56         7.10        10.85 
TCGA-HQ-A5NE TCGA-KQ-A41R TCGA-UY-A9PF TCGA-XF-A9SZ 
       12.16        44.38         3.85        28.24 

$`RBM10 WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
       16.27        16.77        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2I6 
       18.48         2.14        19.00        16.70       130.88        87.32 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 
       17.72        50.27        21.30        23.21         9.67        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       17.98        64.18        76.60        67.36        15.68        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       36.66        38.24        52.01       165.73       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU 
       13.64        56.15        11.18        20.32        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
        1.22        33.04         4.01        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       29.16        46.78        19.79        12.85        27.35         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       58.92         6.28        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       33.01        17.62        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       24.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        8.58        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        9.14        27.68        52.73        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ 
       14.24         1.84        33.14        86.83        51.32         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
       15.98        34.45        14.93         4.21        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       13.74        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA5P 
       94.29         3.48        88.87        34.06        19.69        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       16.83        17.16        34.98        27.62        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
       41.75        51.16        66.54        10.22        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       17.42        40.08         7.33         6.74         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       19.04        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        8.25        17.16        16.18         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       28.41         1.94        23.01        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.10        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
        8.15        20.81        10.55       163.30        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       18.81        19.00        15.35        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 
        5.36        22.16         2.24        16.70         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN 
       26.24         4.24        24.03        24.66        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       12.62        22.52        27.98         5.52        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       14.96        20.91        19.33         5.36        27.45         2.70 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
       13.35         2.27        12.66        10.65         8.94         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
        7.23        20.12        66.02         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91        14.07         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       38.60        64.01        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R 
        1.81        15.42        16.27        11.80         1.15        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       15.58        13.48        12.23        16.67        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       17.62        37.05        22.68        76.01        69.34        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       29.56        17.82         6.21         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9T4 
       64.80        79.66        66.41         5.98        23.64        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       58.72        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        67.20        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  RBM10 MUTATED RBM10 WILD-TYPE 
           0.56            0.62 
  RBM10 MUTATED RBM10 WILD-TYPE 
         108.95          166.03 
  RBM10 MUTATED RBM10 WILD-TYPE 
         12.095          17.735 
[1] "0.6 - 109.0 (12.1)" "0.6 - 166.0 (17.7)"
[1] "hr=" "1.1"
D34V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  RBM10 MUTATED         0        7         5       10
  RBM10 WILD-TYPE       2      115       130      124
D34V3, multiclass
           clus
vv          RBM10 MUTATED RBM10 WILD-TYPE
  STAGE I               0               2
  STAGE II              7             115
  STAGE III             5             130
  STAGE IV             10             124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  RBM10 MUTATED          6  10   5
  RBM10 WILD-TYPE      110 180  52
D34V4, multiclass
          clus
vv         RBM10 MUTATED RBM10 WILD-TYPE
  T0+T1+T2             6             110
  T3                  10             180
  T4                   5              52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RBM10 MUTATED    11   1   9   0
  RBM10 WILD-TYPE 214  45  66   8
D34V5, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  N0            11             214
  N1             1              45
  N2             9              66
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                 cls
clus                0   1
  RBM10 MUTATED    13   0
  RBM10 WILD-TYPE 176  11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED     13    0
  RBM10 WILD-TYPE  176   11
   clus
vv  RBM10 MUTATED RBM10 WILD-TYPE
  0            13             176
  1             0              11
[1] 2 2
[1] FALSE
D34V7, binary
                 cls
clus                0   1
  RBM10 MUTATED     5  17
  RBM10 WILD-TYPE  97 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      5   17
  RBM10 WILD-TYPE   97  276
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  FEMALE             5              97
  MALE              17             276
[1] 2 2
[1] FALSE
D34V8, binary
                 cls
clus                0   1
  RBM10 MUTATED    20   0
  RBM10 WILD-TYPE 330  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED     20    0
  RBM10 WILD-TYPE  330   20
     clus
vv    RBM10 MUTATED RBM10 WILD-TYPE
  NO             20             330
  YES             0              20
[1] 2 2
[1] FALSE
D34V9, continuous
D34V10, continuous
D34V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM10 MUTATED       1                         1    18
  RBM10 WILD-TYPE    38                        21   299
D34V12, multiclass
                           clus
vv                          RBM10 MUTATED RBM10 WILD-TYPE
  ASIAN                                 1              38
  BLACK OR AFRICAN AMERICAN             1              21
  WHITE                                18             299
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, binary
                 cls
clus                0   1
  RBM10 MUTATED     0  20
  RBM10 WILD-TYPE   8 335
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      0   20
  RBM10 WILD-TYPE    8  335
                        clus
vv                       RBM10 MUTATED RBM10 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            20             335
[1] 2 2
[1] FALSE

Clustering(35) Variable = NFE2L2 MUTATION ANALYSIS
D35V1, survival
                  sevent
clus2                0   1
  NFE2L2 MUTATED    12  12
  NFE2L2 WILD-TYPE 205 163
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              24              368 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              12              163 
$`NFE2L2 MUTATED`
TCGA-DK-A3IT TCGA-FD-A3SM TCGA-K4-A3WS TCGA-R3-A69X TCGA-XF-A9SY TCGA-XF-AAN3 
       21.30        17.98        25.02        14.24        21.04        86.30 
TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20U TCGA-BT-A42B TCGA-C4-A0F6 TCGA-DK-A1AE 
        7.33        13.15        14.96        17.56        23.01        16.14 
TCGA-DK-AA6Q TCGA-E5-A2PC TCGA-FD-A3N6 TCGA-FD-A5BU TCGA-G2-A3IB TCGA-G2-AA3C 
       13.58        43.59        27.98        19.33         7.23         6.94 
TCGA-GU-AATQ TCGA-K4-A5RI TCGA-UY-A9PE TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-ZF-AA4U 
        7.00        11.70         6.21        75.39         0.66         8.61 

$`NFE2L2 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      130.88        46.68        87.32         8.22        17.72        50.27 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN 
       33.04         4.01        60.66        24.30        23.41        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       33.01        17.62        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       24.92        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WU 
       27.35         8.58        19.07        22.72         9.01         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ 
       46.98         1.84        33.14        86.83        51.32         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
       15.98        34.45        14.93         4.21        12.76        11.90 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        66.64         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-XF-AAN8 
       98.99        44.32        30.94        61.45        18.58         3.88 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE 
        9.63        13.64        21.11        30.28        94.29         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO 
       88.87        34.06        19.69        57.90        12.23        24.13 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O 
       11.97        94.88       104.65         8.35        44.94        16.83 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 
       17.16        34.98        27.62        50.04         0.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM 
       51.16        66.54        10.22        47.80         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O 
       40.08         2.66         6.74         6.58        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       17.88        19.50         5.06         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 
       16.18         4.67        36.43        28.41         1.94         2.93 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       12.79        12.56        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       12.16        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.19        29.79         1.84        21.86        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
      112.44        17.62        15.62        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 
       15.02        18.81        19.00        15.35        12.03        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        22.16         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SO TCGA-FD-A3SP 
       16.77         8.94        12.62        22.52         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       22.98        14.96        20.91         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        7.10        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        8.94         3.25        22.88        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 
       26.93        59.31        20.12        66.02        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91        14.07         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW 
        7.63        20.05        15.78         4.73        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       19.10         8.48        36.49         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ 
       64.01        12.16        21.24         9.07        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       15.42        16.27        11.80        44.38         1.15        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       15.58        13.48        12.23        16.67        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       17.62        37.05        22.68        76.01        69.34        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       29.56        17.82         3.85         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        79.66        66.41         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       16.27        92.98       110.60         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       56.48        27.06        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       35.84        21.86        28.41        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       47.84        20.22         2.89        59.38        60.16        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        19.40         8.52        54.21        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            0.66             0.56 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           86.30           166.03 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           15.55            17.72 
[1] "0.7 - 86.3 (15.6)"  "0.6 - 166.0 (17.7)"
[1] "hr=" "1.3"
D35V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  NFE2L2 MUTATED         0        3        12        9
  NFE2L2 WILD-TYPE       2      119       123      125
D35V3, multiclass
           clus
vv          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE I                0                2
  STAGE II               3              119
  STAGE III             12              123
  STAGE IV               9              125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  NFE2L2 MUTATED          4  17   1
  NFE2L2 WILD-TYPE      112 173  56
D35V4, multiclass
          clus
vv         NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T0+T1+T2              4              112
  T3                   17              173
  T4                    1               56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  NFE2L2 MUTATED    13   4   4   0
  NFE2L2 WILD-TYPE 212  42  71   8
D35V5, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0             13              212
  N1              4               42
  N2              4               71
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     9   2
  NFE2L2 WILD-TYPE 180   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      9    2
  NFE2L2 WILD-TYPE  180    9
   clus
vv  NFE2L2 MUTATED NFE2L2 WILD-TYPE
  0              9              180
  1              2                9
[1] 2 2
[1] FALSE
D35V7, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED    11  13
  NFE2L2 WILD-TYPE  91 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     11   13
  NFE2L2 WILD-TYPE   91  280
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE             11               91
  MALE               13              280
[1] 2 2
[1] FALSE
D35V8, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED    22   1
  NFE2L2 WILD-TYPE 328  19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     22    1
  NFE2L2 WILD-TYPE  328   19
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  NO              22              328
  YES              1               19
[1] 2 2
[1] FALSE
D35V9, continuous
D35V10, continuous
D35V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NFE2L2 MUTATED       0                         3    20
  NFE2L2 WILD-TYPE    39                        19   297
D35V12, multiclass
                           clus
vv                          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  ASIAN                                  0               39
  BLACK OR AFRICAN AMERICAN              3               19
  WHITE                                 20              297
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V13, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     0  23
  NFE2L2 WILD-TYPE   8 332
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      0   23
  NFE2L2 WILD-TYPE    8  332
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO             23              332
[1] 2 2
[1] FALSE

Clustering(36) Variable = CUL1 MUTATION ANALYSIS
D36V1, survival
                sevent
clus2              0   1
  CUL1 MUTATED    11   8
  CUL1 WILD-TYPE 206 167
  CUL1 MUTATED CUL1 WILD-TYPE 
            19            373 
  CUL1 MUTATED CUL1 WILD-TYPE 
             8            167 
$`CUL1 MUTATED`
TCGA-CU-A0YO TCGA-DK-AA6M TCGA-FD-A6TD TCGA-FD-A6TH TCGA-G2-A3VY TCGA-YF-AA3M 
        4.90        52.01        12.69         4.31        17.62        13.64 
TCGA-ZF-A9R4 TCGA-ZF-A9RL TCGA-BT-A0S7 TCGA-C4-A0F1 TCGA-CU-A3YL TCGA-DK-A1A3 
       30.28        88.87         6.58         2.93        29.79        21.86 
TCGA-DK-A3WW TCGA-E7-A7XN TCGA-G2-A2EC TCGA-GV-A3JX TCGA-K4-A5RI TCGA-UY-A9PE 
       20.81        14.07        22.88        19.10        11.70         6.21 
TCGA-XF-A9SX 
       23.64 

$`CUL1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YR 
       28.70         8.98         2.04        18.58        12.92        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
      165.73       166.03        13.64        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
        6.28        62.86        18.81         6.15        12.36         3.06 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-AA3D 
        9.67        31.07        17.23        11.08        33.01        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 
       21.40        19.13        17.75        24.92        10.92        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       32.98        19.82        20.28        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       22.72         9.01        25.02         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
       27.68        52.73        50.56        35.97        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK 
        1.84        33.14        86.83        51.32         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       34.45        14.93         4.21        12.76        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        66.64         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       98.99        44.32        30.94        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R 
        3.88         9.63        21.11        94.29         3.48        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       19.69        57.90        12.23        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65         8.35        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       10.22        47.80         2.50        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        2.66         6.74        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       16.18         4.67        17.56        36.43        28.41         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       23.01        12.79        12.56        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       13.08         5.19         1.84        66.41        18.41       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P 
        4.80        13.58         8.15        10.55       163.30        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       13.58        18.81        19.00        15.35        12.03        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         5.36        22.16         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
        0.56         0.66        26.96        26.24         4.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       24.66        13.68        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       12.66        10.65         8.94         3.25        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       15.95        26.93        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        29.36        20.71        15.81        15.91        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91        26.70         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        2.20        11.31        18.97         7.63        20.05        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QI 
        4.73         7.00        14.27        21.34         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
        9.07        17.72         1.81        15.42        16.27        11.80 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       44.38         1.15        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF 
       76.01        69.34        35.24        29.56        17.82         3.85 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT 
        5.98        28.24        16.27        92.98       110.60         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC 
        8.32         6.77        56.48        27.06        75.39         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       11.97        22.36        25.41        31.20        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       28.41        13.41        64.08        58.72        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
        2.89         8.61        59.38        60.16        67.20        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        19.40         8.52        54.21        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  CUL1 MUTATED CUL1 WILD-TYPE 
          2.93           0.56 
  CUL1 MUTATED CUL1 WILD-TYPE 
         88.87         166.03 
  CUL1 MUTATED CUL1 WILD-TYPE 
         17.62          17.62 
[1] "2.9 - 88.9 (17.6)"  "0.6 - 166.0 (17.6)"
[1] "hr=" "1.1"
D36V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  CUL1 MUTATED         0        6         8        5
  CUL1 WILD-TYPE       2      116       127      129
D36V3, multiclass
           clus
vv          CUL1 MUTATED CUL1 WILD-TYPE
  STAGE I              0              2
  STAGE II             6            116
  STAGE III            8            127
  STAGE IV             5            129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  CUL1 MUTATED          4  10   2
  CUL1 WILD-TYPE      112 180  55
D36V4, multiclass
          clus
vv         CUL1 MUTATED CUL1 WILD-TYPE
  T0+T1+T2            4            112
  T3                 10            180
  T4                  2             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CUL1 MUTATED    10   0   5   0
  CUL1 WILD-TYPE 215  46  70   8
D36V5, multiclass
    clus
vv   CUL1 MUTATED CUL1 WILD-TYPE
  N0           10            215
  N1            0             46
  N2            5             70
  N3            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                cls
clus               0   1
  CUL1 MUTATED     8   0
  CUL1 WILD-TYPE 181  11
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED      8    0
  CUL1 WILD-TYPE  181   11
   clus
vv  CUL1 MUTATED CUL1 WILD-TYPE
  0            8            181
  1            0             11
[1] 2 2
[1] FALSE
D36V7, binary
                cls
clus               0   1
  CUL1 MUTATED     4  15
  CUL1 WILD-TYPE  98 278
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED      4   15
  CUL1 WILD-TYPE   98  278
        clus
vv       CUL1 MUTATED CUL1 WILD-TYPE
  FEMALE            4             98
  MALE             15            278
[1] 2 2
[1] FALSE
D36V8, binary
                cls
clus               0   1
  CUL1 MUTATED    17   0
  CUL1 WILD-TYPE 333  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED     17    0
  CUL1 WILD-TYPE  333   20
     clus
vv    CUL1 MUTATED CUL1 WILD-TYPE
  NO            17            333
  YES            0             20
[1] 2 2
[1] FALSE
D36V9, continuous
D36V10, continuous
D36V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CUL1 MUTATED       2                         1    14
  CUL1 WILD-TYPE    37                        21   303
D36V12, multiclass
                           clus
vv                          CUL1 MUTATED CUL1 WILD-TYPE
  ASIAN                                2             37
  BLACK OR AFRICAN AMERICAN            1             21
  WHITE                               14            303
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, binary
                cls
clus               0   1
  CUL1 MUTATED     1  17
  CUL1 WILD-TYPE   7 338
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED      1   17
  CUL1 WILD-TYPE    7  338
                        clus
vv                       CUL1 MUTATED CUL1 WILD-TYPE
  HISPANIC OR LATINO                1              7
  NOT HISPANIC OR LATINO           17            338
[1] 2 2
[1] FALSE

Clustering(37) Variable = HLA-A MUTATION ANALYSIS
D37V1, survival
                 sevent
clus2               0   1
  HLA-A MUTATED     2   3
  HLA-A WILD-TYPE 215 172
  HLA-A MUTATED HLA-A WILD-TYPE 
              5             387 
  HLA-A MUTATED HLA-A WILD-TYPE 
              3             172 
$`HLA-A MUTATED`
TCGA-CU-A0YO TCGA-XF-AAN1 TCGA-BL-A13J TCGA-DK-A3WW TCGA-SY-A9G5 
        4.90        30.94         2.66        20.81        38.99 

$`HLA-A WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YR 
       28.70         8.98         2.04        18.58        12.92        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       29.16        46.78        19.79        12.85        27.35         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.36         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       11.08        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       17.75        24.92        10.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       20.28        27.35         8.58        19.07        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
       25.02         3.45         2.76         9.14        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       50.56        35.97        46.98        14.24         1.84        33.14 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       86.83        51.32         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
        4.21        12.76        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
        2.24        66.64         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63        71.57        91.73        98.99        44.32 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       61.45        86.30        18.58         3.88         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
       21.11        30.28        94.29         3.48        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       19.69        57.90        12.23        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65         8.35        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       10.22        47.80         2.50        17.42        40.08         7.33 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       16.18         4.67        17.56        36.43        28.41         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
        2.93        23.01        12.79        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.87        13.08         5.19        29.79         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       66.41        18.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       17.95         7.79       142.78         4.80        13.58         8.15 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       10.55       163.30        15.02        13.58        18.81        19.00 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.35        12.03        43.59        38.83        29.72         5.36 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
       22.16         2.24        16.70         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN 
       26.24         4.24        24.03        24.66        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       12.62        22.52        27.98         5.52        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       14.96        20.91        19.33         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        7.10        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        8.94         3.25        22.88        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       26.93        59.31         7.23        20.12        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 
       29.36        20.71        15.81        15.91        14.07         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91        26.70         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31        18.97         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        7.00        14.27        21.34        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       11.80        44.38         1.15        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       12.23        16.67        16.54        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        69.34        35.24        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        3.85         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 
      110.60         2.96         8.32         6.77        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       75.39         0.66        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       35.84        21.86        28.41        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       47.84        20.22         2.89         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       67.20        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

  HLA-A MUTATED HLA-A WILD-TYPE 
           2.66            0.56 
  HLA-A MUTATED HLA-A WILD-TYPE 
          38.99          166.03 
  HLA-A MUTATED HLA-A WILD-TYPE 
          20.81           17.62 
[1] "2.7 - 39.0 (20.8)"  "0.6 - 166.0 (17.6)"
[1] "hr=" "1.5"
D37V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  HLA-A MUTATED         0        0         3        2
  HLA-A WILD-TYPE       2      122       132      132
D37V3, multiclass
           clus
vv          HLA-A MUTATED HLA-A WILD-TYPE
  STAGE I               0               2
  STAGE II              0             122
  STAGE III             3             132
  STAGE IV              2             132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  HLA-A MUTATED          0   2   3
  HLA-A WILD-TYPE      116 188  54
D37V4, multiclass
          clus
vv         HLA-A MUTATED HLA-A WILD-TYPE
  T0+T1+T2             0             116
  T3                   2             188
  T4                   3              54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HLA-A MUTATED     3   0   2   0
  HLA-A WILD-TYPE 222  46  73   8
D37V5, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  N0             3             222
  N1             0              46
  N2             2              73
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                 cls
clus                0   1
  HLA-A MUTATED     4   0
  HLA-A WILD-TYPE 185  11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      4    0
  HLA-A WILD-TYPE  185   11
   clus
vv  HLA-A MUTATED HLA-A WILD-TYPE
  0             4             185
  1             0              11
[1] 2 2
[1] FALSE
D37V7, binary
                 cls
clus                0   1
  HLA-A MUTATED     1   4
  HLA-A WILD-TYPE 101 289
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      1    4
  HLA-A WILD-TYPE  101  289
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  FEMALE             1             101
  MALE               4             289
[1] 2 2
[1] FALSE
D37V8, binary
                 cls
clus                0   1
  HLA-A MUTATED     5   0
  HLA-A WILD-TYPE 345  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      5    0
  HLA-A WILD-TYPE  345   20
     clus
vv    HLA-A MUTATED HLA-A WILD-TYPE
  NO              5             345
  YES             0              20
[1] 2 2
[1] FALSE
D37V9, continuous
[1] "Remove cluster labels:" "HLA-A MUTATED"         
clus
  HLA-A MUTATED HLA-A WILD-TYPE 
              2             128 
     TCGA-2F-A9KT      TCGA-DK-A2HX      TCGA-DK-A3IN      TCGA-DK-A3IV 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-A3X2      TCGA-DK-A6B2      TCGA-DK-A6B5      TCGA-DK-A6B6 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-AA6M      TCGA-DK-AA6R      TCGA-DK-AA6S      TCGA-DK-AA6W 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-AA75      TCGA-E5-A4TZ      TCGA-E7-A541      TCGA-E7-A7DU 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-E7-A7DV      TCGA-FT-A61P      TCGA-G2-A2ES      TCGA-G2-A3VY 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GC-A3BM      TCGA-GC-A3YS      TCGA-GV-A3JZ      TCGA-GV-A3QF 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GV-A3QK      TCGA-GV-A40E      TCGA-GV-A40G      TCGA-GV-A6ZA 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-KQ-A41N      TCGA-SY-A9G0      TCGA-UY-A78N      TCGA-XF-A9SJ 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-A9SK      TCGA-XF-A9SM      TCGA-XF-A9SP      TCGA-XF-A9ST 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-A9SV      TCGA-XF-A9SW      TCGA-XF-A9SY      TCGA-XF-A9T0 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-A9T2      TCGA-XF-A9T3      TCGA-XF-A9T5      TCGA-XF-A9T6 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-A9T8      TCGA-XF-AAMF      TCGA-XF-AAMH      TCGA-XF-AAMJ 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-AAML      TCGA-XF-AAMQ      TCGA-XF-AAMR      TCGA-XF-AAMY 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-AAMZ      TCGA-XF-AAN2      TCGA-XF-AAN3      TCGA-XF-AAN7 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-AAN8      TCGA-YF-AA3M      TCGA-2F-A9KO      TCGA-2F-A9KP 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-2F-A9KQ      TCGA-2F-A9KR      TCGA-2F-A9KW      TCGA-CF-A1HS 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-CF-A27C      TCGA-CF-A3MF      TCGA-CF-A3MG      TCGA-CF-A3MH 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-CF-A3MI      TCGA-CF-A47S      TCGA-CF-A47T      TCGA-CF-A47V 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-CF-A47W      TCGA-CF-A47X      TCGA-CF-A47Y      TCGA-CF-A5U8 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-CF-A5UA      TCGA-CF-A7I0      TCGA-DK-A3WX      TCGA-DK-AA6P 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-AA6U      TCGA-DK-AA76      TCGA-E5-A2PC      TCGA-E5-A4U1 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-E7-A519      TCGA-E7-A6MD      TCGA-G2-A2EC      TCGA-G2-A2EF 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-G2-A2EJ      TCGA-G2-A2EK      TCGA-G2-A2EL      TCGA-G2-A2EO 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-G2-A3IB      TCGA-G2-A3IE      TCGA-GC-A3I6      TCGA-GC-A3OO 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GC-A3RC      TCGA-GC-A3RD      TCGA-GC-A6I1      TCGA-GC-A6I3 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GD-A3OS      TCGA-GD-A6C6      TCGA-GV-A3JV      TCGA-GV-A3JW 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GV-A3JX      TCGA-GV-A3QH      TCGA-GV-A3QI      TCGA-UY-A78L 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-UY-A78M      TCGA-XF-A8HH      TCGA-XF-A8HI      TCGA-XF-A9SG 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-A9SH      TCGA-XF-A9SI      TCGA-XF-A9SL      TCGA-XF-A9SU 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-A9SX      TCGA-XF-A9SZ      TCGA-XF-A9T4      TCGA-XF-AAME 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-AAMG      TCGA-XF-AAMT      TCGA-XF-AAMW      TCGA-XF-AAMX 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-AAN0      TCGA-XF-AAN4      TCGA-XF-AAN5      TCGA-YF-AA3L 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
D37V10, continuous
[1] "Remove cluster labels:" "HLA-A MUTATED"         
clus
  HLA-A MUTATED HLA-A WILD-TYPE 
              2             213 
     TCGA-4Z-AA7M      TCGA-4Z-AA89      TCGA-BL-A5ZZ      TCGA-BT-A20N 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-BT-A42C      TCGA-C4-A0EZ      TCGA-CU-A0YN      TCGA-CU-A0YR 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-CU-A3KJ      TCGA-CU-A72E      TCGA-DK-A1A5      TCGA-DK-A1AA 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-A1AC      TCGA-DK-A2HX      TCGA-DK-A2I6      TCGA-DK-A3IN 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-A3IQ      TCGA-DK-A3IU      TCGA-DK-A3IV      TCGA-DK-A3X1 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-A3X2      TCGA-DK-A6AV      TCGA-DK-A6AW      TCGA-DK-A6B0 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-A6B2      TCGA-DK-A6B6      TCGA-DK-AA6L      TCGA-DK-AA6R 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-AA74      TCGA-DK-AA75      TCGA-E5-A4TZ      TCGA-FD-A3B6 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FD-A3B7      TCGA-FD-A3NA      TCGA-FD-A3SJ      TCGA-FD-A3SM 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FD-A3SN      TCGA-FD-A3SQ      TCGA-FD-A3SR      TCGA-FD-A3SS 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FD-A43P      TCGA-FD-A43X      TCGA-FD-A5BT      TCGA-FD-A5BX 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FD-A5C0      TCGA-FD-A6TB      TCGA-FD-A6TC      TCGA-FD-A6TE 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FD-A6TG      TCGA-FD-A6TH      TCGA-FJ-A3ZF      TCGA-FT-A61P 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-G2-A2ES      TCGA-G2-AA3D      TCGA-GC-A3BM      TCGA-GC-A3RB 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GC-A3WC      TCGA-GC-A3YS      TCGA-GU-A42P      TCGA-GU-A763 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GU-AATP      TCGA-GV-A3JZ      TCGA-GV-A3QF      TCGA-GV-A3QG 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GV-A3QK      TCGA-GV-A40E      TCGA-GV-A40G      TCGA-HQ-A5ND 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-K4-A3WS      TCGA-KQ-A41N      TCGA-R3-A69X      TCGA-S5-A6DX 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-SY-A9G0      TCGA-UY-A78N      TCGA-XF-A9SJ      TCGA-XF-A9SK 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-A9SM      TCGA-XF-A9SP      TCGA-XF-A9ST      TCGA-XF-A9SV 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-A9SY      TCGA-XF-A9T3      TCGA-XF-A9T8      TCGA-XF-AAMF 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-AAMH      TCGA-XF-AAMQ      TCGA-XF-AAN2      TCGA-XF-AAN7 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-AAN8      TCGA-YF-AA3M      TCGA-ZF-A9R2      TCGA-ZF-A9RL 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-ZF-AA5P      TCGA-2F-A9KO      TCGA-2F-A9KP      TCGA-2F-A9KR 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-5N-A9KI      TCGA-5N-A9KM      TCGA-BL-A0C8      TCGA-BL-A13I 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-BL-A3JM      TCGA-BT-A20J      TCGA-BT-A2LA      TCGA-BT-A42B 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-BT-A42E      TCGA-C4-A0F0      TCGA-C4-A0F1      TCGA-C4-A0F6 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-CF-A3MH      TCGA-CF-A3MI      TCGA-CF-A47W      TCGA-CF-A47X 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-CF-A5UA      TCGA-CF-A9FH      TCGA-CU-A3QU      TCGA-CU-A3YL 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-CU-A5W6      TCGA-DK-A1A3      TCGA-DK-A1A6      TCGA-DK-A1AE 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-A3IL      TCGA-DK-A3IM      TCGA-DK-A3WX      TCGA-DK-AA6P 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-AA6T      TCGA-DK-AA6U      TCGA-DK-AA76      TCGA-E7-A4XJ 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-E7-A519      TCGA-E7-A5KF      TCGA-E7-A678      TCGA-E7-A6ME 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-E7-A6MF      TCGA-E7-A7PW      TCGA-E7-A7XN      TCGA-E7-A85H 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-E7-A97Q      TCGA-FD-A3B3      TCGA-FD-A3B4      TCGA-FD-A3B5 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FD-A3B8      TCGA-FD-A3N5      TCGA-FD-A3N6      TCGA-FD-A3SO 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FD-A3SP      TCGA-FD-A43N      TCGA-FD-A43S      TCGA-FD-A43U 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FD-A5BU      TCGA-FD-A5BV      TCGA-FD-A62N      TCGA-FD-A6TK 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FJ-A3Z9      TCGA-FJ-A3ZE      TCGA-FJ-A871      TCGA-G2-A2EF 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-G2-A2EJ      TCGA-G2-A2EL      TCGA-G2-A3IE      TCGA-G2-AA3B 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-G2-AA3C      TCGA-G2-AA3F      TCGA-GD-A2C5      TCGA-GD-A3OQ 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GD-A3OS      TCGA-GD-A6C6      TCGA-GU-A42Q      TCGA-GU-A42R 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GU-A764      TCGA-GU-AATQ      TCGA-GV-A3JV      TCGA-GV-A3JX 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GV-A3QH      TCGA-GV-A3QI      TCGA-H4-A2HO      TCGA-H4-A2HQ 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-HQ-A5NE      TCGA-K4-A3WV      TCGA-K4-A5RH      TCGA-K4-A5RI 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-K4-A83P      TCGA-K4-AAQO      TCGA-KQ-A41R      TCGA-PQ-A6FI 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-PQ-A6FN      TCGA-UY-A8OB      TCGA-UY-A9PB      TCGA-UY-A9PE 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-UY-A9PF      TCGA-XF-A9SL      TCGA-XF-A9SU      TCGA-XF-A9SX 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-A9SZ      TCGA-XF-AAMT      TCGA-XF-AAN0      TCGA-XF-AAN4 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-AAN5      TCGA-YF-AA3L      TCGA-ZF-A9R0      TCGA-ZF-A9R3 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-ZF-A9R5      TCGA-ZF-A9R9      TCGA-ZF-A9RD      TCGA-ZF-A9RF 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-ZF-A9RM      TCGA-ZF-AA4U      TCGA-ZF-AA4V      TCGA-ZF-AA51 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-ZF-AA52      TCGA-ZF-AA58      TCGA-ZF-AA5H      TCGA-ZF-AA5N 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GU-AATO 
"HLA-A WILD-TYPE" 
D37V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HLA-A MUTATED       0                         0     4
  HLA-A WILD-TYPE    39                        22   313
D37V12, multiclass
                           clus
vv                          HLA-A MUTATED HLA-A WILD-TYPE
  ASIAN                                 0              39
  BLACK OR AFRICAN AMERICAN             0              22
  WHITE                                 4             313
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, binary
                 cls
clus                0   1
  HLA-A MUTATED     0   5
  HLA-A WILD-TYPE   8 350
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      0    5
  HLA-A WILD-TYPE    8  350
                        clus
vv                       HLA-A MUTATED HLA-A WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO             5             350
[1] 2 2
[1] FALSE

Clustering(38) Variable = GNA13 MUTATION ANALYSIS
D38V1, survival
                 sevent
clus2               0   1
  GNA13 MUTATED     6   6
  GNA13 WILD-TYPE 211 169
  GNA13 MUTATED GNA13 WILD-TYPE 
             12             380 
  GNA13 MUTATED GNA13 WILD-TYPE 
              6             169 
$`GNA13 MUTATED`
TCGA-BT-A42C TCGA-DK-AA6L TCGA-FD-A3SN TCGA-FD-A6TB TCGA-K4-A3WS TCGA-K4-A54R 
       28.70        38.24        29.16        18.81        25.02        27.68 
TCGA-SY-A9G0 TCGA-XF-A9ST TCGA-XF-AAML TCGA-5N-A9KM TCGA-DK-A1AD TCGA-G2-A2EO 
       33.14         4.21         7.63        17.42       112.44        59.31 

$`GNA13 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M 
       76.60        67.36        15.68        50.70        36.66        52.01 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
      165.73       166.03        13.64        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ 
        4.01        60.66        24.30        23.41        17.98        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       19.79        12.85        27.35         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       10.78         5.69         8.25        18.08        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       62.86         6.15        12.69        12.36         3.06         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY 
        9.67        31.07        17.23        11.08        33.01        17.62 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
       70.32        21.40        19.13        17.75        24.92        10.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       32.78        32.98        19.82        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       19.07        22.72         9.01         3.45         2.76         9.14 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX 
       52.73        50.56        35.97        46.98        14.24         1.84 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       86.83        51.32         3.22        15.98        34.45        14.93 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       86.30        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       30.28        94.29         3.48        88.87        34.06        19.69 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       57.90        12.23        24.13        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       50.04         0.62        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80         2.50        40.08         7.33         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 
        4.67        17.56        36.43        28.41         1.94         2.93 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       23.01        12.79        12.56        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       13.08         5.19        29.79         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
       18.41        16.14        17.62        15.62        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX 
      142.78         4.80        13.58         8.15        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
      163.30        15.02        13.58        18.81        19.00        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       12.03        43.59        38.83        29.72         5.36        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70         0.56         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
        4.24        24.03        24.66        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       14.37         8.09        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
       20.91        19.33         5.36        27.45         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       13.35         2.27        10.85        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25        22.88        61.94        48.00        15.95        26.93 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
        7.23        20.12        66.02         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91        14.07         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
       38.60        64.01        12.16        21.24         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       17.72         1.81        15.42        16.27        11.80        44.38 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.15        15.32        15.58        13.48        12.23        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.54        38.99        17.62        37.05        22.68        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34        35.24        29.56        17.82         6.21         3.85 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32         6.77        56.48        27.06        75.39 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       21.86        28.41        13.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       20.22         2.89         8.61        59.38        60.16        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        19.40         8.52        54.21        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  GNA13 MUTATED GNA13 WILD-TYPE 
           4.21            0.56 
  GNA13 MUTATED GNA13 WILD-TYPE 
         112.44          166.03 
  GNA13 MUTATED GNA13 WILD-TYPE 
         28.190          17.395 
[1] "4.2 - 112.4 (28.2)" "0.6 - 166.0 (17.4)"
[1] "hr=" "1.2"
D38V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  GNA13 MUTATED         0        3         6        3
  GNA13 WILD-TYPE       2      119       129      131
D38V3, multiclass
           clus
vv          GNA13 MUTATED GNA13 WILD-TYPE
  STAGE I               0               2
  STAGE II              3             119
  STAGE III             6             129
  STAGE IV              3             131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  GNA13 MUTATED          2   7   2
  GNA13 WILD-TYPE      114 183  55
D38V4, multiclass
          clus
vv         GNA13 MUTATED GNA13 WILD-TYPE
  T0+T1+T2             2             114
  T3                   7             183
  T4                   2              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  GNA13 MUTATED     9   2   1   0
  GNA13 WILD-TYPE 216  44  74   8
D38V5, multiclass
    clus
vv   GNA13 MUTATED GNA13 WILD-TYPE
  N0             9             216
  N1             2              44
  N2             1              74
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                 cls
clus                0   1
  GNA13 MUTATED     4   0
  GNA13 WILD-TYPE 185  11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA13 MUTATED      4    0
  GNA13 WILD-TYPE  185   11
   clus
vv  GNA13 MUTATED GNA13 WILD-TYPE
  0             4             185
  1             0              11
[1] 2 2
[1] FALSE
D38V7, binary
                 cls
clus                0   1
  GNA13 MUTATED     1  11
  GNA13 WILD-TYPE 101 282
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA13 MUTATED      1   11
  GNA13 WILD-TYPE  101  282
        clus
vv       GNA13 MUTATED GNA13 WILD-TYPE
  FEMALE             1             101
  MALE              11             282
[1] 2 2
[1] FALSE
D38V8, binary
                 cls
clus                0   1
  GNA13 MUTATED    12   0
  GNA13 WILD-TYPE 338  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA13 MUTATED     12    0
  GNA13 WILD-TYPE  338   20
     clus
vv    GNA13 MUTATED GNA13 WILD-TYPE
  NO             12             338
  YES             0              20
[1] 2 2
[1] FALSE
D38V9, continuous
D38V10, continuous
D38V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GNA13 MUTATED       0                         0    12
  GNA13 WILD-TYPE    39                        22   305
D38V12, multiclass
                           clus
vv                          GNA13 MUTATED GNA13 WILD-TYPE
  ASIAN                                 0              39
  BLACK OR AFRICAN AMERICAN             0              22
  WHITE                                12             305
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, binary
                 cls
clus                0   1
  GNA13 MUTATED     1  10
  GNA13 WILD-TYPE   7 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA13 MUTATED      1   10
  GNA13 WILD-TYPE    7  345
                        clus
vv                       GNA13 MUTATED GNA13 WILD-TYPE
  HISPANIC OR LATINO                 1               7
  NOT HISPANIC OR LATINO            10             345
[1] 2 2
[1] FALSE

Clustering(39) Variable = NUDT11 MUTATION ANALYSIS
D39V1, survival
                  sevent
clus2                0   1
  NUDT11 MUTATED     3   4
  NUDT11 WILD-TYPE 214 171
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               7              385 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               4              171 
$`NUDT11 MUTATED`
TCGA-DK-AA74 TCGA-E7-A7DU TCGA-2F-A9KQ TCGA-4Z-AA81 TCGA-BL-A13J TCGA-E7-A3X6 
       56.15         0.92        94.88        41.75         2.66        29.72 
TCGA-GU-A762 
        7.63 

$`NUDT11 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      130.88        46.68        87.32         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       21.30        23.21         9.67        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       53.29        76.60        67.36        15.68        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       38.24        52.01       165.73       166.03        13.64        13.64 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B6 
       11.18        20.32        15.35        25.58         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       33.01        17.62        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       24.92        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        3.45         2.76         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       35.97        46.98        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       51.32         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
        7.63        71.57        91.73        98.99        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       61.45        86.30        18.58         3.88         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
       21.11        30.28        94.29         3.48        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR 
       19.69        57.90        12.23        24.13        11.97       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
       50.04         0.62        51.16        66.54        10.22        47.80 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 
        2.50        17.42        40.08         7.33         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       14.96         5.06         8.25        17.16        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       17.56        36.43        28.41         1.94         2.93        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       12.79        12.56        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       12.16        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.19        29.79         1.84        21.86        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX 
      142.78         4.80        13.58         8.15        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
      163.30        15.02        13.58        18.81        19.00        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       12.03        43.59        38.83         5.36        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
       24.03        24.66        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       27.98         5.52        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       19.33         5.36        27.45         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.27        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
        7.23        20.12        66.02         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91        14.07         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05        15.78         4.73         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       19.10         8.48        36.49         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       64.01        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
        1.81        15.42        16.27        11.80        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       15.32        15.58        13.48        12.23        16.67        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       38.99        17.62        37.05        22.68        76.01        69.34 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       35.24        29.56        17.82         6.21         3.85         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
       17.88        48.62        64.80        79.66        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT 
       23.64        28.24        16.27        92.98       110.60         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC 
        8.32         6.77        56.48        27.06        75.39         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       11.97        22.36        25.41        31.20        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       28.41        13.41        64.08        58.72        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
        2.89         8.61        59.38        60.16        67.20        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        19.40         8.52        54.21        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  NUDT11 MUTATED NUDT11 WILD-TYPE 
            0.92             0.56 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           94.88           166.03 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           29.72            17.62 
[1] "0.9 - 94.9 (29.7)"  "0.6 - 166.0 (17.6)"
[1] "hr=" "1.1"
D39V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  NUDT11 MUTATED         0        2         3        2
  NUDT11 WILD-TYPE       2      120       132      132
D39V3, multiclass
           clus
vv          NUDT11 MUTATED NUDT11 WILD-TYPE
  STAGE I                0                2
  STAGE II               2              120
  STAGE III              3              132
  STAGE IV               2              132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  NUDT11 MUTATED          2   3   2
  NUDT11 WILD-TYPE      114 187  55
D39V4, multiclass
          clus
vv         NUDT11 MUTATED NUDT11 WILD-TYPE
  T0+T1+T2              2              114
  T3                    3              187
  T4                    2               55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  NUDT11 MUTATED     4   0   2   0
  NUDT11 WILD-TYPE 221  46  73   8
D39V5, multiclass
    clus
vv   NUDT11 MUTATED NUDT11 WILD-TYPE
  N0              4              221
  N1              0               46
  N2              2               73
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     6   0
  NUDT11 WILD-TYPE 183  11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      6    0
  NUDT11 WILD-TYPE  183   11
   clus
vv  NUDT11 MUTATED NUDT11 WILD-TYPE
  0              6              183
  1              0               11
[1] 2 2
[1] FALSE
D39V7, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     0   7
  NUDT11 WILD-TYPE 102 286
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      0    7
  NUDT11 WILD-TYPE  102  286
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  FEMALE              0              102
  MALE                7              286
[1] 2 2
[1] FALSE
D39V8, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     7   0
  NUDT11 WILD-TYPE 343  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      7    0
  NUDT11 WILD-TYPE  343   20
     clus
vv    NUDT11 MUTATED NUDT11 WILD-TYPE
  NO               7              343
  YES              0               20
[1] 2 2
[1] FALSE
D39V9, continuous
[1] "Remove cluster labels:" "NUDT11 MUTATED"        
clus
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               2              128 
      TCGA-2F-A9KT       TCGA-DK-A2HX       TCGA-DK-A3IN       TCGA-DK-A3IV 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DK-A3X2       TCGA-DK-A6B2       TCGA-DK-A6B5       TCGA-DK-A6B6 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DK-AA6M       TCGA-DK-AA6R       TCGA-DK-AA6S       TCGA-DK-AA6W 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DK-AA75       TCGA-E5-A4TZ       TCGA-E7-A541       TCGA-E7-A7DV 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-FT-A61P       TCGA-G2-A2ES       TCGA-G2-A3VY       TCGA-GC-A3BM 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-GC-A3YS       TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QK 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-GV-A40E       TCGA-GV-A40G       TCGA-GV-A6ZA       TCGA-KQ-A41N 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-SY-A9G0       TCGA-UY-A78N       TCGA-XF-A9SJ       TCGA-XF-A9SK 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-XF-A9SM       TCGA-XF-A9SP       TCGA-XF-A9ST       TCGA-XF-A9SV 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-XF-A9SW       TCGA-XF-A9SY       TCGA-XF-A9T0       TCGA-XF-A9T2 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-XF-A9T3       TCGA-XF-A9T5       TCGA-XF-A9T6       TCGA-XF-A9T8 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-XF-AAMF       TCGA-XF-AAMH       TCGA-XF-AAMJ       TCGA-XF-AAML 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-XF-AAMQ       TCGA-XF-AAMR       TCGA-XF-AAMY       TCGA-XF-AAMZ 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-XF-AAN1       TCGA-XF-AAN2       TCGA-XF-AAN3       TCGA-XF-AAN7 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-XF-AAN8       TCGA-YF-AA3M       TCGA-2F-A9KO       TCGA-2F-A9KP 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-2F-A9KR       TCGA-2F-A9KW       TCGA-CF-A1HS       TCGA-CF-A27C 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CF-A3MF       TCGA-CF-A3MG       TCGA-CF-A3MH       TCGA-CF-A3MI 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CF-A47S       TCGA-CF-A47T       TCGA-CF-A47V       TCGA-CF-A47W 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CF-A47X       TCGA-CF-A47Y       TCGA-CF-A5U8       TCGA-CF-A5UA 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CF-A7I0       TCGA-DK-A3WX       TCGA-DK-AA6P       TCGA-DK-AA6U 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DK-AA76       TCGA-E5-A2PC       TCGA-E5-A4U1       TCGA-E7-A519 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-E7-A6MD       TCGA-G2-A2EC       TCGA-G2-A2EF       TCGA-G2-A2EJ 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-G2-A2EK       TCGA-G2-A2EL       TCGA-G2-A2EO       TCGA-G2-A3IB 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-G2-A3IE       TCGA-GC-A3I6       TCGA-GC-A3OO       TCGA-GC-A3RC 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-GC-A3RD       TCGA-GC-A6I1       TCGA-GC-A6I3       TCGA-GD-A3OS 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-GD-A6C6       TCGA-GV-A3JV       TCGA-GV-A3JW       TCGA-GV-A3JX 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-GV-A3QH       TCGA-GV-A3QI       TCGA-SY-A9G5       TCGA-UY-A78L 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-UY-A78M       TCGA-XF-A8HH       TCGA-XF-A8HI       TCGA-XF-A9SG 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-XF-A9SH       TCGA-XF-A9SI       TCGA-XF-A9SL       TCGA-XF-A9SU 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-XF-A9SX       TCGA-XF-A9SZ       TCGA-XF-A9T4       TCGA-XF-AAME 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-XF-AAMG       TCGA-XF-AAMT       TCGA-XF-AAMW       TCGA-XF-AAMX 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-XF-AAN0       TCGA-XF-AAN4       TCGA-XF-AAN5       TCGA-YF-AA3L 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
D39V10, continuous
[1] "Remove cluster labels:" "NUDT11 MUTATED"        
clus
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               2              213 
      TCGA-4Z-AA7M       TCGA-4Z-AA89       TCGA-BL-A5ZZ       TCGA-BT-A20N 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BT-A42C       TCGA-C4-A0EZ       TCGA-CU-A0YN       TCGA-CU-A0YR 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CU-A3KJ       TCGA-CU-A72E       TCGA-DK-A1A5       TCGA-DK-A1AA 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DK-A1AC       TCGA-DK-A2HX       TCGA-DK-A2I6       TCGA-DK-A3IN 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DK-A3IQ       TCGA-DK-A3IU       TCGA-DK-A3IV       TCGA-DK-A3X1 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DK-A3X2       TCGA-DK-A6AV       TCGA-DK-A6AW       TCGA-DK-A6B0 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DK-A6B2       TCGA-DK-A6B6       TCGA-DK-AA6L       TCGA-DK-AA6R 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DK-AA75       TCGA-E5-A4TZ       TCGA-FD-A3B6       TCGA-FD-A3B7 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-FD-A3NA       TCGA-FD-A3SJ       TCGA-FD-A3SM       TCGA-FD-A3SN 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-FD-A3SQ       TCGA-FD-A3SR       TCGA-FD-A3SS       TCGA-FD-A43P 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-FD-A43X       TCGA-FD-A5BT       TCGA-FD-A5BX       TCGA-FD-A5C0 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-FD-A6TB       TCGA-FD-A6TC       TCGA-FD-A6TE       TCGA-FD-A6TG 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-FD-A6TH       TCGA-FJ-A3ZF       TCGA-FT-A61P       TCGA-G2-A2ES 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-G2-AA3D       TCGA-GC-A3BM       TCGA-GC-A3RB       TCGA-GC-A3WC 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-GC-A3YS       TCGA-GU-A42P       TCGA-GU-A763       TCGA-GU-AATP 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QG       TCGA-GV-A3QK 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-GV-A40E       TCGA-GV-A40G       TCGA-HQ-A5ND       TCGA-K4-A3WS 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KQ-A41N       TCGA-R3-A69X       TCGA-S5-A6DX       TCGA-SY-A9G0 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-UY-A78N       TCGA-XF-A9SJ       TCGA-XF-A9SK       TCGA-XF-A9SM 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-XF-A9SP       TCGA-XF-A9ST       TCGA-XF-A9SV       TCGA-XF-A9SY 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-XF-A9T3       TCGA-XF-A9T8       TCGA-XF-AAMF       TCGA-XF-AAMH 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-XF-AAMQ       TCGA-XF-AAN1       TCGA-XF-AAN2       TCGA-XF-AAN7 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-XF-AAN8       TCGA-YF-AA3M       TCGA-ZF-A9R2       TCGA-ZF-A9RL 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-ZF-AA5P       TCGA-2F-A9KO       TCGA-2F-A9KP       TCGA-2F-A9KR 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-5N-A9KI       TCGA-5N-A9KM       TCGA-BL-A0C8       TCGA-BL-A13I 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BL-A3JM       TCGA-BT-A20J       TCGA-BT-A2LA       TCGA-BT-A42B 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BT-A42E       TCGA-C4-A0F0       TCGA-C4-A0F1       TCGA-C4-A0F6 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CF-A3MH       TCGA-CF-A3MI       TCGA-CF-A47W       TCGA-CF-A47X 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CF-A5UA       TCGA-CF-A9FH       TCGA-CU-A3QU       TCGA-CU-A3YL 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CU-A5W6       TCGA-DK-A1A3       TCGA-DK-A1A6       TCGA-DK-A1AE 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DK-A3IL       TCGA-DK-A3IM       TCGA-DK-A3WX       TCGA-DK-AA6P 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DK-AA6T       TCGA-DK-AA6U       TCGA-DK-AA76       TCGA-E7-A4XJ 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-E7-A519       TCGA-E7-A5KF       TCGA-E7-A678       TCGA-E7-A6ME 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-E7-A6MF       TCGA-E7-A7PW       TCGA-E7-A7XN       TCGA-E7-A85H 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-E7-A97Q       TCGA-FD-A3B3       TCGA-FD-A3B4       TCGA-FD-A3B5 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-FD-A3B8       TCGA-FD-A3N5       TCGA-FD-A3N6       TCGA-FD-A3SO 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-FD-A3SP       TCGA-FD-A43N       TCGA-FD-A43S       TCGA-FD-A43U 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-FD-A5BU       TCGA-FD-A5BV       TCGA-FD-A62N       TCGA-FD-A6TK 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-FJ-A3Z9       TCGA-FJ-A3ZE       TCGA-FJ-A871       TCGA-G2-A2EF 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-G2-A2EJ       TCGA-G2-A2EL       TCGA-G2-A3IE       TCGA-G2-AA3B 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-G2-AA3C       TCGA-G2-AA3F       TCGA-GD-A2C5       TCGA-GD-A3OQ 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-GD-A3OS       TCGA-GD-A6C6       TCGA-GU-A42Q       TCGA-GU-A42R 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-GU-A764       TCGA-GU-AATQ       TCGA-GV-A3JV       TCGA-GV-A3JX 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-GV-A3QH       TCGA-GV-A3QI       TCGA-H4-A2HO       TCGA-H4-A2HQ 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-HQ-A5NE       TCGA-K4-A3WV       TCGA-K4-A5RH       TCGA-K4-A5RI 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-K4-A83P       TCGA-K4-AAQO       TCGA-KQ-A41R       TCGA-PQ-A6FI 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-PQ-A6FN       TCGA-UY-A8OB       TCGA-UY-A9PB       TCGA-UY-A9PE 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-UY-A9PF       TCGA-XF-A9SL       TCGA-XF-A9SU       TCGA-XF-A9SX 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-XF-A9SZ       TCGA-XF-AAMT       TCGA-XF-AAN0       TCGA-XF-AAN4 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-XF-AAN5       TCGA-YF-AA3L       TCGA-ZF-A9R0       TCGA-ZF-A9R3 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-ZF-A9R5       TCGA-ZF-A9R9       TCGA-ZF-A9RD       TCGA-ZF-A9RF 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-ZF-A9RM       TCGA-ZF-AA4U       TCGA-ZF-AA4V       TCGA-ZF-AA51 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-ZF-AA52       TCGA-ZF-AA58       TCGA-ZF-AA5H       TCGA-ZF-AA5N 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-GU-AATO 
"NUDT11 WILD-TYPE" 
D39V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NUDT11 MUTATED       0                         0     7
  NUDT11 WILD-TYPE    39                        22   310
D39V12, multiclass
                           clus
vv                          NUDT11 MUTATED NUDT11 WILD-TYPE
  ASIAN                                  0               39
  BLACK OR AFRICAN AMERICAN              0               22
  WHITE                                  7              310
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V13, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     0   6
  NUDT11 WILD-TYPE   8 349
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      0    6
  NUDT11 WILD-TYPE    8  349
                        clus
vv                       NUDT11 MUTATED NUDT11 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO              6              349
[1] 2 2
[1] FALSE

Clustering(40) Variable = MBD1 MUTATION ANALYSIS
D40V1, survival
                sevent
clus2              0   1
  MBD1 MUTATED     7   5
  MBD1 WILD-TYPE 210 170
  MBD1 MUTATED MBD1 WILD-TYPE 
            12            380 
  MBD1 MUTATED MBD1 WILD-TYPE 
             5            170 
$`MBD1 MUTATED`
TCGA-BT-A3PJ TCGA-FD-A3SR TCGA-G2-A2ES TCGA-K4-A54R TCGA-KQ-A41N TCGA-XF-A9ST 
       25.94        19.79        33.01        27.68        52.73         4.21 
TCGA-XF-AAN2 TCGA-DK-A2I4 TCGA-DK-A3WX TCGA-DK-AA6U TCGA-E5-A4U1 TCGA-E7-A3Y1 
       61.45       142.78        10.55        19.00        38.83         5.36 

$`MBD1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C 
       26.14        14.89         8.35        20.48         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       29.16        46.78        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       17.62        70.32        21.40        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       10.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        8.58        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
        2.76         9.14        50.56        35.97        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK 
        1.84        33.14        86.83        51.32         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       34.45        14.93        12.76        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       18.90         2.24        66.64         2.10        13.74        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       11.31        54.90         7.63        71.57        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       44.32        30.94        86.30        18.58         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL 
       13.64        21.11        30.28        94.29         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       34.06        19.69        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       34.98        27.62        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       66.54        10.22        47.80         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50         5.06        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        8.25        17.16        16.18         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         1.94         2.93        23.01        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.00        12.10        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        1.84        21.86        66.41        18.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL 
       17.62        15.62        17.95         7.79         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
        8.15        20.81       163.30        15.02        13.58        18.81 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        12.03        43.59        29.72        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
       24.03        24.66        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       27.98         5.52        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       19.33         5.36        27.45         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.27        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
        7.23        20.12        66.02         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91        14.07         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
       38.60        64.01        12.16        21.24         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       17.72         1.81        15.42        16.27        11.80        44.38 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.15        15.32        15.58        13.48        12.23        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.54        38.99        17.62        37.05        22.68        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34        35.24        29.56        17.82         6.21         3.85 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32         6.77        56.48        27.06        75.39 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       21.86        28.41        13.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       20.22         2.89         8.61        59.38        60.16        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        19.40         8.52        54.21        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  MBD1 MUTATED MBD1 WILD-TYPE 
          4.21           0.56 
  MBD1 MUTATED MBD1 WILD-TYPE 
        142.78         166.03 
  MBD1 MUTATED MBD1 WILD-TYPE 
         26.81          17.49 
[1] "4.2 - 142.8 (26.8)" "0.6 - 166.0 (17.5)"
[1] "hr=" "1.4"
D40V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MBD1 MUTATED         0        6         5        1
  MBD1 WILD-TYPE       2      116       130      133
D40V3, multiclass
           clus
vv          MBD1 MUTATED MBD1 WILD-TYPE
  STAGE I              0              2
  STAGE II             6            116
  STAGE III            5            130
  STAGE IV             1            133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  MBD1 MUTATED          3   6   1
  MBD1 WILD-TYPE      113 184  56
D40V4, multiclass
          clus
vv         MBD1 MUTATED MBD1 WILD-TYPE
  T0+T1+T2            3            113
  T3                  6            184
  T4                  1             56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MBD1 MUTATED    11   0   1   0
  MBD1 WILD-TYPE 214  46  74   8
D40V5, multiclass
    clus
vv   MBD1 MUTATED MBD1 WILD-TYPE
  N0           11            214
  N1            0             46
  N2            1             74
  N3            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                cls
clus               0   1
  MBD1 MUTATED     8   0
  MBD1 WILD-TYPE 181  11
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD1 MUTATED      8    0
  MBD1 WILD-TYPE  181   11
   clus
vv  MBD1 MUTATED MBD1 WILD-TYPE
  0            8            181
  1            0             11
[1] 2 2
[1] FALSE
D40V7, binary
                cls
clus               0   1
  MBD1 MUTATED     1  11
  MBD1 WILD-TYPE 101 282
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD1 MUTATED      1   11
  MBD1 WILD-TYPE  101  282
        clus
vv       MBD1 MUTATED MBD1 WILD-TYPE
  FEMALE            1            101
  MALE             11            282
[1] 2 2
[1] FALSE
D40V8, binary
                cls
clus               0   1
  MBD1 MUTATED    11   1
  MBD1 WILD-TYPE 339  19
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD1 MUTATED     11    1
  MBD1 WILD-TYPE  339   19
     clus
vv    MBD1 MUTATED MBD1 WILD-TYPE
  NO            11            339
  YES            1             19
[1] 2 2
[1] FALSE
D40V9, continuous
D40V10, continuous
D40V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MBD1 MUTATED       0                         1    10
  MBD1 WILD-TYPE    39                        21   307
D40V12, multiclass
                           clus
vv                          MBD1 MUTATED MBD1 WILD-TYPE
  ASIAN                                0             39
  BLACK OR AFRICAN AMERICAN            1             21
  WHITE                               10            307
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V13, binary
                cls
clus               0   1
  MBD1 MUTATED     0  12
  MBD1 WILD-TYPE   8 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD1 MUTATED      0   12
  MBD1 WILD-TYPE    8  343
                        clus
vv                       MBD1 MUTATED MBD1 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           12            343
[1] 2 2
[1] FALSE

Clustering(41) Variable = SCARF2 MUTATION ANALYSIS
D41V1, survival
                  sevent
clus2                0   1
  SCARF2 MUTATED     6   2
  SCARF2 WILD-TYPE 211 173
  SCARF2 MUTATED SCARF2 WILD-TYPE 
               8              384 
  SCARF2 MUTATED SCARF2 WILD-TYPE 
               2              173 
$`SCARF2 MUTATED`
TCGA-DK-A6B6 TCGA-S5-A6DX TCGA-XF-AAN3 TCGA-4Z-AA83 TCGA-DK-AA6P TCGA-GC-A3RD 
       36.66         1.84        86.30        66.54        15.02        14.07 
TCGA-GU-A767 TCGA-KQ-A41R 
        4.73        44.38 

$`SCARF2 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      130.88        46.68        87.32         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       21.30        23.21         9.67        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       53.29        76.60        67.36        15.68        50.70        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       29.16        46.78        19.79        12.85        27.35         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.36         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       11.08        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       17.75        24.92        10.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       20.28        27.35         8.58        19.07        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
       25.02         3.45         2.76         9.14        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78N 
       50.56        35.97        46.98        14.24        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       51.32         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
        7.63        71.57        91.73        98.99        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       61.45        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       30.28        94.29         3.48        88.87        34.06        19.69 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       57.90        12.23        24.13        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-4Z-AA87 
       50.04         0.62        41.75        51.16        10.22        47.80 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
        2.50        17.42        40.08         7.33         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 
        4.67        17.56        36.43        28.41         1.94         2.93 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       23.01        12.79        12.56        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       13.08         5.19        29.79         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW 
        7.79       142.78         4.80        13.58         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
       10.55       163.30        13.58        18.81        19.00        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       12.03        43.59        38.83        29.72         5.36        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70         0.56         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
        4.24        24.03        24.66        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       14.37         8.09        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
       20.91        19.33         5.36        27.45         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       13.35         2.27        10.85        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25        22.88        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       59.31         7.23        20.12        66.02         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       20.71        15.81        15.91         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        7.63        20.05        15.78         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       19.10         8.48        36.49         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       64.01        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R 
        1.81        15.42        16.27        11.80         1.15        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       15.58        13.48        12.23        16.67        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       17.62        37.05        22.68        76.01        69.34        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         6.21         3.85         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       48.62        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW 
       28.24        16.27        92.98       110.60         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L 
        6.77        56.48        27.06        75.39         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       13.41        64.08        58.72        47.84        20.22         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21        29.49         5.52        10.65 

  SCARF2 MUTATED SCARF2 WILD-TYPE 
            1.84             0.56 
  SCARF2 MUTATED SCARF2 WILD-TYPE 
           86.30           166.03 
  SCARF2 MUTATED SCARF2 WILD-TYPE 
           25.84            17.62 
[1] "1.8 - 86.3 (25.8)"  "0.6 - 166.0 (17.6)"
[1] "hr=" "2.1"
D41V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SCARF2 MUTATED         0        4         1        3
  SCARF2 WILD-TYPE       2      118       134      131
D41V3, multiclass
           clus
vv          SCARF2 MUTATED SCARF2 WILD-TYPE
  STAGE I                0                2
  STAGE II               4              118
  STAGE III              1              134
  STAGE IV               3              131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  SCARF2 MUTATED          2   3   1
  SCARF2 WILD-TYPE      114 187  56
D41V4, multiclass
          clus
vv         SCARF2 MUTATED SCARF2 WILD-TYPE
  T0+T1+T2              2              114
  T3                    3              187
  T4                    1               56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SCARF2 MUTATED     4   0   3   0
  SCARF2 WILD-TYPE 221  46  72   8
D41V5, multiclass
    clus
vv   SCARF2 MUTATED SCARF2 WILD-TYPE
  N0              4              221
  N1              0               46
  N2              3               72
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                  cls
clus                 0   1
  SCARF2 MUTATED     3   0
  SCARF2 WILD-TYPE 186  11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCARF2 MUTATED      3    0
  SCARF2 WILD-TYPE  186   11
   clus
vv  SCARF2 MUTATED SCARF2 WILD-TYPE
  0              3              186
  1              0               11
[1] 2 2
[1] FALSE
D41V7, binary
                  cls
clus                 0   1
  SCARF2 MUTATED     3   5
  SCARF2 WILD-TYPE  99 288
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCARF2 MUTATED      3    5
  SCARF2 WILD-TYPE   99  288
        clus
vv       SCARF2 MUTATED SCARF2 WILD-TYPE
  FEMALE              3               99
  MALE                5              288
[1] 2 2
[1] FALSE
D41V8, binary
                  cls
clus                 0   1
  SCARF2 MUTATED     8   0
  SCARF2 WILD-TYPE 342  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCARF2 MUTATED      8    0
  SCARF2 WILD-TYPE  342   20
     clus
vv    SCARF2 MUTATED SCARF2 WILD-TYPE
  NO               8              342
  YES              0               20
[1] 2 2
[1] FALSE
D41V9, continuous
D41V10, continuous
D41V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SCARF2 MUTATED       0                         0     8
  SCARF2 WILD-TYPE    39                        22   309
D41V12, multiclass
                           clus
vv                          SCARF2 MUTATED SCARF2 WILD-TYPE
  ASIAN                                  0               39
  BLACK OR AFRICAN AMERICAN              0               22
  WHITE                                  8              309
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V13, binary
                  cls
clus                 0   1
  SCARF2 MUTATED     0   7
  SCARF2 WILD-TYPE   8 348
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCARF2 MUTATED      0    7
  SCARF2 WILD-TYPE    8  348
                        clus
vv                       SCARF2 MUTATED SCARF2 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO              7              348
[1] 2 2
[1] FALSE

Clustering(42) Variable = FOXQ1 MUTATION ANALYSIS
D42V1, survival
                 sevent
clus2               0   1
  FOXQ1 MUTATED     9   5
  FOXQ1 WILD-TYPE 208 170
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
             14             378 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              5             170 
$`FOXQ1 MUTATED`
TCGA-DK-A3X1 TCGA-FD-A6TA TCGA-GC-A3RB TCGA-XF-AAMQ TCGA-4Z-AA80 TCGA-CF-A1HR 
       66.05        62.86        19.13        71.57         0.62        12.79 
TCGA-CU-A3YL TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-E7-A97P TCGA-E7-A97Q TCGA-G2-A2EF 
       29.79       142.78         8.15        14.37         8.09        61.94 
TCGA-G2-AA3C TCGA-ZF-AA51 
        6.94        56.35 

$`FOXQ1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      130.88        46.68        87.32         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       21.30        23.21         9.67        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       29.16        46.78        19.79        12.85        27.35         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       58.92         6.28        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GC-A3YS 
       33.01        17.62        70.32        21.40        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       10.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        8.58        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       46.98        14.24         1.84        33.14        86.83        51.32 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
        3.22        15.98        34.45        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.10        13.74        10.82        11.31        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       94.29         3.48        88.87        34.06        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        50.04 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
       41.75        51.16        66.54        10.22        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       17.42        40.08         7.33         2.66         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       14.96         5.06         8.25        17.16        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       17.56        36.43        28.41         1.94         2.93        23.01 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.56        13.97        12.59        12.13        13.08        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU 
       13.12        12.00        12.10        11.87        13.08         5.19 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        1.84        21.86        66.41        18.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL 
       17.62        15.62        17.95         7.79         4.80        13.58 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       19.00        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        22.16         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
       26.96        26.24         4.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       14.07        12.95        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
       20.91        19.33         5.36        27.45         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       13.35         2.27        10.85        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        3.25        22.88        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
        7.23        20.12        66.02        29.36        20.71        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07         8.94        13.91        26.70         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        3.12        20.98         2.20        11.31        18.97         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05        15.78         4.73         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       19.10         8.48        36.49         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       64.01        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
        1.81        15.42        16.27        11.80        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       15.32        15.58        13.48        12.23        16.67        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       38.99        17.62        37.05        22.68        76.01        69.34 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       35.24        29.56        17.82         6.21         3.85         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
       17.88        48.62        64.80        79.66        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT 
       23.64        28.24        16.27        92.98       110.60         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC 
        8.32         6.77        56.48        27.06        75.39         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       11.97        22.36        25.41        31.20        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       28.41        13.41        64.08        58.72        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 
        2.89         8.61        59.38        60.16        67.20        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21        29.49         5.52        10.65 

  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
           0.62            0.56 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
         142.78          166.03 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
          24.46           17.62 
[1] "0.6 - 142.8 (24.5)" "0.6 - 166.0 (17.6)"
[1] "hr=" "1.6"
D42V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  FOXQ1 MUTATED         0        5         6        3
  FOXQ1 WILD-TYPE       2      117       129      131
D42V3, multiclass
           clus
vv          FOXQ1 MUTATED FOXQ1 WILD-TYPE
  STAGE I               0               2
  STAGE II              5             117
  STAGE III             6             129
  STAGE IV              3             131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  FOXQ1 MUTATED          4   7   2
  FOXQ1 WILD-TYPE      112 183  55
D42V4, multiclass
          clus
vv         FOXQ1 MUTATED FOXQ1 WILD-TYPE
  T0+T1+T2             4             112
  T3                   7             183
  T4                   2              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  FOXQ1 MUTATED     9   1   1   1
  FOXQ1 WILD-TYPE 216  45  74   7
D42V5, multiclass
    clus
vv   FOXQ1 MUTATED FOXQ1 WILD-TYPE
  N0             9             216
  N1             1              45
  N2             1              74
  N3             1               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"
D42V6, binary
                 cls
clus                0   1
  FOXQ1 MUTATED    11   0
  FOXQ1 WILD-TYPE 178  11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED     11    0
  FOXQ1 WILD-TYPE  178   11
   clus
vv  FOXQ1 MUTATED FOXQ1 WILD-TYPE
  0            11             178
  1             0              11
[1] 2 2
[1] FALSE
D42V7, binary
                 cls
clus                0   1
  FOXQ1 MUTATED     4  10
  FOXQ1 WILD-TYPE  98 283
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      4   10
  FOXQ1 WILD-TYPE   98  283
        clus
vv       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  FEMALE             4              98
  MALE              10             283
[1] 2 2
[1] FALSE
D42V8, binary
                 cls
clus                0   1
  FOXQ1 MUTATED    13   0
  FOXQ1 WILD-TYPE 337  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED     13    0
  FOXQ1 WILD-TYPE  337   20
     clus
vv    FOXQ1 MUTATED FOXQ1 WILD-TYPE
  NO             13             337
  YES             0              20
[1] 2 2
[1] FALSE
D42V9, continuous
[1] "Remove cluster labels:" "FOXQ1 MUTATED"         
clus
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              2             128 
     TCGA-2F-A9KT      TCGA-DK-A2HX      TCGA-DK-A3IN      TCGA-DK-A3IV 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DK-A3X2      TCGA-DK-A6B2      TCGA-DK-A6B5      TCGA-DK-A6B6 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DK-AA6M      TCGA-DK-AA6R      TCGA-DK-AA6S      TCGA-DK-AA6W 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DK-AA75      TCGA-E5-A4TZ      TCGA-E7-A541      TCGA-E7-A7DU 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-E7-A7DV      TCGA-FT-A61P      TCGA-G2-A2ES      TCGA-G2-A3VY 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-GC-A3BM      TCGA-GC-A3YS      TCGA-GV-A3JZ      TCGA-GV-A3QF 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-GV-A3QK      TCGA-GV-A40E      TCGA-GV-A40G      TCGA-GV-A6ZA 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-KQ-A41N      TCGA-SY-A9G0      TCGA-UY-A78N      TCGA-XF-A9SJ 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-A9SK      TCGA-XF-A9SM      TCGA-XF-A9SP      TCGA-XF-A9ST 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-A9SV      TCGA-XF-A9SW      TCGA-XF-A9SY      TCGA-XF-A9T0 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-A9T2      TCGA-XF-A9T3      TCGA-XF-A9T5      TCGA-XF-A9T6 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-A9T8      TCGA-XF-AAMF      TCGA-XF-AAMH      TCGA-XF-AAMJ 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-AAML      TCGA-XF-AAMR      TCGA-XF-AAMY      TCGA-XF-AAMZ 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-AAN1      TCGA-XF-AAN2      TCGA-XF-AAN3      TCGA-XF-AAN7 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-AAN8      TCGA-YF-AA3M      TCGA-2F-A9KO      TCGA-2F-A9KP 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-2F-A9KQ      TCGA-2F-A9KR      TCGA-2F-A9KW      TCGA-CF-A1HS 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CF-A27C      TCGA-CF-A3MF      TCGA-CF-A3MG      TCGA-CF-A3MH 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CF-A3MI      TCGA-CF-A47S      TCGA-CF-A47T      TCGA-CF-A47V 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CF-A47W      TCGA-CF-A47X      TCGA-CF-A47Y      TCGA-CF-A5U8 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CF-A5UA      TCGA-CF-A7I0      TCGA-DK-A3WX      TCGA-DK-AA6P 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DK-AA6U      TCGA-DK-AA76      TCGA-E5-A2PC      TCGA-E5-A4U1 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-E7-A519      TCGA-E7-A6MD      TCGA-G2-A2EC      TCGA-G2-A2EJ 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-G2-A2EK      TCGA-G2-A2EL      TCGA-G2-A2EO      TCGA-G2-A3IB 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-G2-A3IE      TCGA-GC-A3I6      TCGA-GC-A3OO      TCGA-GC-A3RC 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-GC-A3RD      TCGA-GC-A6I1      TCGA-GC-A6I3      TCGA-GD-A3OS 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-GD-A6C6      TCGA-GV-A3JV      TCGA-GV-A3JW      TCGA-GV-A3JX 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-GV-A3QH      TCGA-GV-A3QI      TCGA-SY-A9G5      TCGA-UY-A78L 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-UY-A78M      TCGA-XF-A8HH      TCGA-XF-A8HI      TCGA-XF-A9SG 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-A9SH      TCGA-XF-A9SI      TCGA-XF-A9SL      TCGA-XF-A9SU 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-A9SX      TCGA-XF-A9SZ      TCGA-XF-A9T4      TCGA-XF-AAME 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-AAMG      TCGA-XF-AAMT      TCGA-XF-AAMW      TCGA-XF-AAMX 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-AAN0      TCGA-XF-AAN4      TCGA-XF-AAN5      TCGA-YF-AA3L 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
D42V10, continuous
D42V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FOXQ1 MUTATED       2                         0    12
  FOXQ1 WILD-TYPE    37                        22   305
D42V12, multiclass
                           clus
vv                          FOXQ1 MUTATED FOXQ1 WILD-TYPE
  ASIAN                                 2              37
  BLACK OR AFRICAN AMERICAN             0              22
  WHITE                                12             305
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V13, binary
                 cls
clus                0   1
  FOXQ1 MUTATED     0  13
  FOXQ1 WILD-TYPE   8 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      0   13
  FOXQ1 WILD-TYPE    8  342
                        clus
vv                       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            13             342
[1] 2 2
[1] FALSE

Clustering(43) Variable = FAM47C MUTATION ANALYSIS
D43V1, survival
                  sevent
clus2                0   1
  FAM47C MUTATED     8  13
  FAM47C WILD-TYPE 209 162
  FAM47C MUTATED FAM47C WILD-TYPE 
              21              371 
  FAM47C MUTATED FAM47C WILD-TYPE 
              13              162 
$`FAM47C MUTATED`
TCGA-BT-A3PJ TCGA-CU-A3KJ TCGA-DK-AA71 TCGA-FD-A62P TCGA-XF-AAML TCGA-5N-A9KI 
       25.94        18.48        13.64         6.28         7.63         2.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-FD-A3N6 TCGA-FD-A5BV 
        5.06        14.96         7.79         8.15        27.98         5.36 
TCGA-G2-A3IE TCGA-GC-A3I6 TCGA-GC-A6I1 TCGA-K4-A5RI TCGA-K4-A83P TCGA-XF-A9SH 
       20.12        20.71         8.94        11.70        16.27        64.80 
TCGA-XF-AAMG TCGA-ZF-A9R1 TCGA-ZF-AA51 
      110.60        25.41        56.35 

$`FAM47C WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C 
       26.14        14.89         8.35        20.48         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       13.58         2.14        19.00        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       87.32         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        66.05        17.98        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       67.36        15.68        50.70        36.66        38.24        52.01 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
      165.73       166.03        13.64        56.15        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       15.35        25.58         0.92         1.22        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
       60.66        24.30        23.41        17.98        29.16        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       19.79        12.85        27.35         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TA 
       10.78         5.69         8.25        18.08        58.92        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         3.06         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY 
        9.67        31.07        17.23        11.08        33.01        17.62 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
       70.32        21.40        19.13        17.75        24.92        10.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       32.78        32.98        19.82        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       19.07        22.72         9.01        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        9.14        27.68        52.73        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ 
       14.24         1.84        33.14        86.83        51.32         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
       15.98        34.45        14.93         4.21        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR 
       13.74        10.82        11.31        54.90        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       98.99        44.32        30.94        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
        3.88         9.63        13.64        21.11        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.48        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       16.83        17.16        34.98        27.62        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM 
       41.75        51.16        66.54        10.22        47.80        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20V TCGA-BT-A20X 
       19.04        12.16        17.88        19.50         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       17.16        16.18         4.67        17.56        36.43        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        1.94         2.93        23.01        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.10        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3WW 
       15.62        17.95       142.78         4.80        13.58        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       10.55       163.30        15.02        13.58        18.81        19.00 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.35        12.03        43.59        38.83        29.72         5.36 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
       22.16         2.24        16.70         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN 
       26.24         4.24        24.03        24.66        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       12.62        22.52         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       20.91        19.33        27.45         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.27        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC 
        7.23        66.02         6.94        29.36        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       14.07        13.91        26.70         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        2.20        11.31        18.97         7.63        20.05        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
        4.73         7.00        14.27        21.34        19.10         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
       36.49         1.51        19.40        38.60        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO 
       21.24         9.07        17.72         1.81        15.42        11.80 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       44.38         1.15        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        69.34        35.24        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SL 
        3.85         1.87        17.88        48.62        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT 
        5.98        23.64        28.24        16.27        92.98         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC 
        8.32         6.77        56.48        27.06        75.39         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       11.97        22.36        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       13.41        64.08        58.72        47.84        20.22         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 
        8.61        59.38        60.16        67.20        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
        8.52        54.21        29.49         5.52        10.65 

  FAM47C MUTATED FAM47C WILD-TYPE 
            2.50             0.56 
  FAM47C MUTATED FAM47C WILD-TYPE 
          110.60           166.03 
  FAM47C MUTATED FAM47C WILD-TYPE 
           14.96            17.72 
[1] "2.5 - 110.6 (15.0)" "0.6 - 166.0 (17.7)"
[1] "hr=" "1.6"
D43V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  FAM47C MUTATED         0        8         9        4
  FAM47C WILD-TYPE       2      114       126      130
D43V3, multiclass
           clus
vv          FAM47C MUTATED FAM47C WILD-TYPE
  STAGE I                0                2
  STAGE II               8              114
  STAGE III              9              126
  STAGE IV               4              130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  FAM47C MUTATED          7  10   3
  FAM47C WILD-TYPE      109 180  54
D43V4, multiclass
          clus
vv         FAM47C MUTATED FAM47C WILD-TYPE
  T0+T1+T2              7              109
  T3                   10              180
  T4                    3               54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FAM47C MUTATED    14   3   0   1
  FAM47C WILD-TYPE 211  43  75   7
D43V5, multiclass
    clus
vv   FAM47C MUTATED FAM47C WILD-TYPE
  N0             14              211
  N1              3               43
  N2              0               75
  N3              1                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"
D43V6, binary
                  cls
clus                 0   1
  FAM47C MUTATED    11   0
  FAM47C WILD-TYPE 178  11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED     11    0
  FAM47C WILD-TYPE  178   11
   clus
vv  FAM47C MUTATED FAM47C WILD-TYPE
  0             11              178
  1              0               11
[1] 2 2
[1] FALSE
D43V7, binary
                  cls
clus                 0   1
  FAM47C MUTATED    10  11
  FAM47C WILD-TYPE  92 282
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED     10   11
  FAM47C WILD-TYPE   92  282
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  FEMALE             10               92
  MALE               11              282
[1] 2 2
[1] FALSE
D43V8, binary
                  cls
clus                 0   1
  FAM47C MUTATED    20   0
  FAM47C WILD-TYPE 330  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED     20    0
  FAM47C WILD-TYPE  330   20
     clus
vv    FAM47C MUTATED FAM47C WILD-TYPE
  NO              20              330
  YES              0               20
[1] 2 2
[1] FALSE
D43V9, continuous
D43V10, continuous
D43V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM47C MUTATED       1                         1    19
  FAM47C WILD-TYPE    38                        21   298
D43V12, multiclass
                           clus
vv                          FAM47C MUTATED FAM47C WILD-TYPE
  ASIAN                                  1               38
  BLACK OR AFRICAN AMERICAN              1               21
  WHITE                                 19              298
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V13, binary
                  cls
clus                 0   1
  FAM47C MUTATED     1  20
  FAM47C WILD-TYPE   7 335
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED      1   20
  FAM47C WILD-TYPE    7  335
                        clus
vv                       FAM47C MUTATED FAM47C WILD-TYPE
  HISPANIC OR LATINO                  1                7
  NOT HISPANIC OR LATINO             20              335
[1] 2 2
[1] FALSE

Clustering(44) Variable = METTL3 MUTATION ANALYSIS
D44V1, survival
                  sevent
clus2                0   1
  METTL3 MUTATED    13   4
  METTL3 WILD-TYPE 204 171
  METTL3 MUTATED METTL3 WILD-TYPE 
              17              375 
  METTL3 MUTATED METTL3 WILD-TYPE 
               4              171 
$`METTL3 MUTATED`
TCGA-DK-A1AC TCGA-DK-A6AW TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6S TCGA-FD-A6TB 
      130.88        53.29        50.70        36.66       166.03        18.81 
TCGA-FD-A6TG TCGA-XF-A9T0 TCGA-XF-AAN2 TCGA-4Z-AA7S TCGA-DK-AA76 TCGA-E7-A85H 
        3.06        26.27        61.45        34.98        12.03        12.95 
TCGA-GD-A6C6 TCGA-K4-A83P TCGA-KQ-A41S TCGA-S5-AA26 TCGA-UY-A78M 
        2.20        16.27         1.15        16.54        22.68 

$`METTL3 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 
       23.21         9.67        66.05        17.98        64.18        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W 
       67.36        15.68        38.24        52.01       165.73        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 
       13.64        56.15        11.18        20.32        15.35        25.58 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
        0.92         1.22        33.04         4.01        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       23.41        17.98        29.16        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       27.35         3.62        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC 
        8.25        18.08        58.92         6.28        62.86         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.69        12.36         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       11.08        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       17.75        24.92        10.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       20.28        27.35         8.58        19.07        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
       25.02         3.45         2.76         9.14        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       50.56        35.97        46.98        14.24         1.84        33.14 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       86.83        51.32         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 
        4.21        12.76        11.90        21.04        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
        7.63        71.57        91.73        98.99        44.32        30.94 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       86.30        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       30.28        94.29         3.48        88.87        34.06        19.69 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       57.90        12.23        24.13        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y 
        8.35        44.94        16.83        17.16        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
        0.62        41.75        51.16        66.54        10.22        47.80 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
        2.50        17.42        40.08         7.33         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 
        4.67        17.56        36.43        28.41         1.94         2.93 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       23.01        12.79        12.56        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       13.08         5.19        29.79         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW 
        7.79       142.78         4.80        13.58         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       10.55       163.30        15.02        13.58        18.81        19.00 
TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       15.35        43.59        38.83        29.72         5.36        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70         0.56         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A97P 
        4.24        24.03        24.66        13.68        14.07        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       27.98         5.52        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       19.33         5.36        27.45         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.27        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
        7.23        20.12        66.02         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91        14.07         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.10         3.12        20.98        11.31        18.97         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05        15.78         4.73         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       19.10         8.48        36.49         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       64.01        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42        11.80        44.38        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       13.48        12.23        16.67        38.99        17.62        37.05 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        69.34        35.24        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        3.85         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 
      110.60         2.96         8.32         6.77        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       75.39         0.66        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       35.84        21.86        28.41        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       47.84        20.22         2.89         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       67.20        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

  METTL3 MUTATED METTL3 WILD-TYPE 
            1.15             0.56 
  METTL3 MUTATED METTL3 WILD-TYPE 
          166.03           165.73 
  METTL3 MUTATED METTL3 WILD-TYPE 
           22.68            17.62 
[1] "1.1 - 166.0 (22.7)" "0.6 - 165.7 (17.6)"
[1] "hr=" "2.4"
D44V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  METTL3 MUTATED         0        4         9        4
  METTL3 WILD-TYPE       2      118       126      130
D44V3, multiclass
           clus
vv          METTL3 MUTATED METTL3 WILD-TYPE
  STAGE I                0                2
  STAGE II               4              118
  STAGE III              9              126
  STAGE IV               4              130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  METTL3 MUTATED          3   8   4
  METTL3 WILD-TYPE      113 182  53
D44V4, multiclass
          clus
vv         METTL3 MUTATED METTL3 WILD-TYPE
  T0+T1+T2              3              113
  T3                    8              182
  T4                    4               53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  METTL3 MUTATED    11   1   3   0
  METTL3 WILD-TYPE 214  45  72   8
D44V5, multiclass
    clus
vv   METTL3 MUTATED METTL3 WILD-TYPE
  N0             11              214
  N1              1               45
  N2              3               72
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                  cls
clus                 0   1
  METTL3 MUTATED     7   0
  METTL3 WILD-TYPE 182  11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL3 MUTATED      7    0
  METTL3 WILD-TYPE  182   11
   clus
vv  METTL3 MUTATED METTL3 WILD-TYPE
  0              7              182
  1              0               11
[1] 2 2
[1] FALSE
D44V7, binary
                  cls
clus                 0   1
  METTL3 MUTATED     3  14
  METTL3 WILD-TYPE  99 279
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL3 MUTATED      3   14
  METTL3 WILD-TYPE   99  279
        clus
vv       METTL3 MUTATED METTL3 WILD-TYPE
  FEMALE              3               99
  MALE               14              279
[1] 2 2
[1] FALSE
D44V8, binary
                  cls
clus                 0   1
  METTL3 MUTATED    15   1
  METTL3 WILD-TYPE 335  19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL3 MUTATED     15    1
  METTL3 WILD-TYPE  335   19
     clus
vv    METTL3 MUTATED METTL3 WILD-TYPE
  NO              15              335
  YES              1               19
[1] 2 2
[1] FALSE
D44V9, continuous
D44V10, continuous
D44V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  METTL3 MUTATED       2                         2    13
  METTL3 WILD-TYPE    37                        20   304
D44V12, multiclass
                           clus
vv                          METTL3 MUTATED METTL3 WILD-TYPE
  ASIAN                                  2               37
  BLACK OR AFRICAN AMERICAN              2               20
  WHITE                                 13              304
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V13, binary
                  cls
clus                 0   1
  METTL3 MUTATED     0  14
  METTL3 WILD-TYPE   8 341
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL3 MUTATED      0   14
  METTL3 WILD-TYPE    8  341
                        clus
vv                       METTL3 MUTATED METTL3 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO             14              341
[1] 2 2
[1] FALSE

Clustering(45) Variable = ZNF185 MUTATION ANALYSIS
D45V1, survival
                  sevent
clus2                0   1
  ZNF185 MUTATED     2   3
  ZNF185 WILD-TYPE 215 172
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               5              387 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               3              172 
$`ZNF185 MUTATED`
TCGA-G2-A2ES TCGA-ZF-A9RC TCGA-FJ-A3Z9 TCGA-GC-A3I6 TCGA-K4-A5RJ 
       33.01        94.29        12.66        20.71        17.72 

$`ZNF185 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      130.88        46.68        87.32         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       21.30        23.21         9.67        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       53.29        76.60        67.36        15.68        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       38.24        52.01       165.73       166.03        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU 
       56.15        11.18        20.32        15.35        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        1.22        33.04         4.01        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       17.98        29.16        46.78        19.79        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
        3.62        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
       18.08        58.92         6.28        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
       12.69        12.36         3.06         4.31         9.67        31.07 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       17.23        11.08        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       17.75        24.92        10.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       20.28        27.35         8.58        19.07        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
       25.02         3.45         2.76         9.14        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       50.56        35.97        46.98        14.24         1.84        33.14 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       86.83        51.32         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
        4.21        12.76        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
        2.24        66.64         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63        71.57        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       30.94        61.45        86.30        18.58         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
       13.64        21.11        30.28         3.48        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       19.69        57.90        12.23        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65         8.35        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       10.22        47.80         2.50        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        2.66         6.74         6.58        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       17.88        19.50         5.06        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       17.16        16.18         4.67        17.56        36.43        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        1.94         2.93        23.01        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.10        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
        8.15        20.81        10.55       163.30        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       18.81        19.00        15.35        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        22.16         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65         8.94         3.25        22.88        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       15.95        26.93        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 
        6.94        29.36        15.81        15.91        14.07         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91        26.70         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31        18.97         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        7.00        14.27        21.34        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
        9.07        11.70         1.81        15.42        16.27        11.80 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       44.38         1.15        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        69.34        35.24        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        3.85         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 
      110.60         2.96         8.32         6.77        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       75.39         0.66        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       35.84        21.86        28.41        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       47.84        20.22         2.89         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       67.20        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

  ZNF185 MUTATED ZNF185 WILD-TYPE 
           12.66             0.56 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
           94.29           166.03 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
           20.71            17.62 
[1] "12.7 - 94.3 (20.7)" "0.6 - 166.0 (17.6)"
[1] "hr=" "1"  
D45V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF185 MUTATED         0        2         2        0
  ZNF185 WILD-TYPE       2      120       133      134
D45V3, multiclass
           clus
vv          ZNF185 MUTATED ZNF185 WILD-TYPE
  STAGE I                0                2
  STAGE II               2              120
  STAGE III              2              133
  STAGE IV               0              134
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  ZNF185 MUTATED          1   3   0
  ZNF185 WILD-TYPE      115 187  57
D45V4, multiclass
          clus
vv         ZNF185 MUTATED ZNF185 WILD-TYPE
  T0+T1+T2              1              115
  T3                    3              187
  T4                    0               57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF185 MUTATED     5   0   0   0
  ZNF185 WILD-TYPE 220  46  75   8
D45V5, multiclass
    clus
vv   ZNF185 MUTATED ZNF185 WILD-TYPE
  N0              5              220
  N1              0               46
  N2              0               75
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                  cls
clus                 0   1
  ZNF185 MUTATED     3   0
  ZNF185 WILD-TYPE 186  11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      3    0
  ZNF185 WILD-TYPE  186   11
   clus
vv  ZNF185 MUTATED ZNF185 WILD-TYPE
  0              3              186
  1              0               11
[1] 2 2
[1] FALSE
D45V7, binary
                  cls
clus                 0   1
  ZNF185 MUTATED     0   5
  ZNF185 WILD-TYPE 102 288
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      0    5
  ZNF185 WILD-TYPE  102  288
        clus
vv       ZNF185 MUTATED ZNF185 WILD-TYPE
  FEMALE              0              102
  MALE                5              288
[1] 2 2
[1] FALSE
D45V8, binary
                  cls
clus                 0   1
  ZNF185 MUTATED     4   0
  ZNF185 WILD-TYPE 346  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      4    0
  ZNF185 WILD-TYPE  346   20
     clus
vv    ZNF185 MUTATED ZNF185 WILD-TYPE
  NO               4              346
  YES              0               20
[1] 2 2
[1] FALSE
D45V9, continuous
[1] "Remove cluster labels:" "ZNF185 MUTATED"        
clus
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               2              128 
      TCGA-2F-A9KT       TCGA-DK-A2HX       TCGA-DK-A3IN       TCGA-DK-A3IV 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-A3X2       TCGA-DK-A6B2       TCGA-DK-A6B5       TCGA-DK-A6B6 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-AA6M       TCGA-DK-AA6R       TCGA-DK-AA6S       TCGA-DK-AA6W 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-AA75       TCGA-E5-A4TZ       TCGA-E7-A541       TCGA-E7-A7DU 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-E7-A7DV       TCGA-FT-A61P       TCGA-G2-A3VY       TCGA-GC-A3BM 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GC-A3YS       TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QK 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GV-A40E       TCGA-GV-A40G       TCGA-GV-A6ZA       TCGA-KQ-A41N 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-SY-A9G0       TCGA-UY-A78N       TCGA-XF-A9SJ       TCGA-XF-A9SK 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-A9SM       TCGA-XF-A9SP       TCGA-XF-A9ST       TCGA-XF-A9SV 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-A9SW       TCGA-XF-A9SY       TCGA-XF-A9T0       TCGA-XF-A9T2 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-A9T3       TCGA-XF-A9T5       TCGA-XF-A9T6       TCGA-XF-A9T8 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-AAMF       TCGA-XF-AAMH       TCGA-XF-AAMJ       TCGA-XF-AAML 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-AAMQ       TCGA-XF-AAMR       TCGA-XF-AAMY       TCGA-XF-AAMZ 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-AAN1       TCGA-XF-AAN2       TCGA-XF-AAN3       TCGA-XF-AAN7 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-AAN8       TCGA-YF-AA3M       TCGA-2F-A9KO       TCGA-2F-A9KP 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-2F-A9KQ       TCGA-2F-A9KR       TCGA-2F-A9KW       TCGA-CF-A1HS 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-CF-A27C       TCGA-CF-A3MF       TCGA-CF-A3MG       TCGA-CF-A3MH 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-CF-A3MI       TCGA-CF-A47S       TCGA-CF-A47T       TCGA-CF-A47V 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-CF-A47W       TCGA-CF-A47X       TCGA-CF-A47Y       TCGA-CF-A5U8 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-CF-A5UA       TCGA-CF-A7I0       TCGA-DK-A3WX       TCGA-DK-AA6P 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-AA6U       TCGA-DK-AA76       TCGA-E5-A2PC       TCGA-E5-A4U1 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-E7-A519       TCGA-E7-A6MD       TCGA-G2-A2EC       TCGA-G2-A2EF 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-G2-A2EJ       TCGA-G2-A2EK       TCGA-G2-A2EL       TCGA-G2-A2EO 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-G2-A3IB       TCGA-G2-A3IE       TCGA-GC-A3OO       TCGA-GC-A3RC 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GC-A3RD       TCGA-GC-A6I1       TCGA-GC-A6I3       TCGA-GD-A3OS 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GD-A6C6       TCGA-GV-A3JV       TCGA-GV-A3JW       TCGA-GV-A3JX 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GV-A3QH       TCGA-GV-A3QI       TCGA-SY-A9G5       TCGA-UY-A78L 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-UY-A78M       TCGA-XF-A8HH       TCGA-XF-A8HI       TCGA-XF-A9SG 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-A9SH       TCGA-XF-A9SI       TCGA-XF-A9SL       TCGA-XF-A9SU 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-A9SX       TCGA-XF-A9SZ       TCGA-XF-A9T4       TCGA-XF-AAME 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-AAMG       TCGA-XF-AAMT       TCGA-XF-AAMW       TCGA-XF-AAMX 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-AAN0       TCGA-XF-AAN4       TCGA-XF-AAN5       TCGA-YF-AA3L 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
D45V10, continuous
[1] "Remove cluster labels:" "ZNF185 MUTATED"        
clus
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               2              213 
      TCGA-4Z-AA7M       TCGA-4Z-AA89       TCGA-BL-A5ZZ       TCGA-BT-A20N 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-BT-A42C       TCGA-C4-A0EZ       TCGA-CU-A0YN       TCGA-CU-A0YR 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-CU-A3KJ       TCGA-CU-A72E       TCGA-DK-A1A5       TCGA-DK-A1AA 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-A1AC       TCGA-DK-A2HX       TCGA-DK-A2I6       TCGA-DK-A3IN 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-A3IQ       TCGA-DK-A3IU       TCGA-DK-A3IV       TCGA-DK-A3X1 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-A3X2       TCGA-DK-A6AV       TCGA-DK-A6AW       TCGA-DK-A6B0 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-A6B2       TCGA-DK-A6B6       TCGA-DK-AA6L       TCGA-DK-AA6R 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-AA74       TCGA-DK-AA75       TCGA-E5-A4TZ       TCGA-FD-A3B6 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FD-A3B7       TCGA-FD-A3NA       TCGA-FD-A3SJ       TCGA-FD-A3SM 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FD-A3SN       TCGA-FD-A3SQ       TCGA-FD-A3SR       TCGA-FD-A3SS 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FD-A43P       TCGA-FD-A43X       TCGA-FD-A5BT       TCGA-FD-A5BX 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FD-A5C0       TCGA-FD-A6TB       TCGA-FD-A6TC       TCGA-FD-A6TE 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FD-A6TG       TCGA-FD-A6TH       TCGA-FJ-A3ZF       TCGA-FT-A61P 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-G2-AA3D       TCGA-GC-A3BM       TCGA-GC-A3RB       TCGA-GC-A3WC 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GC-A3YS       TCGA-GU-A42P       TCGA-GU-A763       TCGA-GU-AATP 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QG       TCGA-GV-A3QK 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GV-A40E       TCGA-GV-A40G       TCGA-HQ-A5ND       TCGA-K4-A3WS 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-KQ-A41N       TCGA-R3-A69X       TCGA-S5-A6DX       TCGA-SY-A9G0 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-UY-A78N       TCGA-XF-A9SJ       TCGA-XF-A9SK       TCGA-XF-A9SM 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-A9SP       TCGA-XF-A9ST       TCGA-XF-A9SV       TCGA-XF-A9SY 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-A9T3       TCGA-XF-A9T8       TCGA-XF-AAMF       TCGA-XF-AAMH 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-AAMQ       TCGA-XF-AAN1       TCGA-XF-AAN2       TCGA-XF-AAN7 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-AAN8       TCGA-YF-AA3M       TCGA-ZF-A9R2       TCGA-ZF-A9RL 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-ZF-AA5P       TCGA-2F-A9KO       TCGA-2F-A9KP       TCGA-2F-A9KR 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-5N-A9KI       TCGA-5N-A9KM       TCGA-BL-A0C8       TCGA-BL-A13I 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-BL-A13J       TCGA-BL-A3JM       TCGA-BT-A20J       TCGA-BT-A2LA 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-BT-A42B       TCGA-BT-A42E       TCGA-C4-A0F0       TCGA-C4-A0F1 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-C4-A0F6       TCGA-CF-A3MH       TCGA-CF-A3MI       TCGA-CF-A47W 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-CF-A47X       TCGA-CF-A5UA       TCGA-CF-A9FH       TCGA-CU-A3QU 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-CU-A3YL       TCGA-CU-A5W6       TCGA-DK-A1A3       TCGA-DK-A1A6 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-A1AE       TCGA-DK-A3IL       TCGA-DK-A3IM       TCGA-DK-A3WX 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-AA6P       TCGA-DK-AA6T       TCGA-DK-AA6U       TCGA-DK-AA76 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-E7-A4XJ       TCGA-E7-A519       TCGA-E7-A5KF       TCGA-E7-A678 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-E7-A6ME       TCGA-E7-A6MF       TCGA-E7-A7PW       TCGA-E7-A7XN 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-E7-A85H       TCGA-E7-A97Q       TCGA-FD-A3B3       TCGA-FD-A3B4 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FD-A3B5       TCGA-FD-A3B8       TCGA-FD-A3N5       TCGA-FD-A3N6 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FD-A3SO       TCGA-FD-A3SP       TCGA-FD-A43N       TCGA-FD-A43S 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FD-A43U       TCGA-FD-A5BU       TCGA-FD-A5BV       TCGA-FD-A62N 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FD-A6TK       TCGA-FJ-A3ZE       TCGA-FJ-A871       TCGA-G2-A2EF 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-G2-A2EJ       TCGA-G2-A2EL       TCGA-G2-A3IE       TCGA-G2-AA3B 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-G2-AA3C       TCGA-G2-AA3F       TCGA-GD-A2C5       TCGA-GD-A3OQ 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GD-A3OS       TCGA-GD-A6C6       TCGA-GU-A42Q       TCGA-GU-A42R 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GU-A764       TCGA-GU-AATQ       TCGA-GV-A3JV       TCGA-GV-A3JX 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GV-A3QH       TCGA-GV-A3QI       TCGA-H4-A2HO       TCGA-H4-A2HQ 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-HQ-A5NE       TCGA-K4-A3WV       TCGA-K4-A5RH       TCGA-K4-A5RI 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-K4-A83P       TCGA-K4-AAQO       TCGA-KQ-A41R       TCGA-PQ-A6FI 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-PQ-A6FN       TCGA-UY-A8OB       TCGA-UY-A9PB       TCGA-UY-A9PE 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-UY-A9PF       TCGA-XF-A9SL       TCGA-XF-A9SU       TCGA-XF-A9SX 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-A9SZ       TCGA-XF-AAMT       TCGA-XF-AAN0       TCGA-XF-AAN4 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-AAN5       TCGA-YF-AA3L       TCGA-ZF-A9R0       TCGA-ZF-A9R3 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-ZF-A9R5       TCGA-ZF-A9R9       TCGA-ZF-A9RD       TCGA-ZF-A9RF 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-ZF-A9RM       TCGA-ZF-AA4U       TCGA-ZF-AA4V       TCGA-ZF-AA51 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-ZF-AA52       TCGA-ZF-AA58       TCGA-ZF-AA5H       TCGA-ZF-AA5N 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GU-AATO 
"ZNF185 WILD-TYPE" 
D45V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF185 MUTATED       0                         0     5
  ZNF185 WILD-TYPE    39                        22   312
D45V12, multiclass
                           clus
vv                          ZNF185 MUTATED ZNF185 WILD-TYPE
  ASIAN                                  0               39
  BLACK OR AFRICAN AMERICAN              0               22
  WHITE                                  5              312
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V13, binary
                  cls
clus                 0   1
  ZNF185 MUTATED     0   5
  ZNF185 WILD-TYPE   8 350
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      0    5
  ZNF185 WILD-TYPE    8  350
                        clus
vv                       ZNF185 MUTATED ZNF185 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO              5              350
[1] 2 2
[1] FALSE

Clustering(46) Variable = ERBB2 MUTATION ANALYSIS
D46V1, survival
                 sevent
clus2               0   1
  ERBB2 MUTATED    31  17
  ERBB2 WILD-TYPE 186 158
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             48             344 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             17             158 
$`ERBB2 MUTATED`
TCGA-2F-A9KT TCGA-BT-A20T TCGA-DK-A2I6 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-FD-A3SN 
      108.95        14.89        87.32        36.66        38.24        29.16 
TCGA-FD-A6TB TCGA-GC-A3YS TCGA-GV-A40G TCGA-GV-A6ZA TCGA-XF-A9SM TCGA-XF-A9ST 
       18.81        24.92        19.07        22.72        34.45         4.21 
TCGA-XF-A9T8 TCGA-XF-AAML TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-ZF-A9RC TCGA-ZF-AA4R 
       13.74         7.63        61.45        86.30        94.29        34.06 
TCGA-2F-A9KP TCGA-4Z-AA7S TCGA-BT-A0YX TCGA-CF-A5UA TCGA-CU-A3YL TCGA-DK-A1A3 
       11.97        34.98        13.15        12.00        29.79        21.86 
TCGA-E7-A7XN TCGA-FD-A5BU TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GU-A766 TCGA-GU-A767 
       14.07        19.33         6.94        15.81        15.78         4.73 
TCGA-HQ-A2OF TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41S TCGA-MV-A51V 
       64.01        17.72         1.81        16.27         1.15        13.48 
TCGA-SY-A9G5 TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 
       38.99        79.66        66.41         6.77        56.48        75.39 
TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4V TCGA-ZF-AA4X 
       31.20        21.86        64.08        58.72        59.38        67.20 

$`ERBB2 WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
       16.27        16.77        15.12        33.83        12.39        26.14 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
        8.35        20.48        25.94         9.96        28.70         8.98 
TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        2.04        18.58        12.92         4.90        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       13.58         2.14        19.00        16.70       130.88        46.68 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       66.05        17.98        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       15.68        50.70        52.01       165.73       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 
       13.64        56.15        11.18        20.32        15.35        25.58 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
        0.92         1.22        33.04         4.01        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       23.41        17.98        46.78        19.79        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
        3.62        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD 
       18.08        58.92         6.28        62.86         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.36         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       11.08        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       17.75        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       27.35         8.58         9.01        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        9.14        27.68        52.73        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ 
       14.24         1.84        33.14        86.83        51.32         3.22 
TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       15.98        14.93        12.76        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH 
       18.90         2.24        66.64         2.10        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
       54.90        71.57        91.73        98.99        44.32        30.94 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO 
        3.48        88.87        19.69        57.90        12.23        24.13 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       10.22        47.80         2.50        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        2.66         6.74         6.58        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       16.18         4.67        17.56        36.43        28.41         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
        2.93        23.01        12.79        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.10        12.62        12.26        13.12        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       13.08         5.19         1.84        66.41        18.41       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       15.02        13.58        18.81        19.00        15.35        12.03 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        38.83        29.72         5.36        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
       24.03        24.66        13.68        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BV 
        5.52        25.74        22.98        14.96        20.91         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
       12.66        10.65         8.94         3.25        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       48.00        15.95        26.93        59.31         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 
       66.02        29.36        20.71        15.91        14.07         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91        26.70         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-AATQ TCGA-GV-A3JV 
       11.31        18.97         7.63        20.05         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB 
       38.60        12.16        21.24         9.07        11.70        15.42 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        44.38        15.32        15.58        12.23        16.67 
TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       16.54        17.62        37.05        22.68        76.01        69.34 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       35.24        29.56        17.82         6.21         3.85         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       17.88        48.62        64.80         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN4 
       16.27        92.98       110.60         2.96         8.32        27.06 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R5 TCGA-ZF-A9R9 
        0.66        11.97        22.36        25.41        35.84        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W 
       13.41        47.84        20.22         2.89         8.61        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        19.40         8.52        54.21        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  ERBB2 MUTATED ERBB2 WILD-TYPE 
           1.15            0.56 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
         108.95          166.03 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
         23.820          16.995 
[1] "1.1 - 109.0 (23.8)" "0.6 - 166.0 (17.0)"
[1] "hr=" "1.7"
D46V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ERBB2 MUTATED         0       16        19       13
  ERBB2 WILD-TYPE       2      106       116      121
D46V3, multiclass
           clus
vv          ERBB2 MUTATED ERBB2 WILD-TYPE
  STAGE I               0               2
  STAGE II             16             106
  STAGE III            19             116
  STAGE IV             13             121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  ERBB2 MUTATED         15  25   6
  ERBB2 WILD-TYPE      101 165  51
D46V4, multiclass
          clus
vv         ERBB2 MUTATED ERBB2 WILD-TYPE
  T0+T1+T2            15             101
  T3                  25             165
  T4                   6              51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ERBB2 MUTATED    29   7   6   0
  ERBB2 WILD-TYPE 196  39  69   8
D46V5, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  N0            29             196
  N1             7              39
  N2             6              69
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                 cls
clus                0   1
  ERBB2 MUTATED    20   0
  ERBB2 WILD-TYPE 169  11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     20    0
  ERBB2 WILD-TYPE  169   11
   clus
vv  ERBB2 MUTATED ERBB2 WILD-TYPE
  0            20             169
  1             0              11
[1] 2 2
[1] FALSE
D46V7, binary
                 cls
clus                0   1
  ERBB2 MUTATED    11  37
  ERBB2 WILD-TYPE  91 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     11   37
  ERBB2 WILD-TYPE   91  256
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  FEMALE            11              91
  MALE              37             256
[1] 2 2
[1] FALSE
D46V8, binary
                 cls
clus                0   1
  ERBB2 MUTATED    44   1
  ERBB2 WILD-TYPE 306  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     44    1
  ERBB2 WILD-TYPE  306   19
     clus
vv    ERBB2 MUTATED ERBB2 WILD-TYPE
  NO             44             306
  YES             1              19
[1] 2 2
[1] FALSE
D46V9, continuous
D46V10, continuous
D46V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERBB2 MUTATED       3                         3    41
  ERBB2 WILD-TYPE    36                        19   276
D46V12, multiclass
                           clus
vv                          ERBB2 MUTATED ERBB2 WILD-TYPE
  ASIAN                                 3              36
  BLACK OR AFRICAN AMERICAN             3              19
  WHITE                                41             276
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V13, binary
                 cls
clus                0   1
  ERBB2 MUTATED     1  44
  ERBB2 WILD-TYPE   7 311
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      1   44
  ERBB2 WILD-TYPE    7  311
                        clus
vv                       ERBB2 MUTATED ERBB2 WILD-TYPE
  HISPANIC OR LATINO                 1               7
  NOT HISPANIC OR LATINO            44             311
[1] 2 2
[1] FALSE

Clustering(47) Variable = ATM MUTATION ANALYSIS
D47V1, survival
               sevent
clus2             0   1
  ATM MUTATED    32  20
  ATM WILD-TYPE 185 155
  ATM MUTATED ATM WILD-TYPE 
           52           340 
  ATM MUTATED ATM WILD-TYPE 
           20           155 
$`ATM MUTATED`
TCGA-4Z-AA84 TCGA-BT-A3PK TCGA-CU-A0YR TCGA-DK-A6AW TCGA-FD-A43P TCGA-FD-A6TI 
       15.12         9.96        15.12        53.29        27.35         9.67 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A3WU TCGA-KQ-A41N TCGA-KQ-A41O 
        8.58        22.72        25.02         3.45        52.73        50.56 
TCGA-R3-A69X TCGA-UY-A9PH TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAML TCGA-ZF-A9RC 
       14.24        51.32        66.64        13.74         7.63        94.29 
TCGA-2F-A9KO TCGA-5N-A9KM TCGA-BT-A0YX TCGA-BT-A20U TCGA-BT-A3PH TCGA-BT-A42E 
       24.13        17.42        13.15        14.96         4.67        36.43 
TCGA-DK-A1AG TCGA-DK-A3IK TCGA-DK-A3WW TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A85H 
       15.62         4.80        20.81         2.24         0.66        12.95 
TCGA-FD-A3B5 TCGA-FD-A3N6 TCGA-FD-A43N TCGA-FT-A3EE TCGA-G2-A3IE TCGA-G2-AA3B 
        8.94        27.98        22.98         3.25        20.12        66.02 
TCGA-G2-AA3C TCGA-GD-A6C6 TCGA-K4-A6MB TCGA-MV-A51V TCGA-S5-AA26 TCGA-SY-A9G5 
        6.94         2.20        15.42        13.48        16.54        38.99 
TCGA-UY-A8OB TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-AAME 
       69.34        29.56         3.85        17.88        79.66        92.98 
TCGA-XF-AAMG TCGA-YC-A9TC TCGA-ZF-A9RF TCGA-ZF-AA4X 
      110.60         0.66        64.08        67.20 

$`ATM WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        16.77        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ 
       14.89         8.35        20.48        25.94        28.70         8.98 
TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E 
        2.04        18.58        12.92         4.90        18.48        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 
        2.14        19.00        16.70       130.88        46.68        87.32 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       66.05        17.98        64.18        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S 
       50.70        36.66        38.24        52.01       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       13.64        13.64        56.15        11.18        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       25.58         0.92         1.22        33.04         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
       24.30        23.41        17.98        29.16        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       12.85         3.62        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
        8.25        18.08        58.92         6.28        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 
        6.15        12.69        12.36         3.06         4.31        31.07 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM 
       17.23        11.08        33.01        17.62        70.32        21.40 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP 
       19.13        17.75        24.92        10.92        32.78        32.98 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A4AB 
       19.82        20.28        27.35        19.07         9.01         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-S5-A6DX TCGA-SY-A9G0 
        9.14        27.68        35.97        46.98         1.84        33.14 
TCGA-UY-A78N TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       86.83         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR 
        2.10        10.82        11.31        54.90        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       98.99        44.32        30.94        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RE 
        3.88         9.63        13.64        21.11        30.28         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KP 
       88.87        34.06        19.69        57.90        12.23        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       34.98        27.62        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13I 
       66.54        10.22        47.80         2.50        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        2.66         6.74         6.58        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       19.50         5.06         5.06         8.25        17.16        16.18 
TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR 
       17.56        28.41         1.94         2.93        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.56        13.97        12.59        12.13        13.08        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU 
       13.12        12.00        12.10        11.87        13.08         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       29.79         1.84        21.86        66.41        18.41       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL 
       16.14        17.62        17.95         7.79       142.78        13.58 
TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
        8.15        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       19.00        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 
        5.36        22.16        16.70         0.56        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A97P 
        4.24        24.03        24.66        13.68        14.07        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SO 
        8.09        32.02        16.77        12.62        22.52         5.52 
TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       25.74        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.70         7.10        13.35         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       10.65         8.94        22.88        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       26.93        59.31         7.23        29.36        20.71        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07         8.94        13.91        26.70         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
        3.12        20.98        11.31        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       15.78         4.73         7.00        14.27        21.34        19.10 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.48        36.49         1.51        19.40        38.60        64.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       12.16        21.24         9.07        11.70        17.72         1.81 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       16.27        11.80        44.38         1.15        15.32        15.58 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       12.23        16.67        17.62        37.05        22.68        76.01 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH 
       35.24        17.82         6.21         1.87        48.62        64.80 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAMT 
       66.41         5.98        23.64        28.24        16.27         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YF-AA3L 
        8.32         6.77        56.48        27.06        75.39        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       13.41        58.72        47.84        20.22         2.89         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       59.38        60.16        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  ATM MUTATED ATM WILD-TYPE 
         0.66          0.56 
  ATM MUTATED ATM WILD-TYPE 
       110.60        166.03 
  ATM MUTATED ATM WILD-TYPE 
        16.98         17.67 
[1] "0.7 - 110.6 (17.0)" "0.6 - 166.0 (17.7)"
[1] "hr=" "1.3"
D47V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  ATM MUTATED         0       16        21       16
  ATM WILD-TYPE       2      106       114      118
D47V3, multiclass
           clus
vv          ATM MUTATED ATM WILD-TYPE
  STAGE I             0             2
  STAGE II           16           106
  STAGE III          21           114
  STAGE IV           16           118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1+T2  T3  T4
  ATM MUTATED         17  27   6
  ATM WILD-TYPE       99 163  51
D47V4, multiclass
          clus
vv         ATM MUTATED ATM WILD-TYPE
  T0+T1+T2          17            99
  T3                27           163
  T4                 6            51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  ATM MUTATED    33   8   6   1
  ATM WILD-TYPE 192  38  69   7
D47V5, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  N0          33           192
  N1           8            38
  N2           6            69
  N3           1             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"
D47V6, binary
               cls
clus              0   1
  ATM MUTATED    21   2
  ATM WILD-TYPE 168   9
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     21    2
  ATM WILD-TYPE  168    9
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0          21           168
  1           2             9
[1] 2 2
[1] FALSE
D47V7, binary
               cls
clus              0   1
  ATM MUTATED    10  43
  ATM WILD-TYPE  92 250
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     10   43
  ATM WILD-TYPE   92  250
        clus
vv       ATM MUTATED ATM WILD-TYPE
  FEMALE          10            92
  MALE            43           250
[1] 2 2
[1] FALSE
D47V8, binary
               cls
clus              0   1
  ATM MUTATED    47   2
  ATM WILD-TYPE 303  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     47    2
  ATM WILD-TYPE  303   18
     clus
vv    ATM MUTATED ATM WILD-TYPE
  NO           47           303
  YES           2            18
[1] 2 2
[1] FALSE
D47V9, continuous
D47V10, continuous
D47V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATM MUTATED       4                         5    43
  ATM WILD-TYPE    35                        17   274
D47V12, multiclass
                           clus
vv                          ATM MUTATED ATM WILD-TYPE
  ASIAN                               4            35
  BLACK OR AFRICAN AMERICAN           5            17
  WHITE                              43           274
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V13, binary
               cls
clus              0   1
  ATM MUTATED     2  49
  ATM WILD-TYPE   6 306
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      2   49
  ATM WILD-TYPE    6  306
                        clus
vv                       ATM MUTATED ATM WILD-TYPE
  HISPANIC OR LATINO               2             6
  NOT HISPANIC OR LATINO          49           306
[1] 2 2
[1] FALSE

Clustering(48) Variable = UNC93B1 MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  UNC93B1 MUTATED     2   5
  UNC93B1 WILD-TYPE 215 170
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                7               385 
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                5               170 
$`UNC93B1 MUTATED`
TCGA-FD-A3SJ TCGA-XF-AAML TCGA-4Z-AA7W TCGA-BT-A3PH TCGA-XF-AAN0 TCGA-ZF-AA4N 
       24.30         7.63        27.62         4.67        56.48         2.89 
TCGA-ZF-AA4W 
       60.16 

$`UNC93B1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      130.88        46.68        87.32         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       21.30        23.21         9.67        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       53.29        76.60        67.36        15.68        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       38.24        52.01       165.73       166.03        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU 
       56.15        11.18        20.32        15.35        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM 
        1.22        33.04         4.01        60.66        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       29.16        46.78        19.79        12.85        27.35         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.36         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       11.08        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       17.75        24.92        10.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       20.28        27.35         8.58        19.07        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
       25.02         3.45         2.76         9.14        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       50.56        35.97        46.98        14.24         1.84        33.14 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       86.83        51.32         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
        4.21        12.76        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
        2.24        66.64         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
       54.90        71.57        91.73        98.99        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       61.45        86.30        18.58         3.88         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
       21.11        30.28        94.29         3.48        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       19.69        57.90        12.23        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65         8.35        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       50.04         0.62        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 
       16.18        17.56        36.43        28.41         1.94         2.93 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       23.01        12.79        12.56        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       13.08         5.19        29.79         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW 
        7.79       142.78         4.80        13.58         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       10.55       163.30        15.02        13.58        18.81        19.00 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.35        12.03        43.59        38.83        29.72         5.36 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
       22.16         2.24        16.70         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN 
       26.24         4.24        24.03        24.66        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       12.62        22.52        27.98         5.52        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       14.96        20.91        19.33         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        7.10        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        8.94         3.25        22.88        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       26.93        59.31         7.23        20.12        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 
       29.36        20.71        15.81        15.91        14.07         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91        26.70         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31        18.97         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        7.00        14.27        21.34        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       11.80        44.38         1.15        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       12.23        16.67        16.54        38.99        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       22.68        76.01        69.34        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        6.21         3.85         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       79.66        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN4 
       92.98       110.60         2.96         8.32         6.77        27.06 
TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       75.39         0.66        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       35.84        21.86        28.41        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 
       47.84        20.22         8.61        59.38        67.20        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        19.40         8.52        54.21        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
             2.89              0.56 
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
            60.16            166.03 
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
            24.30             17.62 
[1] "2.9 - 60.2 (24.3)"  "0.6 - 166.0 (17.6)"
[1] "hr=" "1.6"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  UNC93B1 MUTATED         0        3         1        3
  UNC93B1 WILD-TYPE       2      119       134      131
D48V3, multiclass
           clus
vv          UNC93B1 MUTATED UNC93B1 WILD-TYPE
  STAGE I                 0                 2
  STAGE II                3               119
  STAGE III               1               134
  STAGE IV                3               131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  UNC93B1 MUTATED          3   2   1
  UNC93B1 WILD-TYPE      113 188  56
D48V4, multiclass
          clus
vv         UNC93B1 MUTATED UNC93B1 WILD-TYPE
  T0+T1+T2               3               113
  T3                     2               188
  T4                     1                56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  UNC93B1 MUTATED     3   0   3   0
  UNC93B1 WILD-TYPE 222  46  72   8
D48V5, multiclass
    clus
vv   UNC93B1 MUTATED UNC93B1 WILD-TYPE
  N0               3               222
  N1               0                46
  N2               3                72
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                   cls
clus                  0   1
  UNC93B1 MUTATED     2   0
  UNC93B1 WILD-TYPE 187  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UNC93B1 MUTATED      2    0
  UNC93B1 WILD-TYPE  187   11
   clus
vv  UNC93B1 MUTATED UNC93B1 WILD-TYPE
  0               2               187
  1               0                11
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  UNC93B1 MUTATED     0   7
  UNC93B1 WILD-TYPE 102 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UNC93B1 MUTATED      0    7
  UNC93B1 WILD-TYPE  102  286
        clus
vv       UNC93B1 MUTATED UNC93B1 WILD-TYPE
  FEMALE               0               102
  MALE                 7               286
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  UNC93B1 MUTATED     7   0
  UNC93B1 WILD-TYPE 343  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UNC93B1 MUTATED      7    0
  UNC93B1 WILD-TYPE  343   20
     clus
vv    UNC93B1 MUTATED UNC93B1 WILD-TYPE
  NO                7               343
  YES               0                20
[1] 2 2
[1] FALSE
D48V9, continuous
[1] "Remove cluster labels:" "UNC93B1 MUTATED"       
clus
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                2               128 
       TCGA-2F-A9KT        TCGA-DK-A2HX        TCGA-DK-A3IN        TCGA-DK-A3IV 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-A3X2        TCGA-DK-A6B2        TCGA-DK-A6B5        TCGA-DK-A6B6 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-AA6M        TCGA-DK-AA6R        TCGA-DK-AA6S        TCGA-DK-AA6W 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-AA75        TCGA-E5-A4TZ        TCGA-E7-A541        TCGA-E7-A7DU 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-E7-A7DV        TCGA-FT-A61P        TCGA-G2-A2ES        TCGA-G2-A3VY 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GC-A3BM        TCGA-GC-A3YS        TCGA-GV-A3JZ        TCGA-GV-A3QF 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GV-A3QK        TCGA-GV-A40E        TCGA-GV-A40G        TCGA-GV-A6ZA 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-KQ-A41N        TCGA-SY-A9G0        TCGA-UY-A78N        TCGA-XF-A9SJ 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-A9SK        TCGA-XF-A9SM        TCGA-XF-A9SP        TCGA-XF-A9ST 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-A9SV        TCGA-XF-A9SW        TCGA-XF-A9SY        TCGA-XF-A9T0 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-A9T2        TCGA-XF-A9T3        TCGA-XF-A9T5        TCGA-XF-A9T6 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-A9T8        TCGA-XF-AAMF        TCGA-XF-AAMH        TCGA-XF-AAMJ 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-AAMQ        TCGA-XF-AAMR        TCGA-XF-AAMY        TCGA-XF-AAMZ 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-AAN1        TCGA-XF-AAN2        TCGA-XF-AAN3        TCGA-XF-AAN7 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-AAN8        TCGA-YF-AA3M        TCGA-2F-A9KO        TCGA-2F-A9KP 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-2F-A9KQ        TCGA-2F-A9KR        TCGA-2F-A9KW        TCGA-CF-A1HS 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-CF-A27C        TCGA-CF-A3MF        TCGA-CF-A3MG        TCGA-CF-A3MH 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-CF-A3MI        TCGA-CF-A47S        TCGA-CF-A47T        TCGA-CF-A47V 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-CF-A47W        TCGA-CF-A47X        TCGA-CF-A47Y        TCGA-CF-A5U8 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-CF-A5UA        TCGA-CF-A7I0        TCGA-DK-A3WX        TCGA-DK-AA6P 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-AA6U        TCGA-DK-AA76        TCGA-E5-A2PC        TCGA-E5-A4U1 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-E7-A519        TCGA-E7-A6MD        TCGA-G2-A2EC        TCGA-G2-A2EF 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL        TCGA-G2-A2EO 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-G2-A3IB        TCGA-G2-A3IE        TCGA-GC-A3I6        TCGA-GC-A3OO 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GC-A3RC        TCGA-GC-A3RD        TCGA-GC-A6I1        TCGA-GC-A6I3 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GD-A3OS        TCGA-GD-A6C6        TCGA-GV-A3JV        TCGA-GV-A3JW 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GV-A3JX        TCGA-GV-A3QH        TCGA-GV-A3QI        TCGA-SY-A9G5 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-UY-A78L        TCGA-UY-A78M        TCGA-XF-A8HH        TCGA-XF-A8HI 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-A9SG        TCGA-XF-A9SH        TCGA-XF-A9SI        TCGA-XF-A9SL 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-A9SU        TCGA-XF-A9SX        TCGA-XF-A9SZ        TCGA-XF-A9T4 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-AAME        TCGA-XF-AAMG        TCGA-XF-AAMT        TCGA-XF-AAMW 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-AAMX        TCGA-XF-AAN4        TCGA-XF-AAN5        TCGA-YF-AA3L 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
D48V10, continuous
[1] "Remove cluster labels:" "UNC93B1 MUTATED"       
clus
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                2               213 
       TCGA-4Z-AA7M        TCGA-4Z-AA89        TCGA-BL-A5ZZ        TCGA-BT-A20N 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-BT-A42C        TCGA-C4-A0EZ        TCGA-CU-A0YN        TCGA-CU-A0YR 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-CU-A3KJ        TCGA-CU-A72E        TCGA-DK-A1A5        TCGA-DK-A1AA 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-A1AC        TCGA-DK-A2HX        TCGA-DK-A2I6        TCGA-DK-A3IN 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-A3IQ        TCGA-DK-A3IU        TCGA-DK-A3IV        TCGA-DK-A3X1 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-A3X2        TCGA-DK-A6AV        TCGA-DK-A6AW        TCGA-DK-A6B0 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-A6B2        TCGA-DK-A6B6        TCGA-DK-AA6L        TCGA-DK-AA6R 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-AA74        TCGA-DK-AA75        TCGA-E5-A4TZ        TCGA-FD-A3B6 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FD-A3B7        TCGA-FD-A3NA        TCGA-FD-A3SM        TCGA-FD-A3SN 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FD-A3SQ        TCGA-FD-A3SR        TCGA-FD-A3SS        TCGA-FD-A43P 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FD-A43X        TCGA-FD-A5BT        TCGA-FD-A5BX        TCGA-FD-A5C0 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FD-A6TB        TCGA-FD-A6TC        TCGA-FD-A6TE        TCGA-FD-A6TG 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FD-A6TH        TCGA-FJ-A3ZF        TCGA-FT-A61P        TCGA-G2-A2ES 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-G2-AA3D        TCGA-GC-A3BM        TCGA-GC-A3RB        TCGA-GC-A3WC 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GC-A3YS        TCGA-GU-A42P        TCGA-GU-A763        TCGA-GU-AATP 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GV-A3JZ        TCGA-GV-A3QF        TCGA-GV-A3QG        TCGA-GV-A3QK 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GV-A40E        TCGA-GV-A40G        TCGA-HQ-A5ND        TCGA-K4-A3WS 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-KQ-A41N        TCGA-R3-A69X        TCGA-S5-A6DX        TCGA-SY-A9G0 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-UY-A78N        TCGA-XF-A9SJ        TCGA-XF-A9SK        TCGA-XF-A9SM 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-A9SP        TCGA-XF-A9ST        TCGA-XF-A9SV        TCGA-XF-A9SY 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-A9T3        TCGA-XF-A9T8        TCGA-XF-AAMF        TCGA-XF-AAMH 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-AAMQ        TCGA-XF-AAN1        TCGA-XF-AAN2        TCGA-XF-AAN7 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-AAN8        TCGA-YF-AA3M        TCGA-ZF-A9R2        TCGA-ZF-A9RL 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-ZF-AA5P        TCGA-2F-A9KO        TCGA-2F-A9KP        TCGA-2F-A9KR 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-5N-A9KI        TCGA-5N-A9KM        TCGA-BL-A0C8        TCGA-BL-A13I 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-BL-A13J        TCGA-BL-A3JM        TCGA-BT-A20J        TCGA-BT-A2LA 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-BT-A42B        TCGA-BT-A42E        TCGA-C4-A0F0        TCGA-C4-A0F1 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A3MH        TCGA-CF-A3MI        TCGA-CF-A47W 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-CF-A47X        TCGA-CF-A5UA        TCGA-CF-A9FH        TCGA-CU-A3QU 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-CU-A3YL        TCGA-CU-A5W6        TCGA-DK-A1A3        TCGA-DK-A1A6 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-A1AE        TCGA-DK-A3IL        TCGA-DK-A3IM        TCGA-DK-A3WX 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-AA6P        TCGA-DK-AA6T        TCGA-DK-AA6U        TCGA-DK-AA76 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-E7-A4XJ        TCGA-E7-A519        TCGA-E7-A5KF        TCGA-E7-A678 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-E7-A6ME        TCGA-E7-A6MF        TCGA-E7-A7PW        TCGA-E7-A7XN 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-E7-A85H        TCGA-E7-A97Q        TCGA-FD-A3B3        TCGA-FD-A3B4 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FD-A3B5        TCGA-FD-A3B8        TCGA-FD-A3N5        TCGA-FD-A3N6 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FD-A3SO        TCGA-FD-A3SP        TCGA-FD-A43N        TCGA-FD-A43S 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FD-A43U        TCGA-FD-A5BU        TCGA-FD-A5BV        TCGA-FD-A62N 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FD-A6TK        TCGA-FJ-A3Z9        TCGA-FJ-A3ZE        TCGA-FJ-A871 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EL        TCGA-G2-A3IE 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-G2-AA3B        TCGA-G2-AA3C        TCGA-G2-AA3F        TCGA-GD-A2C5 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GD-A3OQ        TCGA-GD-A3OS        TCGA-GD-A6C6        TCGA-GU-A42Q 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GU-A42R        TCGA-GU-A764        TCGA-GU-AATQ        TCGA-GV-A3JV 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GV-A3JX        TCGA-GV-A3QH        TCGA-GV-A3QI        TCGA-H4-A2HO 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-H4-A2HQ        TCGA-HQ-A5NE        TCGA-K4-A3WV        TCGA-K4-A5RH 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-K4-A5RI        TCGA-K4-A83P        TCGA-K4-AAQO        TCGA-KQ-A41R 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-PQ-A6FI        TCGA-PQ-A6FN        TCGA-UY-A8OB        TCGA-UY-A9PB 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-UY-A9PE        TCGA-UY-A9PF        TCGA-XF-A9SL        TCGA-XF-A9SU 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-A9SX        TCGA-XF-A9SZ        TCGA-XF-AAMT        TCGA-XF-AAN4 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-AAN5        TCGA-YF-AA3L        TCGA-ZF-A9R0        TCGA-ZF-A9R3 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-ZF-A9R5        TCGA-ZF-A9R9        TCGA-ZF-A9RD        TCGA-ZF-A9RF 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-ZF-A9RM        TCGA-ZF-AA4U        TCGA-ZF-AA4V        TCGA-ZF-AA51 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-ZF-AA52        TCGA-ZF-AA58        TCGA-ZF-AA5H        TCGA-ZF-AA5N 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GU-AATO 
"UNC93B1 WILD-TYPE" 
D48V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UNC93B1 MUTATED       0                         0     7
  UNC93B1 WILD-TYPE    39                        22   310
D48V12, multiclass
                           clus
vv                          UNC93B1 MUTATED UNC93B1 WILD-TYPE
  ASIAN                                   0                39
  BLACK OR AFRICAN AMERICAN               0                22
  WHITE                                   7               310
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V13, binary
                   cls
clus                  0   1
  UNC93B1 MUTATED     0   6
  UNC93B1 WILD-TYPE   8 349
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UNC93B1 MUTATED      0    6
  UNC93B1 WILD-TYPE    8  349
                        clus
vv                       UNC93B1 MUTATED UNC93B1 WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               6               349
[1] 2 2
[1] FALSE

Clustering(49) Variable = SF1 MUTATION ANALYSIS
D49V1, survival
               sevent
clus2             0   1
  SF1 MUTATED     6   4
  SF1 WILD-TYPE 211 171
  SF1 MUTATED SF1 WILD-TYPE 
           10           382 
  SF1 MUTATED SF1 WILD-TYPE 
            4           171 
$`SF1 MUTATED`
TCGA-DK-A1AC TCGA-E7-A7DV TCGA-G2-AA3D TCGA-GC-A3YS TCGA-XF-A9SK TCGA-XF-AAN7 
      130.88         1.22        70.32        24.92        15.98        18.58 
TCGA-4Z-AA82 TCGA-CF-A47W TCGA-DK-A3IK TCGA-ZF-A9RM 
       51.16        12.10         4.80        47.84 

$`SF1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B6 
       11.18        20.32        15.35        25.58         0.92        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P 
       33.01        17.62        21.40        19.13        17.75        10.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       32.78        32.98        19.82        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       19.07        22.72         9.01        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        9.14        27.68        52.73        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ 
       14.24         1.84        33.14        86.83        51.32         3.22 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       34.45        14.93         4.21        12.76        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        66.64         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 
       98.99        44.32        30.94        61.45        86.30         3.88 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE 
        9.63        13.64        21.11        30.28        94.29         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO 
       88.87        34.06        19.69        57.90        12.23        24.13 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O 
       11.97        94.88       104.65         8.35        44.94        16.83 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 
       17.16        34.98        27.62        50.04         0.62        41.75 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       66.54        10.22        47.80         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50         5.06        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        8.25        17.16        16.18         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         1.94         2.93        23.01        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.10        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM 
       15.62        17.95         7.79       142.78        13.58         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       19.00        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        22.16         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
       26.96        26.24         4.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.70         7.10        13.35         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65         8.94         3.25        22.88        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       15.95        26.93        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        29.36        20.71        15.81        15.91        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91        26.70         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        2.20        11.31        18.97         7.63        20.05        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
        4.73         7.00        14.27        21.34        19.10         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
       36.49         1.51        19.40        38.60        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       21.24         9.07        11.70        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       16.27        11.80        44.38         1.15        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       13.48        12.23        16.67        16.54        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       37.05        22.68        76.01        69.34        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         6.21         3.85         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        79.66        66.41         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       16.27        92.98       110.60         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
       56.48        27.06        75.39         0.66        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       25.41        31.20        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       64.08        58.72        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        67.20        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  SF1 MUTATED SF1 WILD-TYPE 
         1.22          0.56 
  SF1 MUTATED SF1 WILD-TYPE 
       130.88        166.03 
  SF1 MUTATED SF1 WILD-TYPE 
        21.75         17.62 
[1] "1.2 - 130.9 (21.8)" "0.6 - 166.0 (17.6)"
[1] "hr=" "1.4"
D49V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  SF1 MUTATED         0        2         1        7
  SF1 WILD-TYPE       2      120       134      127
D49V3, multiclass
           clus
vv          SF1 MUTATED SF1 WILD-TYPE
  STAGE I             0             2
  STAGE II            2           120
  STAGE III           1           134
  STAGE IV            7           127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1+T2  T3  T4
  SF1 MUTATED          3   6   1
  SF1 WILD-TYPE      113 184  56
D49V4, multiclass
          clus
vv         SF1 MUTATED SF1 WILD-TYPE
  T0+T1+T2           3           113
  T3                 6           184
  T4                 1            56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  SF1 MUTATED     3   4   2   1
  SF1 WILD-TYPE 222  42  73   7
D49V5, multiclass
    clus
vv   SF1 MUTATED SF1 WILD-TYPE
  N0           3           222
  N1           4            42
  N2           2            73
  N3           1             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"
D49V6, binary
               cls
clus              0   1
  SF1 MUTATED     5   0
  SF1 WILD-TYPE 184  11
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED      5    0
  SF1 WILD-TYPE  184   11
   clus
vv  SF1 MUTATED SF1 WILD-TYPE
  0           5           184
  1           0            11
[1] 2 2
[1] FALSE
D49V7, binary
               cls
clus              0   1
  SF1 MUTATED     0  10
  SF1 WILD-TYPE 102 283
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED      0   10
  SF1 WILD-TYPE  102  283
        clus
vv       SF1 MUTATED SF1 WILD-TYPE
  FEMALE           0           102
  MALE            10           283
[1] 2 2
[1] FALSE
D49V8, binary
               cls
clus              0   1
  SF1 MUTATED     9   0
  SF1 WILD-TYPE 341  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED      9    0
  SF1 WILD-TYPE  341   20
     clus
vv    SF1 MUTATED SF1 WILD-TYPE
  NO            9           341
  YES           0            20
[1] 2 2
[1] FALSE
D49V9, continuous
D49V10, continuous
D49V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SF1 MUTATED       1                         1     8
  SF1 WILD-TYPE    38                        21   309
D49V12, multiclass
                           clus
vv                          SF1 MUTATED SF1 WILD-TYPE
  ASIAN                               1            38
  BLACK OR AFRICAN AMERICAN           1            21
  WHITE                               8           309
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V13, binary
               cls
clus              0   1
  SF1 MUTATED     0   8
  SF1 WILD-TYPE   8 347
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED      0    8
  SF1 WILD-TYPE    8  347
                        clus
vv                       SF1 MUTATED SF1 WILD-TYPE
  HISPANIC OR LATINO               0             8
  NOT HISPANIC OR LATINO           8           347
[1] 2 2
[1] FALSE

Clustering(50) Variable = BCL2L1 MUTATION ANALYSIS
D50V1, survival
                  sevent
clus2                0   1
  BCL2L1 MUTATED     0   4
  BCL2L1 WILD-TYPE 217 171
  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
               4              388 
  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
               4              171 
$`BCL2L1 MUTATED`
TCGA-BT-A20N TCGA-DK-AA75 TCGA-FD-A62O TCGA-GC-A3I6 
       26.14        11.18         7.10        20.71 

$`BCL2L1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       33.01        17.62        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       24.92        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        3.45         2.76         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       35.97        46.98        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       51.32         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
        7.63        71.57        91.73        98.99        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       61.45        86.30        18.58         3.88         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
       21.11        30.28        94.29         3.48        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       19.69        57.90        12.23        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65         8.35        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       10.22        47.80         2.50        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        2.66         6.74         6.58        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       17.88        19.50         5.06        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       17.16        16.18         4.67        17.56        36.43        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        1.94         2.93        23.01        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.10        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
        8.15        20.81        10.55       163.30        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       18.81        19.00        15.35        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        22.16         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
       27.45         2.70        13.35         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65         8.94         3.25        22.88        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       15.95        26.93        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 
        6.94        29.36        15.81        15.91        14.07         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91        26.70         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31        18.97         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        7.00        14.27        21.34        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       11.80        44.38         1.15        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       12.23        16.67        16.54        38.99        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       22.68        76.01        69.34        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        6.21         3.85         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       79.66        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       58.72        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        67.20        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
            7.10             0.56 
  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
           26.14           166.03 
  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
          15.945           17.620 
[1] "7.1 - 26.1 (15.9)"  "0.6 - 166.0 (17.6)"
[1] "hr=" "2.9"
D50V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  BCL2L1 MUTATED         0        0         3        1
  BCL2L1 WILD-TYPE       2      122       132      133
D50V3, multiclass
           clus
vv          BCL2L1 MUTATED BCL2L1 WILD-TYPE
  STAGE I                0                2
  STAGE II               0              122
  STAGE III              3              132
  STAGE IV               1              133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  BCL2L1 MUTATED          0   4   0
  BCL2L1 WILD-TYPE      116 186  57
D50V4, multiclass
          clus
vv         BCL2L1 MUTATED BCL2L1 WILD-TYPE
  T0+T1+T2              0              116
  T3                    4              186
  T4                    0               57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  BCL2L1 MUTATED     3   0   1   0
  BCL2L1 WILD-TYPE 222  46  74   8
D50V5, multiclass
    clus
vv   BCL2L1 MUTATED BCL2L1 WILD-TYPE
  N0              3              222
  N1              0               46
  N2              1               74
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                  cls
clus                 0   1
  BCL2L1 MUTATED     2   0
  BCL2L1 WILD-TYPE 187  11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL2L1 MUTATED      2    0
  BCL2L1 WILD-TYPE  187   11
   clus
vv  BCL2L1 MUTATED BCL2L1 WILD-TYPE
  0              2              187
  1              0               11
[1] 2 2
[1] FALSE
D50V7, binary
                  cls
clus                 0   1
  BCL2L1 MUTATED     0   4
  BCL2L1 WILD-TYPE 102 289
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL2L1 MUTATED      0    4
  BCL2L1 WILD-TYPE  102  289
        clus
vv       BCL2L1 MUTATED BCL2L1 WILD-TYPE
  FEMALE              0              102
  MALE                4              289
[1] 2 2
[1] FALSE
D50V8, binary
                  cls
clus                 0   1
  BCL2L1 MUTATED     4   0
  BCL2L1 WILD-TYPE 346  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL2L1 MUTATED      4    0
  BCL2L1 WILD-TYPE  346   20
     clus
vv    BCL2L1 MUTATED BCL2L1 WILD-TYPE
  NO               4              346
  YES              0               20
[1] 2 2
[1] FALSE
D50V9, continuous
[1] "Remove cluster labels:" "BCL2L1 MUTATED"        
clus
  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
               2              128 
      TCGA-2F-A9KT       TCGA-DK-A2HX       TCGA-DK-A3IN       TCGA-DK-A3IV 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A3X2       TCGA-DK-A6B2       TCGA-DK-A6B5       TCGA-DK-A6B6 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-AA6M       TCGA-DK-AA6R       TCGA-DK-AA6S       TCGA-DK-AA6W 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-E5-A4TZ       TCGA-E7-A541       TCGA-E7-A7DU       TCGA-E7-A7DV 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FT-A61P       TCGA-G2-A2ES       TCGA-G2-A3VY       TCGA-GC-A3BM 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GC-A3YS       TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QK 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GV-A40E       TCGA-GV-A40G       TCGA-GV-A6ZA       TCGA-KQ-A41N 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-SY-A9G0       TCGA-UY-A78N       TCGA-XF-A9SJ       TCGA-XF-A9SK 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9SM       TCGA-XF-A9SP       TCGA-XF-A9ST       TCGA-XF-A9SV 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9SW       TCGA-XF-A9SY       TCGA-XF-A9T0       TCGA-XF-A9T2 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9T3       TCGA-XF-A9T5       TCGA-XF-A9T6       TCGA-XF-A9T8 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAMF       TCGA-XF-AAMH       TCGA-XF-AAMJ       TCGA-XF-AAML 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAMQ       TCGA-XF-AAMR       TCGA-XF-AAMY       TCGA-XF-AAMZ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAN1       TCGA-XF-AAN2       TCGA-XF-AAN3       TCGA-XF-AAN7 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAN8       TCGA-YF-AA3M       TCGA-2F-A9KO       TCGA-2F-A9KP 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-2F-A9KQ       TCGA-2F-A9KR       TCGA-2F-A9KW       TCGA-CF-A1HS 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CF-A27C       TCGA-CF-A3MF       TCGA-CF-A3MG       TCGA-CF-A3MH 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CF-A3MI       TCGA-CF-A47S       TCGA-CF-A47T       TCGA-CF-A47V 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CF-A47W       TCGA-CF-A47X       TCGA-CF-A47Y       TCGA-CF-A5U8 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CF-A5UA       TCGA-CF-A7I0       TCGA-DK-A3WX       TCGA-DK-AA6P 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-AA6U       TCGA-DK-AA76       TCGA-E5-A2PC       TCGA-E5-A4U1 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-E7-A519       TCGA-E7-A6MD       TCGA-G2-A2EC       TCGA-G2-A2EF 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-G2-A2EJ       TCGA-G2-A2EK       TCGA-G2-A2EL       TCGA-G2-A2EO 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-G2-A3IB       TCGA-G2-A3IE       TCGA-GC-A3OO       TCGA-GC-A3RC 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GC-A3RD       TCGA-GC-A6I1       TCGA-GC-A6I3       TCGA-GD-A3OS 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GD-A6C6       TCGA-GV-A3JV       TCGA-GV-A3JW       TCGA-GV-A3JX 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GV-A3QH       TCGA-GV-A3QI       TCGA-SY-A9G5       TCGA-UY-A78L 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-UY-A78M       TCGA-XF-A8HH       TCGA-XF-A8HI       TCGA-XF-A9SG 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9SH       TCGA-XF-A9SI       TCGA-XF-A9SL       TCGA-XF-A9SU 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9SX       TCGA-XF-A9SZ       TCGA-XF-A9T4       TCGA-XF-AAME 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAMG       TCGA-XF-AAMT       TCGA-XF-AAMW       TCGA-XF-AAMX 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAN0       TCGA-XF-AAN4       TCGA-XF-AAN5       TCGA-YF-AA3L 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
D50V10, continuous
[1] "Remove cluster labels:" "BCL2L1 MUTATED"        
clus
  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
               2              213 
      TCGA-4Z-AA7M       TCGA-4Z-AA89       TCGA-BL-A5ZZ       TCGA-BT-A42C 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-C4-A0EZ       TCGA-CU-A0YN       TCGA-CU-A0YR       TCGA-CU-A3KJ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CU-A72E       TCGA-DK-A1A5       TCGA-DK-A1AA       TCGA-DK-A1AC 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A2HX       TCGA-DK-A2I6       TCGA-DK-A3IN       TCGA-DK-A3IQ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A3IU       TCGA-DK-A3IV       TCGA-DK-A3X1       TCGA-DK-A3X2 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A6AV       TCGA-DK-A6AW       TCGA-DK-A6B0       TCGA-DK-A6B2 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A6B6       TCGA-DK-AA6L       TCGA-DK-AA6R       TCGA-DK-AA74 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-E5-A4TZ       TCGA-FD-A3B6       TCGA-FD-A3B7       TCGA-FD-A3NA 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A3SJ       TCGA-FD-A3SM       TCGA-FD-A3SN       TCGA-FD-A3SQ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A3SR       TCGA-FD-A3SS       TCGA-FD-A43P       TCGA-FD-A43X 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A5BT       TCGA-FD-A5BX       TCGA-FD-A5C0       TCGA-FD-A6TB 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A6TC       TCGA-FD-A6TE       TCGA-FD-A6TG       TCGA-FD-A6TH 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FJ-A3ZF       TCGA-FT-A61P       TCGA-G2-A2ES       TCGA-G2-AA3D 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GC-A3BM       TCGA-GC-A3RB       TCGA-GC-A3WC       TCGA-GC-A3YS 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GU-A42P       TCGA-GU-A763       TCGA-GU-AATP       TCGA-GV-A3JZ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GV-A3QF       TCGA-GV-A3QG       TCGA-GV-A3QK       TCGA-GV-A40E 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GV-A40G       TCGA-HQ-A5ND       TCGA-K4-A3WS       TCGA-KQ-A41N 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-R3-A69X       TCGA-S5-A6DX       TCGA-SY-A9G0       TCGA-UY-A78N 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9SJ       TCGA-XF-A9SK       TCGA-XF-A9SM       TCGA-XF-A9SP 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9ST       TCGA-XF-A9SV       TCGA-XF-A9SY       TCGA-XF-A9T3 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9T8       TCGA-XF-AAMF       TCGA-XF-AAMH       TCGA-XF-AAMQ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAN1       TCGA-XF-AAN2       TCGA-XF-AAN7       TCGA-XF-AAN8 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-YF-AA3M       TCGA-ZF-A9R2       TCGA-ZF-A9RL       TCGA-ZF-AA5P 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-2F-A9KO       TCGA-2F-A9KP       TCGA-2F-A9KR       TCGA-5N-A9KI 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-5N-A9KM       TCGA-BL-A0C8       TCGA-BL-A13I       TCGA-BL-A13J 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-BL-A3JM       TCGA-BT-A20J       TCGA-BT-A2LA       TCGA-BT-A42B 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-BT-A42E       TCGA-C4-A0F0       TCGA-C4-A0F1       TCGA-C4-A0F6 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CF-A3MH       TCGA-CF-A3MI       TCGA-CF-A47W       TCGA-CF-A47X 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CF-A5UA       TCGA-CF-A9FH       TCGA-CU-A3QU       TCGA-CU-A3YL 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CU-A5W6       TCGA-DK-A1A3       TCGA-DK-A1A6       TCGA-DK-A1AE 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A3IL       TCGA-DK-A3IM       TCGA-DK-A3WX       TCGA-DK-AA6P 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-AA6T       TCGA-DK-AA6U       TCGA-DK-AA76       TCGA-E7-A4XJ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-E7-A519       TCGA-E7-A5KF       TCGA-E7-A678       TCGA-E7-A6ME 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-E7-A6MF       TCGA-E7-A7PW       TCGA-E7-A7XN       TCGA-E7-A85H 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-E7-A97Q       TCGA-FD-A3B3       TCGA-FD-A3B4       TCGA-FD-A3B5 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A3B8       TCGA-FD-A3N5       TCGA-FD-A3N6       TCGA-FD-A3SO 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A3SP       TCGA-FD-A43N       TCGA-FD-A43S       TCGA-FD-A43U 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A5BU       TCGA-FD-A5BV       TCGA-FD-A62N       TCGA-FD-A6TK 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FJ-A3Z9       TCGA-FJ-A3ZE       TCGA-FJ-A871       TCGA-G2-A2EF 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-G2-A2EJ       TCGA-G2-A2EL       TCGA-G2-A3IE       TCGA-G2-AA3B 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-G2-AA3C       TCGA-G2-AA3F       TCGA-GD-A2C5       TCGA-GD-A3OQ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GD-A3OS       TCGA-GD-A6C6       TCGA-GU-A42Q       TCGA-GU-A42R 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GU-A764       TCGA-GU-AATQ       TCGA-GV-A3JV       TCGA-GV-A3JX 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GV-A3QH       TCGA-GV-A3QI       TCGA-H4-A2HO       TCGA-H4-A2HQ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-HQ-A5NE       TCGA-K4-A3WV       TCGA-K4-A5RH       TCGA-K4-A5RI 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-K4-A83P       TCGA-K4-AAQO       TCGA-KQ-A41R       TCGA-PQ-A6FI 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-PQ-A6FN       TCGA-UY-A8OB       TCGA-UY-A9PB       TCGA-UY-A9PE 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-UY-A9PF       TCGA-XF-A9SL       TCGA-XF-A9SU       TCGA-XF-A9SX 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9SZ       TCGA-XF-AAMT       TCGA-XF-AAN0       TCGA-XF-AAN4 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAN5       TCGA-YF-AA3L       TCGA-ZF-A9R0       TCGA-ZF-A9R3 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-ZF-A9R5       TCGA-ZF-A9R9       TCGA-ZF-A9RD       TCGA-ZF-A9RF 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-ZF-A9RM       TCGA-ZF-AA4U       TCGA-ZF-AA4V       TCGA-ZF-AA51 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-ZF-AA52       TCGA-ZF-AA58       TCGA-ZF-AA5H       TCGA-ZF-AA5N 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GU-AATO 
"BCL2L1 WILD-TYPE" 
D50V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCL2L1 MUTATED       0                         0     3
  BCL2L1 WILD-TYPE    39                        22   314
D50V12, multiclass
                           clus
vv                          BCL2L1 MUTATED BCL2L1 WILD-TYPE
  ASIAN                                  0               39
  BLACK OR AFRICAN AMERICAN              0               22
  WHITE                                  3              314
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V13, binary
                  cls
clus                 0   1
  BCL2L1 MUTATED     0   3
  BCL2L1 WILD-TYPE   8 352
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL2L1 MUTATED      0    3
  BCL2L1 WILD-TYPE    8  352
                        clus
vv                       BCL2L1 MUTATED BCL2L1 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO              3              352
[1] 2 2
[1] FALSE

Clustering(51) Variable = DNAH6 MUTATION ANALYSIS
D51V1, survival
                 sevent
clus2               0   1
  DNAH6 MUTATED    11   5
  DNAH6 WILD-TYPE 206 170
  DNAH6 MUTATED DNAH6 WILD-TYPE 
             16             376 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
              5             170 
$`DNAH6 MUTATED`
TCGA-DK-A6B6 TCGA-E7-A541 TCGA-GV-A3QF TCGA-GV-A6ZA TCGA-XF-A9SW TCGA-4Z-AA80 
       36.66        25.58        20.28        22.72        11.90         0.62 
TCGA-CF-A47V TCGA-CU-A3QU TCGA-DK-AA6P TCGA-E7-A6MD TCGA-FD-A3B8 TCGA-GD-A3OP 
       12.46         5.19        15.02         4.24        12.62         2.10 
TCGA-K4-A83P TCGA-MV-A51V TCGA-UY-A9PD TCGA-XF-A8HI 
       16.27        13.48        17.82        17.88 

$`DNAH6 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      130.88        46.68        87.32         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       21.30        23.21         9.67        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       53.29        76.60        67.36        15.68        50.70        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       11.18        20.32        15.35         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       33.01        17.62        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK 
       24.92        10.92        32.78        32.98        19.82        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
        8.58        19.07         9.01        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        9.14        27.68        52.73        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ 
       14.24         1.84        33.14        86.83        51.32         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SY 
       15.98        34.45        14.93         4.21        12.76        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        66.64         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       98.99        44.32        30.94        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
        3.88         9.63        13.64        21.11        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.48        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 
       16.83        17.16        34.98        27.62        50.04        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM 
       51.16        66.54        10.22        47.80         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       19.04        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
        5.06         8.25        17.16        16.18         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR 
       36.43        28.41         1.94         2.93        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.56        13.97        12.59        12.13        13.08        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       10.95        12.66        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 
       12.00        12.10        11.87        13.08        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T 
        8.15        20.81        10.55       163.30        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       19.00        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        22.16         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN 
       26.96        26.24        24.03        24.66        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
       20.91        19.33         5.36        27.45         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       13.35         2.27        10.85        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25        22.88        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       59.31         7.23        20.12        66.02         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 
       20.71        15.81        15.91        14.07         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
       26.70         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
       38.60        64.01        12.16        21.24         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
       17.72         1.81        15.42        11.80        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       15.32        15.58        12.23        16.67        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       17.62        37.05        22.68        76.01        69.34        35.24 
TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH 
       29.56         6.21         3.85         1.87        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       79.66        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       58.72        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        67.20        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  DNAH6 MUTATED DNAH6 WILD-TYPE 
           0.62            0.56 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
          36.66          166.03 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
          14.25           17.72 
[1] "0.6 - 36.7 (14.2)"  "0.6 - 166.0 (17.7)"
[1] "hr=" "1"  
D51V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  DNAH6 MUTATED         0        7         2        7
  DNAH6 WILD-TYPE       2      115       133      127
D51V3, multiclass
           clus
vv          DNAH6 MUTATED DNAH6 WILD-TYPE
  STAGE I               0               2
  STAGE II              7             115
  STAGE III             2             133
  STAGE IV              7             127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  DNAH6 MUTATED          7   4   3
  DNAH6 WILD-TYPE      109 186  54
D51V4, multiclass
          clus
vv         DNAH6 MUTATED DNAH6 WILD-TYPE
  T0+T1+T2             7             109
  T3                   4             186
  T4                   3              54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DNAH6 MUTATED     8   3   4   0
  DNAH6 WILD-TYPE 217  43  71   8
D51V5, multiclass
    clus
vv   DNAH6 MUTATED DNAH6 WILD-TYPE
  N0             8             217
  N1             3              43
  N2             4              71
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                 cls
clus                0   1
  DNAH6 MUTATED     6   0
  DNAH6 WILD-TYPE 183  11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH6 MUTATED      6    0
  DNAH6 WILD-TYPE  183   11
   clus
vv  DNAH6 MUTATED DNAH6 WILD-TYPE
  0             6             183
  1             0              11
[1] 2 2
[1] FALSE
D51V7, binary
                 cls
clus                0   1
  DNAH6 MUTATED     3  13
  DNAH6 WILD-TYPE  99 280
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH6 MUTATED      3   13
  DNAH6 WILD-TYPE   99  280
        clus
vv       DNAH6 MUTATED DNAH6 WILD-TYPE
  FEMALE             3              99
  MALE              13             280
[1] 2 2
[1] FALSE
D51V8, binary
                 cls
clus                0   1
  DNAH6 MUTATED    13   1
  DNAH6 WILD-TYPE 337  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH6 MUTATED     13    1
  DNAH6 WILD-TYPE  337   19
     clus
vv    DNAH6 MUTATED DNAH6 WILD-TYPE
  NO             13             337
  YES             1              19
[1] 2 2
[1] FALSE
D51V9, continuous
D51V10, continuous
D51V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DNAH6 MUTATED       1                         0    15
  DNAH6 WILD-TYPE    38                        22   302
D51V12, multiclass
                           clus
vv                          DNAH6 MUTATED DNAH6 WILD-TYPE
  ASIAN                                 1              38
  BLACK OR AFRICAN AMERICAN             0              22
  WHITE                                15             302
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V13, binary
                 cls
clus                0   1
  DNAH6 MUTATED     1  14
  DNAH6 WILD-TYPE   7 341
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH6 MUTATED      1   14
  DNAH6 WILD-TYPE    7  341
                        clus
vv                       DNAH6 MUTATED DNAH6 WILD-TYPE
  HISPANIC OR LATINO                 1               7
  NOT HISPANIC OR LATINO            14             341
[1] 2 2
[1] FALSE

Clustering(52) Variable = HES1 MUTATION ANALYSIS
D52V1, survival
                sevent
clus2              0   1
  HES1 MUTATED     7   4
  HES1 WILD-TYPE 210 171
  HES1 MUTATED HES1 WILD-TYPE 
            11            381 
  HES1 MUTATED HES1 WILD-TYPE 
             4            171 
$`HES1 MUTATED`
TCGA-CU-A72E TCGA-DK-A1AC TCGA-DK-AA71 TCGA-GV-A3QF TCGA-S5-A6DX TCGA-4Z-AA80 
       13.58       130.88        13.64        20.28         1.84         0.62 
TCGA-DK-A2I4 TCGA-DK-A3WW TCGA-FD-A5BU TCGA-KQ-A41R TCGA-ZF-AA4V 
      142.78        20.81        19.33        44.38        59.38 

$`HES1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX 
       15.12        18.48         2.14        19.00        16.70        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       87.32         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        66.05        17.98        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       67.36        15.68        50.70        36.66        38.24        52.01 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
      165.73       166.03        13.64        56.15        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       15.35        25.58         0.92         1.22        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
       60.66        24.30        23.41        17.98        29.16        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       19.79        12.85        27.35         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       10.78         5.69         8.25        18.08        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
       62.86        18.81         6.15        12.69        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        4.31         9.67        31.07        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       17.62        70.32        21.40        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E 
       10.92        32.78        32.98        19.82        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       19.07        22.72         9.01        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        9.14        27.68        52.73        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK 
       14.24        33.14        86.83        51.32         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       34.45        14.93         4.21        12.76        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        66.64         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       98.99        44.32        30.94        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
        3.88         9.63        13.64        21.11        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.48        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 
       16.83        17.16        34.98        27.62        50.04        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM 
       51.16        66.54        10.22        47.80         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       19.04        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
        5.06         8.25        17.16        16.18         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR 
       36.43        28.41         1.94         2.93        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.56        13.97        12.59        12.13        13.08        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU 
       13.12        12.00        12.10        11.87        13.08         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       29.79         1.84        21.86        66.41        18.41       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK 
       16.14        17.62        15.62        17.95         7.79         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
       13.58         8.15        10.55       163.30        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       18.81        19.00        15.35        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        22.16         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ 
       25.74        22.98        14.96        20.91         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.70         7.10        13.35         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65         8.94         3.25        22.88        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       15.95        26.93        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        29.36        20.71        15.81        15.91        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91        26.70         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        2.20        11.31        18.97         7.63        20.05        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
        4.73         7.00        14.27        21.34        19.10         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
       36.49         1.51        19.40        38.60        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       21.24         9.07        11.70        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       16.27        11.80         1.15        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       12.23        16.67        16.54        38.99        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       22.68        76.01        69.34        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        6.21         3.85         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       79.66        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W 
       58.72        47.84        20.22         2.89         8.61        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       67.20        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

  HES1 MUTATED HES1 WILD-TYPE 
          0.62           0.56 
  HES1 MUTATED HES1 WILD-TYPE 
        142.78         166.03 
  HES1 MUTATED HES1 WILD-TYPE 
         20.28          17.62 
[1] "0.6 - 142.8 (20.3)" "0.6 - 166.0 (17.6)"
[1] "hr=" "1.6"
D52V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  HES1 MUTATED         0        4         4        3
  HES1 WILD-TYPE       2      118       131      131
D52V3, multiclass
           clus
vv          HES1 MUTATED HES1 WILD-TYPE
  STAGE I              0              2
  STAGE II             4            118
  STAGE III            4            131
  STAGE IV             3            131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  HES1 MUTATED          4   6   1
  HES1 WILD-TYPE      112 184  56
D52V4, multiclass
          clus
vv         HES1 MUTATED HES1 WILD-TYPE
  T0+T1+T2            4            112
  T3                  6            184
  T4                  1             56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  HES1 MUTATED     8   0   3   0
  HES1 WILD-TYPE 217  46  72   8
D52V5, multiclass
    clus
vv   HES1 MUTATED HES1 WILD-TYPE
  N0            8            217
  N1            0             46
  N2            3             72
  N3            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                cls
clus               0   1
  HES1 MUTATED     7   0
  HES1 WILD-TYPE 182  11
[1] "tbl2"
                cls
clus             [,1] [,2]
  HES1 MUTATED      7    0
  HES1 WILD-TYPE  182   11
   clus
vv  HES1 MUTATED HES1 WILD-TYPE
  0            7            182
  1            0             11
[1] 2 2
[1] FALSE
D52V7, binary
                cls
clus               0   1
  HES1 MUTATED     2   9
  HES1 WILD-TYPE 100 284
[1] "tbl2"
                cls
clus             [,1] [,2]
  HES1 MUTATED      2    9
  HES1 WILD-TYPE  100  284
        clus
vv       HES1 MUTATED HES1 WILD-TYPE
  FEMALE            2            100
  MALE              9            284
[1] 2 2
[1] FALSE
D52V8, binary
                cls
clus               0   1
  HES1 MUTATED    11   0
  HES1 WILD-TYPE 339  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  HES1 MUTATED     11    0
  HES1 WILD-TYPE  339   20
     clus
vv    HES1 MUTATED HES1 WILD-TYPE
  NO            11            339
  YES            0             20
[1] 2 2
[1] FALSE
D52V9, continuous
[1] "Remove cluster labels:" "HES1 MUTATED"          
clus
  HES1 MUTATED HES1 WILD-TYPE 
             1            129 
    TCGA-2F-A9KT     TCGA-DK-A2HX     TCGA-DK-A3IN     TCGA-DK-A3IV 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-DK-A3X2     TCGA-DK-A6B2     TCGA-DK-A6B5     TCGA-DK-A6B6 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-DK-AA6M     TCGA-DK-AA6R     TCGA-DK-AA6S     TCGA-DK-AA6W 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-DK-AA75     TCGA-E5-A4TZ     TCGA-E7-A541     TCGA-E7-A7DU 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-E7-A7DV     TCGA-FT-A61P     TCGA-G2-A2ES     TCGA-G2-A3VY 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-GC-A3BM     TCGA-GC-A3YS     TCGA-GV-A3JZ     TCGA-GV-A3QK 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-GV-A40E     TCGA-GV-A40G     TCGA-GV-A6ZA     TCGA-KQ-A41N 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-SY-A9G0     TCGA-UY-A78N     TCGA-XF-A9SJ     TCGA-XF-A9SK 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-A9SM     TCGA-XF-A9SP     TCGA-XF-A9ST     TCGA-XF-A9SV 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-A9SW     TCGA-XF-A9SY     TCGA-XF-A9T0     TCGA-XF-A9T2 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-A9T3     TCGA-XF-A9T5     TCGA-XF-A9T6     TCGA-XF-A9T8 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-AAMF     TCGA-XF-AAMH     TCGA-XF-AAMJ     TCGA-XF-AAML 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-AAMQ     TCGA-XF-AAMR     TCGA-XF-AAMY     TCGA-XF-AAMZ 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-AAN1     TCGA-XF-AAN2     TCGA-XF-AAN3     TCGA-XF-AAN7 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-AAN8     TCGA-YF-AA3M     TCGA-2F-A9KO     TCGA-2F-A9KP 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-2F-A9KQ     TCGA-2F-A9KR     TCGA-2F-A9KW     TCGA-CF-A1HS 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-CF-A27C     TCGA-CF-A3MF     TCGA-CF-A3MG     TCGA-CF-A3MH 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-CF-A3MI     TCGA-CF-A47S     TCGA-CF-A47T     TCGA-CF-A47V 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-CF-A47W     TCGA-CF-A47X     TCGA-CF-A47Y     TCGA-CF-A5U8 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-CF-A5UA     TCGA-CF-A7I0     TCGA-DK-A3WX     TCGA-DK-AA6P 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-DK-AA6U     TCGA-DK-AA76     TCGA-E5-A2PC     TCGA-E5-A4U1 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-E7-A519     TCGA-E7-A6MD     TCGA-G2-A2EC     TCGA-G2-A2EF 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-G2-A2EJ     TCGA-G2-A2EK     TCGA-G2-A2EL     TCGA-G2-A2EO 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-G2-A3IB     TCGA-G2-A3IE     TCGA-GC-A3I6     TCGA-GC-A3OO 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-GC-A3RC     TCGA-GC-A3RD     TCGA-GC-A6I1     TCGA-GC-A6I3 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-GD-A3OS     TCGA-GD-A6C6     TCGA-GV-A3JV     TCGA-GV-A3JW 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-GV-A3JX     TCGA-GV-A3QH     TCGA-GV-A3QI     TCGA-SY-A9G5 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-UY-A78L     TCGA-UY-A78M     TCGA-XF-A8HH     TCGA-XF-A8HI 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-A9SG     TCGA-XF-A9SH     TCGA-XF-A9SI     TCGA-XF-A9SL 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-A9SU     TCGA-XF-A9SX     TCGA-XF-A9SZ     TCGA-XF-A9T4 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-AAME     TCGA-XF-AAMG     TCGA-XF-AAMT     TCGA-XF-AAMW 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-AAMX     TCGA-XF-AAN0     TCGA-XF-AAN4     TCGA-XF-AAN5 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-YF-AA3L 
"HES1 WILD-TYPE" 
D52V10, continuous
D52V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HES1 MUTATED       0                         1    10
  HES1 WILD-TYPE    39                        21   307
D52V12, multiclass
                           clus
vv                          HES1 MUTATED HES1 WILD-TYPE
  ASIAN                                0             39
  BLACK OR AFRICAN AMERICAN            1             21
  WHITE                               10            307
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V13, binary
                cls
clus               0   1
  HES1 MUTATED     0   9
  HES1 WILD-TYPE   8 346
[1] "tbl2"
                cls
clus             [,1] [,2]
  HES1 MUTATED      0    9
  HES1 WILD-TYPE    8  346
                        clus
vv                       HES1 MUTATED HES1 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO            9            346
[1] 2 2
[1] FALSE

Clustering(53) Variable = ERBB3 MUTATION ANALYSIS
D53V1, survival
                 sevent
clus2               0   1
  ERBB3 MUTATED    20  21
  ERBB3 WILD-TYPE 197 154
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             41             351 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             21             154 
$`ERBB3 MUTATED`
TCGA-4Z-AA7Q TCGA-DK-A1AA TCGA-DK-A3IN TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6S 
       16.77        19.00         8.22        67.36        36.66       166.03 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3B6 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A6TB 
       15.35        25.58        33.04        24.30        29.16        18.81 
TCGA-FD-A6TG TCGA-FJ-A3ZF TCGA-UY-A9PH TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAML 
        3.06        17.23        51.32        13.74        10.82         7.63 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-AA53 TCGA-2F-A9KW TCGA-4Z-AA81 TCGA-BT-A20R 
        9.63        13.64        57.90         8.35        41.75         5.06 
TCGA-DK-A1AG TCGA-DK-A3IL TCGA-DK-AA6P TCGA-DK-AA6X TCGA-E7-A4IJ TCGA-FD-A62O 
       15.62        13.58        15.02        15.35        22.16         7.10 
TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-AA3B TCGA-GD-A3OQ TCGA-GU-A42R TCGA-HQ-A2OE 
       61.94        59.31        66.02         3.12        18.97        38.60 
TCGA-HQ-A5NE TCGA-K4-A6FZ TCGA-MV-A51V TCGA-XF-A8HH TCGA-ZF-AA4U 
       12.16         1.81        13.48         1.87         8.61 

$`ERBB3 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       18.48        13.58         2.14        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       87.32        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 
       66.05        17.98        64.18        53.29        76.60        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA71 
       50.70        38.24        52.01       165.73        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B7 
       56.15        11.18        20.32         0.92         1.22         4.01 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       60.66        23.41        17.98        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       27.35         3.62        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC 
        8.25        18.08        58.92         6.28        62.86         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FT-A61P 
       12.69        12.36         4.31         9.67        31.07        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       33.01        17.62        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       24.92        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        3.45         2.76         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       35.97        46.98        14.24         1.84        33.14        86.83 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
        3.22        15.98        34.45        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
        2.10        11.31        54.90        71.57        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 
       44.32        30.94        61.45        86.30        18.58         3.88 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
       21.11        30.28        94.29         3.48        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       19.69        12.23        24.13        11.97        94.88       104.65 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
        0.62        51.16        66.54        10.22        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       17.42        40.08         7.33         2.66         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U 
       13.15        19.04        12.16        17.88        19.50        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
        5.06         8.25        17.16        16.18         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR 
       36.43        28.41         1.94         2.93        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.56        13.97        12.59        12.13        13.08        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU 
       13.12        12.00        12.10        11.87        13.08         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       29.79         1.84        21.86        66.41        18.41       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       16.14        17.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T 
        8.15        20.81        10.55       163.30        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       19.00        12.03        43.59        38.83        29.72         5.36 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70         0.56         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
        4.24        24.03        24.66        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       14.37         8.09        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62S 
       20.91        19.33         5.36        27.45         2.70        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.27        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EC TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE 
       22.88        48.00        15.95        26.93         7.23        20.12 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        29.36        20.71        15.81        15.91        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 
        8.94        13.91        26.70         2.10        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       11.31         7.63        20.05        15.78         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
       14.27        21.34        19.10         8.48        36.49         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       19.40        64.01        21.24         9.07        11.70        17.72 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       15.42        16.27        11.80        44.38         1.15        15.32 
TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       15.58        12.23        16.67        16.54        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       37.05        22.68        76.01        69.34        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       17.82         6.21         3.85        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       79.66        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W 
       58.72        47.84        20.22         2.89        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       67.20        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

  ERBB3 MUTATED ERBB3 WILD-TYPE 
           1.81            0.56 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
         166.03          165.73 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
          15.62           17.72 
[1] "1.8 - 166.0 (15.6)" "0.6 - 165.7 (17.7)"
[1] "hr=" "1.2"
D53V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ERBB3 MUTATED         0       15        15       10
  ERBB3 WILD-TYPE       2      107       120      124
D53V3, multiclass
           clus
vv          ERBB3 MUTATED ERBB3 WILD-TYPE
  STAGE I               0               2
  STAGE II             15             107
  STAGE III            15             120
  STAGE IV             10             124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  ERBB3 MUTATED         13  17   6
  ERBB3 WILD-TYPE      103 173  51
D53V4, multiclass
          clus
vv         ERBB3 MUTATED ERBB3 WILD-TYPE
  T0+T1+T2            13             103
  T3                  17             173
  T4                   6              51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ERBB3 MUTATED    24   2   9   0
  ERBB3 WILD-TYPE 201  44  66   8
D53V5, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  N0            24             201
  N1             2              44
  N2             9              66
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                 cls
clus                0   1
  ERBB3 MUTATED    20   0
  ERBB3 WILD-TYPE 169  11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     20    0
  ERBB3 WILD-TYPE  169   11
   clus
vv  ERBB3 MUTATED ERBB3 WILD-TYPE
  0            20             169
  1             0              11
[1] 2 2
[1] FALSE
D53V7, binary
                 cls
clus                0   1
  ERBB3 MUTATED     7  34
  ERBB3 WILD-TYPE  95 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      7   34
  ERBB3 WILD-TYPE   95  259
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  FEMALE             7              95
  MALE              34             259
[1] 2 2
[1] FALSE
D53V8, binary
                 cls
clus                0   1
  ERBB3 MUTATED    37   1
  ERBB3 WILD-TYPE 313  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     37    1
  ERBB3 WILD-TYPE  313   19
     clus
vv    ERBB3 MUTATED ERBB3 WILD-TYPE
  NO             37             313
  YES             1              19
[1] 2 2
[1] FALSE
D53V9, continuous
D53V10, continuous
D53V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERBB3 MUTATED       1                         0    37
  ERBB3 WILD-TYPE    38                        22   280
D53V12, multiclass
                           clus
vv                          ERBB3 MUTATED ERBB3 WILD-TYPE
  ASIAN                                 1              38
  BLACK OR AFRICAN AMERICAN             0              22
  WHITE                                37             280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, binary
                 cls
clus                0   1
  ERBB3 MUTATED     2  35
  ERBB3 WILD-TYPE   6 320
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      2   35
  ERBB3 WILD-TYPE    6  320
                        clus
vv                       ERBB3 MUTATED ERBB3 WILD-TYPE
  HISPANIC OR LATINO                 2               6
  NOT HISPANIC OR LATINO            35             320
[1] 2 2
[1] FALSE

Clustering(54) Variable = TXNIP MUTATION ANALYSIS
D54V1, survival
                 sevent
clus2               0   1
  TXNIP MUTATED    10   7
  TXNIP WILD-TYPE 207 168
  TXNIP MUTATED TXNIP WILD-TYPE 
             17             375 
  TXNIP MUTATED TXNIP WILD-TYPE 
              7             168 
$`TXNIP MUTATED`
TCGA-BT-A20T TCGA-FD-A43P TCGA-GC-A3WC TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WU 
       14.89        27.35        17.75        19.07        22.72         3.45 
TCGA-4Z-AA7R TCGA-BT-A3PH TCGA-DK-A1A6 TCGA-FD-A3SO TCGA-G2-A2EC TCGA-G2-A2EO 
       17.16         4.67        66.41         5.52        22.88        59.31 
TCGA-KQ-A41S TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-AAMG TCGA-ZF-AA56 
        1.15         6.21         3.85       110.60         8.52 

$`TXNIP WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       26.14         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A5BR 
       29.16        46.78        19.79        12.85         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3YS 
       33.01        17.62        70.32        21.40        19.13        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       10.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        8.58         9.01        25.02         2.76         9.14        27.68 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX 
       52.73        50.56        35.97        46.98        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
       33.14        86.83        51.32         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       14.93         4.21        12.76        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       18.90         2.24        66.64         2.10        13.74        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       11.31        54.90         7.63        71.57        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 
       44.32        30.94        61.45        86.30        18.58         3.88 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE 
        9.63        13.64        21.11        30.28        94.29         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO 
       88.87        34.06        19.69        57.90        12.23        24.13 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O 
       11.97        94.88       104.65         8.35        44.94        16.83 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       34.98        27.62        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       66.54        10.22        47.80         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50         5.06        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
        8.25        17.16        16.18        17.56        36.43        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        1.94         2.93        23.01        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.10        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       21.86        18.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       17.95         7.79       142.78         4.80        13.58         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       19.00        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        22.16         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
       26.96        26.24         4.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FD-A43N 
        8.94        12.62        22.52        27.98        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       14.96        20.91        19.33         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        7.10        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25        61.94        48.00        15.95        26.93 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
        7.23        20.12        66.02         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91        14.07         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
       38.60        64.01        12.16        21.24         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       17.72         1.81        15.42        16.27        11.80        44.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       15.32        15.58        13.48        12.23        16.67        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       38.99        17.62        37.05        22.68        76.01        69.34 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       35.24        29.56        17.82         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        79.66        66.41         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       16.27        92.98         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       58.72        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 
       60.16        67.20        56.35        35.41        19.40        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

  TXNIP MUTATED TXNIP WILD-TYPE 
           1.15            0.56 
  TXNIP MUTATED TXNIP WILD-TYPE 
         110.60          166.03 
  TXNIP MUTATED TXNIP WILD-TYPE 
          17.16           17.62 
[1] "1.1 - 110.6 (17.2)" "0.6 - 166.0 (17.6)"
[1] "hr=" "1"  
D54V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TXNIP MUTATED         0        4         6        7
  TXNIP WILD-TYPE       2      118       129      127
D54V3, multiclass
           clus
vv          TXNIP MUTATED TXNIP WILD-TYPE
  STAGE I               0               2
  STAGE II              4             118
  STAGE III             6             129
  STAGE IV              7             127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  TXNIP MUTATED          5   6   5
  TXNIP WILD-TYPE      111 184  52
D54V4, multiclass
          clus
vv         TXNIP MUTATED TXNIP WILD-TYPE
  T0+T1+T2             5             111
  T3                   6             184
  T4                   5              52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TXNIP MUTATED    10   3   3   0
  TXNIP WILD-TYPE 215  43  72   8
D54V5, multiclass
    clus
vv   TXNIP MUTATED TXNIP WILD-TYPE
  N0            10             215
  N1             3              43
  N2             3              72
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                 cls
clus                0   1
  TXNIP MUTATED     5   0
  TXNIP WILD-TYPE 184  11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXNIP MUTATED      5    0
  TXNIP WILD-TYPE  184   11
   clus
vv  TXNIP MUTATED TXNIP WILD-TYPE
  0             5             184
  1             0              11
[1] 2 2
[1] FALSE
D54V7, binary
                 cls
clus                0   1
  TXNIP MUTATED     4  13
  TXNIP WILD-TYPE  98 280
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXNIP MUTATED      4   13
  TXNIP WILD-TYPE   98  280
        clus
vv       TXNIP MUTATED TXNIP WILD-TYPE
  FEMALE             4              98
  MALE              13             280
[1] 2 2
[1] FALSE
D54V8, binary
                 cls
clus                0   1
  TXNIP MUTATED    17   0
  TXNIP WILD-TYPE 333  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXNIP MUTATED     17    0
  TXNIP WILD-TYPE  333   20
     clus
vv    TXNIP MUTATED TXNIP WILD-TYPE
  NO             17             333
  YES             0              20
[1] 2 2
[1] FALSE
D54V9, continuous
D54V10, continuous
D54V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TXNIP MUTATED       0                         3    14
  TXNIP WILD-TYPE    39                        19   303
D54V12, multiclass
                           clus
vv                          TXNIP MUTATED TXNIP WILD-TYPE
  ASIAN                                 0              39
  BLACK OR AFRICAN AMERICAN             3              19
  WHITE                                14             303
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V13, binary
                 cls
clus                0   1
  TXNIP MUTATED     1  13
  TXNIP WILD-TYPE   7 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXNIP MUTATED      1   13
  TXNIP WILD-TYPE    7  342
                        clus
vv                       TXNIP MUTATED TXNIP WILD-TYPE
  HISPANIC OR LATINO                 1               7
  NOT HISPANIC OR LATINO            13             342
[1] 2 2
[1] FALSE

Clustering(55) Variable = THRAP3 MUTATION ANALYSIS
D55V1, survival
                  sevent
clus2                0   1
  THRAP3 MUTATED    10   4
  THRAP3 WILD-TYPE 207 171
  THRAP3 MUTATED THRAP3 WILD-TYPE 
              14              378 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
               4              171 
$`THRAP3 MUTATED`
TCGA-DK-A3X1 TCGA-FD-A3SN TCGA-FD-A43X TCGA-K4-A3WU TCGA-ZF-A9RE TCGA-BT-A2LB 
       66.05        29.16         3.62         3.45         3.48        16.18 
TCGA-GC-A3RC TCGA-GC-A6I1 TCGA-GU-A767 TCGA-GV-A3QI TCGA-MV-A51V TCGA-UY-A9PF 
       15.91         8.94         4.73        36.49        13.48         3.85 
TCGA-XF-AAMG TCGA-ZF-AA4W 
      110.60        60.16 

$`THRAP3 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      130.88        46.68        87.32         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       21.30        23.21         9.67        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A5BR TCGA-FD-A5BS 
       46.78        19.79        12.85        27.35        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       10.78         5.69         8.25        18.08        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
       62.86        18.81         6.15        12.69        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        4.31         9.67        31.07        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       17.62        70.32        21.40        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       10.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AB 
        8.58        19.07        22.72         9.01        25.02         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        9.14        27.68        52.73        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ 
       14.24         1.84        33.14        86.83        51.32         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
       15.98        34.45        14.93         4.21        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       13.74        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
       94.29        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       16.83        17.16        34.98        27.62        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
       41.75        51.16        66.54        10.22        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       17.42        40.08         7.33         2.66         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B 
       14.96         5.06         8.25        17.16         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR 
       36.43        28.41         1.94         2.93        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.56        13.97        12.59        12.13        13.08        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU 
       13.12        12.00        12.10        11.87        13.08         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       29.79         1.84        21.86        66.41        18.41       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       15.02        13.58        18.81        19.00        15.35        12.03 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        38.83        29.72         5.36        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
       24.03        24.66        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       27.98         5.52        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       19.33         5.36        27.45         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.27        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
        7.23        20.12        66.02         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       15.81        14.07        13.91        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
       20.98         2.20        11.31        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
       15.78         7.00        14.27        21.34        19.10         8.48 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI 
       11.80        44.38         1.15        15.32        15.58        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        69.34        35.24        29.56        17.82         6.21 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT 
        5.98        23.64        28.24        16.27        92.98         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC 
        8.32         6.77        56.48        27.06        75.39         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       11.97        22.36        25.41        31.20        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       28.41        13.41        64.08        58.72        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        2.89         8.61        59.38        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21        29.49         5.52        10.65 

  THRAP3 MUTATED THRAP3 WILD-TYPE 
            3.45             0.56 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
          110.60           166.03 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
          14.695           17.720 
[1] "3.5 - 110.6 (14.7)" "0.6 - 166.0 (17.7)"
[1] "hr=" "1.5"
D55V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  THRAP3 MUTATED         0        4         8        2
  THRAP3 WILD-TYPE       2      118       127      132
D55V3, multiclass
           clus
vv          THRAP3 MUTATED THRAP3 WILD-TYPE
  STAGE I                0                2
  STAGE II               4              118
  STAGE III              8              127
  STAGE IV               2              132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  THRAP3 MUTATED          3   8   2
  THRAP3 WILD-TYPE      113 182  55
D55V4, multiclass
          clus
vv         THRAP3 MUTATED THRAP3 WILD-TYPE
  T0+T1+T2              3              113
  T3                    8              182
  T4                    2               55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  THRAP3 MUTATED    11   0   2   0
  THRAP3 WILD-TYPE 214  46  73   8
D55V5, multiclass
    clus
vv   THRAP3 MUTATED THRAP3 WILD-TYPE
  N0             11              214
  N1              0               46
  N2              2               73
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                  cls
clus                 0   1
  THRAP3 MUTATED     4   0
  THRAP3 WILD-TYPE 185  11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THRAP3 MUTATED      4    0
  THRAP3 WILD-TYPE  185   11
   clus
vv  THRAP3 MUTATED THRAP3 WILD-TYPE
  0              4              185
  1              0               11
[1] 2 2
[1] FALSE
D55V7, binary
                  cls
clus                 0   1
  THRAP3 MUTATED     4  10
  THRAP3 WILD-TYPE  98 283
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THRAP3 MUTATED      4   10
  THRAP3 WILD-TYPE   98  283
        clus
vv       THRAP3 MUTATED THRAP3 WILD-TYPE
  FEMALE              4               98
  MALE               10              283
[1] 2 2
[1] FALSE
D55V8, binary
                  cls
clus                 0   1
  THRAP3 MUTATED    13   1
  THRAP3 WILD-TYPE 337  19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THRAP3 MUTATED     13    1
  THRAP3 WILD-TYPE  337   19
     clus
vv    THRAP3 MUTATED THRAP3 WILD-TYPE
  NO              13              337
  YES              1               19
[1] 2 2
[1] FALSE
D55V9, continuous
D55V10, continuous
D55V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  THRAP3 MUTATED       0                         0    14
  THRAP3 WILD-TYPE    39                        22   303
D55V12, multiclass
                           clus
vv                          THRAP3 MUTATED THRAP3 WILD-TYPE
  ASIAN                                  0               39
  BLACK OR AFRICAN AMERICAN              0               22
  WHITE                                 14              303
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V13, binary
                  cls
clus                 0   1
  THRAP3 MUTATED     2  12
  THRAP3 WILD-TYPE   6 343
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THRAP3 MUTATED      2   12
  THRAP3 WILD-TYPE    6  343
                        clus
vv                       THRAP3 MUTATED THRAP3 WILD-TYPE
  HISPANIC OR LATINO                  2                6
  NOT HISPANIC OR LATINO             12              343
[1] 2 2
[1] FALSE

Clustering(56) Variable = SPTAN1 MUTATION ANALYSIS
D56V1, survival
                  sevent
clus2                0   1
  SPTAN1 MUTATED    28  16
  SPTAN1 WILD-TYPE 189 159
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
              44              348 
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
              16              159 
$`SPTAN1 MUTATED`
TCGA-BT-A42C TCGA-DK-A1AA TCGA-DK-A6B5 TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
       28.70        19.00        50.70        29.16        46.78        19.79 
TCGA-FD-A6TB TCGA-FD-A6TI TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GV-A6ZA TCGA-UY-A9PH 
       18.81         9.67        17.62        21.40        22.72        51.32 
TCGA-XF-A9SV TCGA-XF-A9T8 TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-ZF-A9RL TCGA-2F-A9KQ 
       12.76        13.74        98.99        30.94        88.87        94.88 
TCGA-4Z-AA7O TCGA-4Z-AA7W TCGA-4Z-AA87 TCGA-BT-A0YX TCGA-BT-A20R TCGA-BT-A42E 
       16.83        27.62        47.80        13.15         5.06        36.43 
TCGA-BT-A42F TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-DK-A1A6 
       28.41        10.95        12.46        12.10        11.87        66.41 
TCGA-DK-A2I1 TCGA-DK-A3WY TCGA-E7-A3X6 TCGA-FD-A5BZ TCGA-FD-A6TK TCGA-G2-A2EC 
       17.95       163.30        29.72        27.45        10.85        22.88 
TCGA-G2-A2EO TCGA-G2-A3IE TCGA-GU-A766 TCGA-GV-A3JX TCGA-MV-A51V TCGA-UY-A78K 
       59.31        20.12        15.78        19.10        13.48        17.62 
TCGA-XF-AAMG TCGA-XF-AAN0 
      110.60        56.48 

$`SPTAN1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       18.48        13.58         2.14        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       87.32         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        66.05        17.98        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       67.36        15.68        36.66        38.24        52.01       165.73 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
      166.03        13.64        13.64        56.15        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       15.35        25.58         0.92         1.22        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SS TCGA-FD-A43P 
       60.66        24.30        23.41        17.98        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
        3.62        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD 
       18.08        58.92         6.28        62.86         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
       12.36         3.06         4.31        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
       33.01        70.32        19.13        17.75        24.92        10.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       32.78        32.98        19.82        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       19.07         9.01        25.02         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
       27.68        52.73        50.56        35.97        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
        1.84        33.14        86.83         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
       14.93         4.21        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.24        66.64         2.10        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN3 
        7.63        71.57        91.73        44.32        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
       94.29         3.48        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7R 
       24.13        11.97       104.65         8.35        44.94        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       34.98        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74         6.58        19.04        12.16        17.88        19.50 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       14.96         5.06         8.25        17.16        16.18         4.67 
TCGA-BT-A42B TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       17.56         1.94         2.93        23.01        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47T 
       13.97        12.59        12.13        13.08        12.16        12.66 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A9FM 
       12.10        12.62        12.26        13.12        12.00        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AD 
        5.19        29.79         1.84        21.86        18.41       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       16.14        17.62        15.62         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-AA6P TCGA-DK-AA6Q 
       13.58         8.15        20.81        10.55        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       18.81        19.00        15.35        12.03        43.59        38.83 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        22.16         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
       26.96        26.24         4.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A62N 
       22.98        14.96        20.91        19.33         5.36         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        7.10        13.35         2.27        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
        3.25        61.94        48.00        15.95        26.93         7.23 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       66.02         6.94        29.36        20.71        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07         8.94        13.91        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
       20.98         2.20        11.31        18.97         7.63        20.05 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QI 
        4.73         7.00        14.27        21.34         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI 
       11.80        44.38         1.15        15.32        15.58        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.67        16.54        38.99        37.05        22.68        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34        35.24        29.56        17.82         6.21         3.85 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT 
        5.98        23.64        28.24        16.27        92.98         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L 
        8.32         6.77        27.06        75.39         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       13.41        64.08        58.72        47.84        20.22         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21        29.49         5.52        10.65 

  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
            5.06             0.56 
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
          163.30           166.03 
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
          22.060           16.735 
[1] "5.1 - 163.3 (22.1)" "0.6 - 166.0 (16.7)"
[1] "hr=" "1.7"
D56V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SPTAN1 MUTATED         0       18        16       11
  SPTAN1 WILD-TYPE       2      104       119      123
D56V3, multiclass
           clus
vv          SPTAN1 MUTATED SPTAN1 WILD-TYPE
  STAGE I                0                2
  STAGE II              18              104
  STAGE III             16              119
  STAGE IV              11              123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  SPTAN1 MUTATED         14  16   9
  SPTAN1 WILD-TYPE      102 174  48
D56V4, multiclass
          clus
vv         SPTAN1 MUTATED SPTAN1 WILD-TYPE
  T0+T1+T2             14              102
  T3                   16              174
  T4                    9               48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SPTAN1 MUTATED    30   5   6   0
  SPTAN1 WILD-TYPE 195  41  69   8
D56V5, multiclass
    clus
vv   SPTAN1 MUTATED SPTAN1 WILD-TYPE
  N0             30              195
  N1              5               41
  N2              6               69
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                  cls
clus                 0   1
  SPTAN1 MUTATED    25   1
  SPTAN1 WILD-TYPE 164  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPTAN1 MUTATED     25    1
  SPTAN1 WILD-TYPE  164   10
   clus
vv  SPTAN1 MUTATED SPTAN1 WILD-TYPE
  0             25              164
  1              1               10
[1] 2 2
[1] FALSE
D56V7, binary
                  cls
clus                 0   1
  SPTAN1 MUTATED     7  38
  SPTAN1 WILD-TYPE  95 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPTAN1 MUTATED      7   38
  SPTAN1 WILD-TYPE   95  255
        clus
vv       SPTAN1 MUTATED SPTAN1 WILD-TYPE
  FEMALE              7               95
  MALE               38              255
[1] 2 2
[1] FALSE
D56V8, binary
                  cls
clus                 0   1
  SPTAN1 MUTATED    41   2
  SPTAN1 WILD-TYPE 309  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPTAN1 MUTATED     41    2
  SPTAN1 WILD-TYPE  309   18
     clus
vv    SPTAN1 MUTATED SPTAN1 WILD-TYPE
  NO              41              309
  YES              2               18
[1] 2 2
[1] FALSE
D56V9, continuous
D56V10, continuous
D56V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPTAN1 MUTATED       6                         3    35
  SPTAN1 WILD-TYPE    33                        19   282
D56V12, multiclass
                           clus
vv                          SPTAN1 MUTATED SPTAN1 WILD-TYPE
  ASIAN                                  6               33
  BLACK OR AFRICAN AMERICAN              3               19
  WHITE                                 35              282
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V13, binary
                  cls
clus                 0   1
  SPTAN1 MUTATED     2  39
  SPTAN1 WILD-TYPE   6 316
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPTAN1 MUTATED      2   39
  SPTAN1 WILD-TYPE    6  316
                        clus
vv                       SPTAN1 MUTATED SPTAN1 WILD-TYPE
  HISPANIC OR LATINO                  2                6
  NOT HISPANIC OR LATINO             39              316
[1] 2 2
[1] FALSE

Clustering(57) Variable = ARID1B MUTATION ANALYSIS
D57V1, survival
                  sevent
clus2                0   1
  ARID1B MUTATED    11  12
  ARID1B WILD-TYPE 206 163
  ARID1B MUTATED ARID1B WILD-TYPE 
              23              369 
  ARID1B MUTATED ARID1B WILD-TYPE 
              12              163 
$`ARID1B MUTATED`
TCGA-CU-A0YR TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-AA74 TCGA-E7-A541 TCGA-FD-A6TA 
       15.12        66.05        53.29        56.15        25.58        62.86 
TCGA-FD-A6TC TCGA-GU-AATP TCGA-KQ-A41P TCGA-XF-A9SK TCGA-XF-AAML TCGA-ZF-A9R4 
        6.15        32.98        35.97        15.98         7.63        30.28 
TCGA-2F-A9KO TCGA-4Z-AA80 TCGA-BL-A13I TCGA-BT-A3PH TCGA-DK-A1A3 TCGA-E7-A4IJ 
       24.13         0.62         7.33         4.67        21.86        22.16 
TCGA-ZF-A9R7 TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA5N TCGA-GU-AATO 
       21.86        59.38        56.35         5.52        10.65 

$`ARID1B WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 
       23.21         9.67        17.98        64.18        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       15.68        50.70        36.66        38.24        52.01       165.73 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
      166.03        13.64        13.64        11.18        20.32        15.35 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
        0.92         1.22        33.04         4.01        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       23.41        17.98        29.16        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       27.35         3.62        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TD 
        8.25        18.08        58.92         6.28        18.81        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.36         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       11.08        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QF 
       17.75        24.92        10.92        32.78        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        3.45         2.76         9.14        27.68        52.73        50.56 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       46.98        14.24         1.84        33.14        86.83        51.32 
TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
        3.22        34.45        14.93         4.21        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR 
       13.74        10.82        11.31        54.90        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       98.99        44.32        30.94        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE 
        3.88         9.63        13.64        21.11        94.29         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KP 
       88.87        34.06        19.69        57.90        12.23        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       34.98        27.62        50.04        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J 
       10.22        47.80         2.50        17.42        40.08         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 
       16.18        17.56        36.43        28.41         1.94         2.93 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       23.01        12.79        12.56        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 
       13.08         5.19        29.79         1.84        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX 
      142.78         4.80        13.58         8.15        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
      163.30        15.02        13.58        18.81        19.00        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       12.03        43.59        38.83        29.72         5.36         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
       24.03        24.66        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       27.98         5.52        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       19.33         5.36        27.45         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.27        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
        7.23        20.12        66.02         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91        14.07         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
       38.60        64.01        12.16        21.24         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       17.72         1.81        15.42        16.27        11.80        44.38 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.15        15.32        15.58        13.48        12.23        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.54        38.99        17.62        37.05        22.68        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34        35.24        29.56        17.82         6.21         3.85 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32         6.77        56.48        27.06        75.39 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       28.41        13.41        64.08        58.72        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 
        2.89         8.61        60.16        67.20        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
        8.52        54.21        29.49 

  ARID1B MUTATED ARID1B WILD-TYPE 
            0.62             0.56 
  ARID1B MUTATED ARID1B WILD-TYPE 
           66.05           166.03 
  ARID1B MUTATED ARID1B WILD-TYPE 
           22.16            17.56 
[1] "0.6 - 66.0 (22.2)"  "0.6 - 166.0 (17.6)"
[1] "hr=" "1.1"
D57V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ARID1B MUTATED         0        8         5       10
  ARID1B WILD-TYPE       2      114       130      124
D57V3, multiclass
           clus
vv          ARID1B MUTATED ARID1B WILD-TYPE
  STAGE I                0                2
  STAGE II               8              114
  STAGE III              5              130
  STAGE IV              10              124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  ARID1B MUTATED         10  10   2
  ARID1B WILD-TYPE      106 180  55
D57V4, multiclass
          clus
vv         ARID1B MUTATED ARID1B WILD-TYPE
  T0+T1+T2             10              106
  T3                   10              180
  T4                    2               55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ARID1B MUTATED     9   2   6   1
  ARID1B WILD-TYPE 216  44  69   7
D57V5, multiclass
    clus
vv   ARID1B MUTATED ARID1B WILD-TYPE
  N0              9              216
  N1              2               44
  N2              6               69
  N3              1                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"
D57V6, binary
                  cls
clus                 0   1
  ARID1B MUTATED    13   2
  ARID1B WILD-TYPE 176   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED     13    2
  ARID1B WILD-TYPE  176    9
   clus
vv  ARID1B MUTATED ARID1B WILD-TYPE
  0             13              176
  1              2                9
[1] 2 2
[1] FALSE
D57V7, binary
                  cls
clus                 0   1
  ARID1B MUTATED     6  17
  ARID1B WILD-TYPE  96 276
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED      6   17
  ARID1B WILD-TYPE   96  276
        clus
vv       ARID1B MUTATED ARID1B WILD-TYPE
  FEMALE              6               96
  MALE               17              276
[1] 2 2
[1] FALSE
D57V8, binary
                  cls
clus                 0   1
  ARID1B MUTATED    22   0
  ARID1B WILD-TYPE 328  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED     22    0
  ARID1B WILD-TYPE  328   20
     clus
vv    ARID1B MUTATED ARID1B WILD-TYPE
  NO              22              328
  YES              0               20
[1] 2 2
[1] FALSE
D57V9, continuous
D57V10, continuous
D57V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1B MUTATED       1                         0    22
  ARID1B WILD-TYPE    38                        22   295
D57V12, multiclass
                           clus
vv                          ARID1B MUTATED ARID1B WILD-TYPE
  ASIAN                                  1               38
  BLACK OR AFRICAN AMERICAN              0               22
  WHITE                                 22              295
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V13, binary
                  cls
clus                 0   1
  ARID1B MUTATED     0  22
  ARID1B WILD-TYPE   8 333
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED      0   22
  ARID1B WILD-TYPE    8  333
                        clus
vv                       ARID1B MUTATED ARID1B WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO             22              333
[1] 2 2
[1] FALSE

Clustering(58) Variable = NRAS MUTATION ANALYSIS
D58V1, survival
                sevent
clus2              0   1
  NRAS MUTATED     5   2
  NRAS WILD-TYPE 212 173
  NRAS MUTATED NRAS WILD-TYPE 
             7            385 
  NRAS MUTATED NRAS WILD-TYPE 
             2            173 
$`NRAS MUTATED`
TCGA-BT-A20W TCGA-FD-A43P TCGA-ZF-A9RL TCGA-4Z-AA82 TCGA-G2-A2EF TCGA-UY-A9PD 
        8.35        27.35        88.87        51.16        61.94        17.82 
TCGA-ZF-A9R5 
       35.84 

$`NRAS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       26.14        14.89        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A5BR 
       29.16        46.78        19.79        12.85         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       33.01        17.62        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       24.92        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        3.45         2.76         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       35.97        46.98        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       51.32         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
        7.63        71.57        91.73        98.99        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       61.45        86.30        18.58         3.88         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA4T 
       21.11        30.28        94.29         3.48        34.06        19.69 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       57.90        12.23        24.13        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
       50.04         0.62        41.75        66.54        10.22        47.80 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
        2.50        17.42        40.08         7.33         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 
        4.67        17.56        36.43        28.41         1.94         2.93 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       23.01        12.79        12.56        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       13.08         5.19        29.79         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW 
        7.79       142.78         4.80        13.58         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       10.55       163.30        15.02        13.58        18.81        19.00 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.35        12.03        43.59        38.83        29.72         5.36 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
       22.16         2.24        16.70         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN 
       26.24         4.24        24.03        24.66        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       12.62        22.52        27.98         5.52        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       14.96        20.91        19.33         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        7.10        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25        22.88        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       59.31         7.23        20.12        66.02         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 
       20.71        15.81        15.91        14.07         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       26.70         2.10         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       18.97         7.63        20.05        15.78         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
       14.27        21.34        19.10         8.48        36.49         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
       19.40        38.60        64.01        12.16        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70        17.72         1.81        15.42        16.27        11.80 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       44.38         1.15        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF 
       76.01        69.34        35.24        29.56         6.21         3.85 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32         6.77        56.48        27.06        75.39 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R7 
        0.66        11.97        22.36        25.41        31.20        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       28.41        13.41        64.08        58.72        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
        2.89         8.61        59.38        60.16        67.20        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        19.40         8.52        54.21        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  NRAS MUTATED NRAS WILD-TYPE 
          8.35           0.56 
  NRAS MUTATED NRAS WILD-TYPE 
         88.87         166.03 
  NRAS MUTATED NRAS WILD-TYPE 
         35.84          17.56 
[1] "8.3 - 88.9 (35.8)"  "0.6 - 166.0 (17.6)"
[1] "hr=" "2.4"
D58V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NRAS MUTATED         0        4         2        1
  NRAS WILD-TYPE       2      118       133      133
D58V3, multiclass
           clus
vv          NRAS MUTATED NRAS WILD-TYPE
  STAGE I              0              2
  STAGE II             4            118
  STAGE III            2            133
  STAGE IV             1            133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  NRAS MUTATED          3   2   0
  NRAS WILD-TYPE      113 188  57
D58V4, multiclass
          clus
vv         NRAS MUTATED NRAS WILD-TYPE
  T0+T1+T2            3            113
  T3                  2            188
  T4                  0             57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  NRAS MUTATED     5   1   0   0
  NRAS WILD-TYPE 220  45  75   8
D58V5, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  N0            5            220
  N1            1             45
  N2            0             75
  N3            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                cls
clus               0   1
  NRAS MUTATED     4   0
  NRAS WILD-TYPE 185  11
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      4    0
  NRAS WILD-TYPE  185   11
   clus
vv  NRAS MUTATED NRAS WILD-TYPE
  0            4            185
  1            0             11
[1] 2 2
[1] FALSE
D58V7, binary
                cls
clus               0   1
  NRAS MUTATED     0   7
  NRAS WILD-TYPE 102 286
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0    7
  NRAS WILD-TYPE  102  286
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            0            102
  MALE              7            286
[1] 2 2
[1] FALSE
D58V8, binary
                cls
clus               0   1
  NRAS MUTATED     7   0
  NRAS WILD-TYPE 343  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      7    0
  NRAS WILD-TYPE  343   20
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             7            343
  YES            0             20
[1] 2 2
[1] FALSE
D58V9, continuous
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             1            129 
    TCGA-2F-A9KT     TCGA-DK-A2HX     TCGA-DK-A3IN     TCGA-DK-A3IV 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-DK-A3X2     TCGA-DK-A6B2     TCGA-DK-A6B5     TCGA-DK-A6B6 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-DK-AA6M     TCGA-DK-AA6R     TCGA-DK-AA6S     TCGA-DK-AA6W 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-DK-AA75     TCGA-E5-A4TZ     TCGA-E7-A541     TCGA-E7-A7DU 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-E7-A7DV     TCGA-FT-A61P     TCGA-G2-A2ES     TCGA-G2-A3VY 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GC-A3BM     TCGA-GC-A3YS     TCGA-GV-A3JZ     TCGA-GV-A3QF 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GV-A3QK     TCGA-GV-A40E     TCGA-GV-A40G     TCGA-GV-A6ZA 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-KQ-A41N     TCGA-SY-A9G0     TCGA-UY-A78N     TCGA-XF-A9SJ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-A9SK     TCGA-XF-A9SM     TCGA-XF-A9SP     TCGA-XF-A9ST 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-A9SV     TCGA-XF-A9SW     TCGA-XF-A9SY     TCGA-XF-A9T0 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-A9T2     TCGA-XF-A9T3     TCGA-XF-A9T5     TCGA-XF-A9T6 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-A9T8     TCGA-XF-AAMF     TCGA-XF-AAMH     TCGA-XF-AAMJ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-AAML     TCGA-XF-AAMQ     TCGA-XF-AAMR     TCGA-XF-AAMY 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-AAMZ     TCGA-XF-AAN1     TCGA-XF-AAN2     TCGA-XF-AAN3 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-AAN7     TCGA-XF-AAN8     TCGA-YF-AA3M     TCGA-2F-A9KO 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-2F-A9KP     TCGA-2F-A9KQ     TCGA-2F-A9KR     TCGA-2F-A9KW 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-CF-A1HS     TCGA-CF-A27C     TCGA-CF-A3MF     TCGA-CF-A3MG 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-CF-A3MH     TCGA-CF-A3MI     TCGA-CF-A47S     TCGA-CF-A47T 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-CF-A47V     TCGA-CF-A47W     TCGA-CF-A47X     TCGA-CF-A47Y 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-CF-A5U8     TCGA-CF-A5UA     TCGA-CF-A7I0     TCGA-DK-A3WX 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-DK-AA6P     TCGA-DK-AA6U     TCGA-DK-AA76     TCGA-E5-A2PC 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-E5-A4U1     TCGA-E7-A519     TCGA-E7-A6MD     TCGA-G2-A2EC 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-G2-A2EJ     TCGA-G2-A2EK     TCGA-G2-A2EL     TCGA-G2-A2EO 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-G2-A3IB     TCGA-G2-A3IE     TCGA-GC-A3I6     TCGA-GC-A3OO 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GC-A3RC     TCGA-GC-A3RD     TCGA-GC-A6I1     TCGA-GC-A6I3 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GD-A3OS     TCGA-GD-A6C6     TCGA-GV-A3JV     TCGA-GV-A3JW 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GV-A3JX     TCGA-GV-A3QH     TCGA-GV-A3QI     TCGA-SY-A9G5 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-UY-A78L     TCGA-UY-A78M     TCGA-XF-A8HH     TCGA-XF-A8HI 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-A9SG     TCGA-XF-A9SH     TCGA-XF-A9SI     TCGA-XF-A9SL 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-A9SU     TCGA-XF-A9SX     TCGA-XF-A9SZ     TCGA-XF-A9T4 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-AAME     TCGA-XF-AAMG     TCGA-XF-AAMT     TCGA-XF-AAMW 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-AAMX     TCGA-XF-AAN0     TCGA-XF-AAN4     TCGA-XF-AAN5 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-YF-AA3L 
"NRAS WILD-TYPE" 
D58V10, continuous
D58V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED       0                         2     5
  NRAS WILD-TYPE    39                        20   312
D58V12, multiclass
                           clus
vv                          NRAS MUTATED NRAS WILD-TYPE
  ASIAN                                0             39
  BLACK OR AFRICAN AMERICAN            2             20
  WHITE                                5            312
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V13, binary
                cls
clus               0   1
  NRAS MUTATED     0   6
  NRAS WILD-TYPE   8 349
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0    6
  NRAS WILD-TYPE    8  349
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO            6            349
[1] 2 2
[1] FALSE

Clustering(59) Variable = RPTN MUTATION ANALYSIS
D59V1, survival
                sevent
clus2              0   1
  RPTN MUTATED     8   7
  RPTN WILD-TYPE 209 168
  RPTN MUTATED RPTN WILD-TYPE 
            15            377 
  RPTN MUTATED RPTN WILD-TYPE 
             7            168 
$`RPTN MUTATED`
TCGA-BT-A3PK TCGA-DK-A3IT TCGA-XF-AAMY TCGA-XF-AAN2 TCGA-ZF-A9RE TCGA-4Z-AA86 
        9.96        21.30        98.99        61.45         3.48        10.22 
TCGA-CU-A3YL TCGA-DK-A3WW TCGA-DK-AA6X TCGA-E7-A97Q TCGA-G2-A3IE TCGA-G2-AA3B 
       29.79        20.81        15.35         8.09        20.12        66.02 
TCGA-K4-A5RH TCGA-MV-A51V TCGA-ZF-AA52 
        9.07        13.48        35.41 

$`RPTN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C 
       26.14        14.89         8.35        20.48        25.94        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU 
       46.68        87.32         8.22        17.72        50.27        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        66.05        17.98        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       67.36        15.68        50.70        36.66        38.24        52.01 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
      165.73       166.03        13.64        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       33.01        17.62        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       24.92        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        3.45         2.76         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       35.97        46.98        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       51.32         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 
        7.63        71.57        91.73        44.32        30.94        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
       94.29        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       16.83        17.16        34.98        27.62        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM 
       41.75        51.16        66.54        47.80         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       19.04        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
        5.06         8.25        17.16        16.18         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR 
       36.43        28.41         1.94         2.93        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.56        13.97        12.59        12.13        13.08        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU 
       13.12        12.00        12.10        11.87        13.08         5.19 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        1.84        21.86        66.41        18.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
       13.58         8.15        10.55       163.30        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       18.81        19.00        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        22.16         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
       26.96        26.24         4.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       14.07        12.95        14.37        32.02        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       12.62        22.52        27.98         5.52        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       14.96        20.91        19.33         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        7.10        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        8.94         3.25        22.88        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
       26.93        59.31         7.23         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91        14.07         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A5RJ 
       38.60        64.01        12.16        21.24        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
        1.81        15.42        16.27        11.80        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       15.32        15.58        12.23        16.67        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       17.62        37.05        22.68        76.01        69.34        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         6.21         3.85         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       48.62        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW 
       28.24        16.27        92.98       110.60         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L 
        6.77        56.48        27.06        75.39         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       13.41        64.08        58.72        47.84        20.22         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA54 
        8.61        59.38        60.16        67.20        56.35        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
        8.52        54.21        29.49         5.52        10.65 

  RPTN MUTATED RPTN WILD-TYPE 
          3.48           0.56 
  RPTN MUTATED RPTN WILD-TYPE 
         98.99         166.03 
  RPTN MUTATED RPTN WILD-TYPE 
         20.12          17.62 
[1] "3.5 - 99.0 (20.1)"  "0.6 - 166.0 (17.6)"
[1] "hr=" "1"  
D59V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RPTN MUTATED         0        6         7        2
  RPTN WILD-TYPE       2      116       128      132
D59V3, multiclass
           clus
vv          RPTN MUTATED RPTN WILD-TYPE
  STAGE I              0              2
  STAGE II             6            116
  STAGE III            7            128
  STAGE IV             2            132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  RPTN MUTATED          3   7   2
  RPTN WILD-TYPE      113 183  55
D59V4, multiclass
          clus
vv         RPTN MUTATED RPTN WILD-TYPE
  T0+T1+T2            3            113
  T3                  7            183
  T4                  2             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RPTN MUTATED    10   1   0   1
  RPTN WILD-TYPE 215  45  75   7
D59V5, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  N0           10            215
  N1            1             45
  N2            0             75
  N3            1              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"
D59V6, binary
                cls
clus               0   1
  RPTN MUTATED     7   0
  RPTN WILD-TYPE 182  11
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      7    0
  RPTN WILD-TYPE  182   11
   clus
vv  RPTN MUTATED RPTN WILD-TYPE
  0            7            182
  1            0             11
[1] 2 2
[1] FALSE
D59V7, binary
                cls
clus               0   1
  RPTN MUTATED     3  12
  RPTN WILD-TYPE  99 281
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      3   12
  RPTN WILD-TYPE   99  281
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  FEMALE            3             99
  MALE             12            281
[1] 2 2
[1] FALSE
D59V8, binary
                cls
clus               0   1
  RPTN MUTATED    14   1
  RPTN WILD-TYPE 336  19
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED     14    1
  RPTN WILD-TYPE  336   19
     clus
vv    RPTN MUTATED RPTN WILD-TYPE
  NO            14            336
  YES            1             19
[1] 2 2
[1] FALSE
D59V9, continuous
D59V10, continuous
D59V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RPTN MUTATED       0                         1    14
  RPTN WILD-TYPE    39                        21   303
D59V12, multiclass
                           clus
vv                          RPTN MUTATED RPTN WILD-TYPE
  ASIAN                                0             39
  BLACK OR AFRICAN AMERICAN            1             21
  WHITE                               14            303
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V13, binary
                cls
clus               0   1
  RPTN MUTATED     0  14
  RPTN WILD-TYPE   8 341
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      0   14
  RPTN WILD-TYPE    8  341
                        clus
vv                       RPTN MUTATED RPTN WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           14            341
[1] 2 2
[1] FALSE

Clustering(60) Variable = RAI1 MUTATION ANALYSIS
D60V1, survival
                sevent
clus2              0   1
  RAI1 MUTATED    16   5
  RAI1 WILD-TYPE 201 170
  RAI1 MUTATED RAI1 WILD-TYPE 
            21            371 
  RAI1 MUTATED RAI1 WILD-TYPE 
             5            170 
$`RAI1 MUTATED`
TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BT-A3PJ TCGA-DK-A6AW TCGA-FD-A62P TCGA-KQ-A41P 
       15.12        33.83        25.94        53.29         6.28        35.97 
TCGA-XF-A9ST TCGA-YC-A8S6 TCGA-2F-A9KQ TCGA-4Z-AA80 TCGA-4Z-AA83 TCGA-BT-A3PH 
        4.21         9.63        94.88         0.62        66.54         4.67 
TCGA-CF-A1HR TCGA-CU-A3YL TCGA-E7-A5KE TCGA-GV-A3QI TCGA-LT-A5Z6 TCGA-UY-A9PF 
       12.79        29.79         0.56        36.49        15.58         3.85 
TCGA-XF-AAMG TCGA-XF-AAMX TCGA-XF-AAN5 
      110.60         6.77        75.39 

$`RAI1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
      108.95        16.27        16.77        12.39        26.14        14.89 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 
        8.35        20.48         9.96        28.70         8.98         2.04 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E 
       18.58        12.92         4.90        15.12        18.48        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 
        2.14        19.00        16.70       130.88        46.68        87.32 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       66.05        17.98        64.18        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S 
       50.70        36.66        38.24        52.01       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       13.64        13.64        56.15        11.18        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       25.58         0.92         1.22        33.04         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
       24.30        23.41        17.98        29.16        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       12.85        27.35         3.62        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB 
        5.69         8.25        18.08        58.92        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.15        12.69        12.36         3.06         4.31         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D 
       31.07        17.23        11.08        33.01        17.62        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 
       21.40        19.13        17.75        24.92        10.92        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       32.98        19.82        20.28        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       22.72         9.01        25.02         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX 
       27.68        52.73        50.56        46.98        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
       33.14        86.83        51.32         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
       14.93        12.76        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
        2.24        66.64         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63        71.57        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YF-AA3M 
       30.94        61.45        86.30        18.58         3.88        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
       21.11        30.28        94.29         3.48        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR 
       19.69        57.90        12.23        24.13        11.97       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
       50.04        41.75        51.16        10.22        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       17.42        40.08         7.33         2.66         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42B 
       14.96         5.06         8.25        17.16        16.18        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HS 
       36.43        28.41         1.94         2.93        23.01        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A5W6 
       12.00        12.10        11.87        13.08         5.19         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
        8.15        20.81        10.55       163.30        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       18.81        19.00        15.35        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF 
       29.72         5.36        22.16         2.24        16.70         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
       26.96        26.24         4.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.70         7.10        13.35         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65         8.94         3.25        22.88        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       15.95        26.93        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        29.36        20.71        15.81        15.91        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91        26.70         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        2.20        11.31        18.97         7.63        20.05        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
        4.73         7.00        14.27        21.34        19.10         8.48 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI 
       11.80        44.38         1.15        15.32        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        69.34        35.24        29.56        17.82         6.21 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT 
        5.98        23.64        28.24        16.27        92.98         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
        8.32        56.48        27.06         0.66        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       25.41        31.20        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       64.08        58.72        47.84        20.22         2.89         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 
       59.38        60.16        67.20        56.35        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
        8.52        54.21        29.49         5.52        10.65 

  RAI1 MUTATED RAI1 WILD-TYPE 
          0.56           0.66 
  RAI1 MUTATED RAI1 WILD-TYPE 
        110.60         166.03 
  RAI1 MUTATED RAI1 WILD-TYPE 
         15.58          17.62 
[1] "0.6 - 110.6 (15.6)" "0.7 - 166.0 (17.6)"
[1] "hr=" "2.1"
D60V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RAI1 MUTATED         0        7         9        5
  RAI1 WILD-TYPE       2      115       126      129
D60V3, multiclass
           clus
vv          RAI1 MUTATED RAI1 WILD-TYPE
  STAGE I              0              2
  STAGE II             7            115
  STAGE III            9            126
  STAGE IV             5            129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  RAI1 MUTATED          6  11   3
  RAI1 WILD-TYPE      110 179  54
D60V4, multiclass
          clus
vv         RAI1 MUTATED RAI1 WILD-TYPE
  T0+T1+T2            6            110
  T3                 11            179
  T4                  3             54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RAI1 MUTATED    16   0   3   1
  RAI1 WILD-TYPE 209  46  72   7
D60V5, multiclass
    clus
vv   RAI1 MUTATED RAI1 WILD-TYPE
  N0           16            209
  N1            0             46
  N2            3             72
  N3            1              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"
D60V6, binary
                cls
clus               0   1
  RAI1 MUTATED     9   2
  RAI1 WILD-TYPE 180   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED      9    2
  RAI1 WILD-TYPE  180    9
   clus
vv  RAI1 MUTATED RAI1 WILD-TYPE
  0            9            180
  1            2              9
[1] 2 2
[1] FALSE
D60V7, binary
                cls
clus               0   1
  RAI1 MUTATED     3  18
  RAI1 WILD-TYPE  99 275
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED      3   18
  RAI1 WILD-TYPE   99  275
        clus
vv       RAI1 MUTATED RAI1 WILD-TYPE
  FEMALE            3             99
  MALE             18            275
[1] 2 2
[1] FALSE
D60V8, binary
                cls
clus               0   1
  RAI1 MUTATED    21   0
  RAI1 WILD-TYPE 329  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED     21    0
  RAI1 WILD-TYPE  329   20
     clus
vv    RAI1 MUTATED RAI1 WILD-TYPE
  NO            21            329
  YES            0             20
[1] 2 2
[1] FALSE
D60V9, continuous
D60V10, continuous
D60V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAI1 MUTATED       2                         1    18
  RAI1 WILD-TYPE    37                        21   299
D60V12, multiclass
                           clus
vv                          RAI1 MUTATED RAI1 WILD-TYPE
  ASIAN                                2             37
  BLACK OR AFRICAN AMERICAN            1             21
  WHITE                               18            299
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V13, binary
                cls
clus               0   1
  RAI1 MUTATED     1  16
  RAI1 WILD-TYPE   7 339
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED      1   16
  RAI1 WILD-TYPE    7  339
                        clus
vv                       RAI1 MUTATED RAI1 WILD-TYPE
  HISPANIC OR LATINO                1              7
  NOT HISPANIC OR LATINO           16            339
[1] 2 2
[1] FALSE

Clustering(61) Variable = TMCO4 MUTATION ANALYSIS
D61V1, survival
                 sevent
clus2               0   1
  TMCO4 MUTATED     7   5
  TMCO4 WILD-TYPE 210 170
  TMCO4 MUTATED TMCO4 WILD-TYPE 
             12             380 
  TMCO4 MUTATED TMCO4 WILD-TYPE 
              5             170 
$`TMCO4 MUTATED`
TCGA-E7-A7DU TCGA-HQ-A5ND TCGA-XF-AAML TCGA-2F-A9KR TCGA-4Z-AA7O TCGA-E5-A4U1 
        0.92         9.01         7.63       104.65        16.83        38.83 
TCGA-E7-A4IJ TCGA-E7-A5KF TCGA-E7-A6MD TCGA-H4-A2HQ TCGA-MV-A51V TCGA-XF-AAN0 
       22.16         0.66         4.24        19.40        13.48        56.48 

$`TMCO4 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      130.88        46.68        87.32         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       21.30        23.21         9.67        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       53.29        76.60        67.36        15.68        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       38.24        52.01       165.73       166.03        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV 
       56.15        11.18        20.32        15.35        25.58         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       29.16        46.78        19.79        12.85        27.35         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.36         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       11.08        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       17.75        24.92        10.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WS 
       20.28        27.35         8.58        19.07        22.72        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        3.45         2.76         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       35.97        46.98        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       51.32         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       86.30        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       30.28        94.29         3.48        88.87        34.06        19.69 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW 
       57.90        12.23        24.13        11.97        94.88         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       44.94        17.16        34.98        27.62        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
       41.75        51.16        66.54        10.22        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       17.42        40.08         7.33         2.66         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       14.96         5.06         8.25        17.16        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       17.56        36.43        28.41         1.94         2.93        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       12.79        12.56        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       12.16        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.19        29.79         1.84        21.86        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX 
      142.78         4.80        13.58         8.15        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
      163.30        15.02        13.58        18.81        19.00        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       12.03        43.59        29.72         5.36         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
        0.56        26.96        26.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.70         7.10        13.35         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65         8.94         3.25        22.88        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       15.95        26.93        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        29.36        20.71        15.81        15.91        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91        26.70         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        2.20        11.31        18.97         7.63        20.05        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
        4.73         7.00        14.27        21.34        19.10         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
       36.49         1.51        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI 
       11.80        44.38         1.15        15.32        15.58        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        69.34        35.24        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        3.85         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-XF-AAN5 
      110.60         2.96         8.32         6.77        27.06        75.39 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       21.86        28.41        13.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       20.22         2.89         8.61        59.38        60.16        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        19.40         8.52        54.21        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  TMCO4 MUTATED TMCO4 WILD-TYPE 
           0.66            0.56 
  TMCO4 MUTATED TMCO4 WILD-TYPE 
         104.65          166.03 
  TMCO4 MUTATED TMCO4 WILD-TYPE 
         15.155          17.670 
[1] "0.7 - 104.7 (15.2)" "0.6 - 166.0 (17.7)"
[1] "hr=" "1"  
D61V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TMCO4 MUTATED         0        5         3        4
  TMCO4 WILD-TYPE       2      117       132      130
D61V3, multiclass
           clus
vv          TMCO4 MUTATED TMCO4 WILD-TYPE
  STAGE I               0               2
  STAGE II              5             117
  STAGE III             3             132
  STAGE IV              4             130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  TMCO4 MUTATED          5   4   2
  TMCO4 WILD-TYPE      111 186  55
D61V4, multiclass
          clus
vv         TMCO4 MUTATED TMCO4 WILD-TYPE
  T0+T1+T2             5             111
  T3                   4             186
  T4                   2              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TMCO4 MUTATED     7   2   1   0
  TMCO4 WILD-TYPE 218  44  74   8
D61V5, multiclass
    clus
vv   TMCO4 MUTATED TMCO4 WILD-TYPE
  N0             7             218
  N1             2              44
  N2             1              74
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                 cls
clus                0   1
  TMCO4 MUTATED    10   1
  TMCO4 WILD-TYPE 179  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO4 MUTATED     10    1
  TMCO4 WILD-TYPE  179   10
   clus
vv  TMCO4 MUTATED TMCO4 WILD-TYPE
  0            10             179
  1             1              10
[1] 2 2
[1] FALSE
D61V7, binary
                 cls
clus                0   1
  TMCO4 MUTATED     2  10
  TMCO4 WILD-TYPE 100 283
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO4 MUTATED      2   10
  TMCO4 WILD-TYPE  100  283
        clus
vv       TMCO4 MUTATED TMCO4 WILD-TYPE
  FEMALE             2             100
  MALE              10             283
[1] 2 2
[1] FALSE
D61V8, binary
                 cls
clus                0   1
  TMCO4 MUTATED    10   0
  TMCO4 WILD-TYPE 340  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO4 MUTATED     10    0
  TMCO4 WILD-TYPE  340   20
     clus
vv    TMCO4 MUTATED TMCO4 WILD-TYPE
  NO             10             340
  YES             0              20
[1] 2 2
[1] FALSE
D61V9, continuous
D61V10, continuous
D61V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMCO4 MUTATED       2                         2     5
  TMCO4 WILD-TYPE    37                        20   312
D61V12, multiclass
                           clus
vv                          TMCO4 MUTATED TMCO4 WILD-TYPE
  ASIAN                                 2              37
  BLACK OR AFRICAN AMERICAN             2              20
  WHITE                                 5             312
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V13, binary
                 cls
clus                0   1
  TMCO4 MUTATED     0   9
  TMCO4 WILD-TYPE   8 346
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO4 MUTATED      0    9
  TMCO4 WILD-TYPE    8  346
                        clus
vv                       TMCO4 MUTATED TMCO4 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO             9             346
[1] 2 2
[1] FALSE

Clustering(62) Variable = CNOT1 MUTATION ANALYSIS
D62V1, survival
                 sevent
clus2               0   1
  CNOT1 MUTATED    17   4
  CNOT1 WILD-TYPE 200 171
  CNOT1 MUTATED CNOT1 WILD-TYPE 
             21             371 
  CNOT1 MUTATED CNOT1 WILD-TYPE 
              4             171 
$`CNOT1 MUTATED`
TCGA-4Z-AA7M TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B6 TCGA-DK-AA71 
       16.27        66.05        53.29        76.60        36.66        13.64 
TCGA-E7-A541 TCGA-FD-A3SN TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GV-A3QF 
       25.58        29.16        11.08        33.01        17.62        20.28 
TCGA-GV-A6ZA TCGA-K4-A4AB TCGA-XF-AAMR TCGA-ZF-A9RL TCGA-DK-A1AE TCGA-DK-A2I1 
       22.72         2.76        91.73        88.87        16.14        17.95 
TCGA-UY-A8OB TCGA-XF-A9SG TCGA-ZF-A9RD 
       69.34        48.62        13.41 

$`CNOT1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.77        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 
       23.21         9.67        17.98        64.18        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       50.70        38.24        52.01       165.73       166.03        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-E7-A7DV 
       56.15        11.18        20.32        15.35         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-AA3D 
        3.06         4.31         9.67        31.07        17.23        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 
       21.40        19.13        17.75        24.92        10.92        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND 
       32.98        19.82        27.35         8.58        19.07         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
       25.02         3.45         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       35.97        46.98        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       51.32         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
        7.63        71.57        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       86.30        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       30.28        94.29         3.48        34.06        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
        0.62        41.75        51.16        66.54        10.22        47.80 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
        2.50        17.42        40.08         7.33         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 
        4.67        17.56        36.43        28.41         1.94         2.93 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       23.01        12.79        12.56        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       13.08         5.19        29.79         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 
       18.41       112.44        17.62        15.62         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       15.02        13.58        18.81        19.00        15.35        12.03 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        38.83        29.72         5.36        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
       24.03        24.66        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       27.98         5.52        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       19.33         5.36        27.45         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.27        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
        7.23        20.12        66.02         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91        14.07         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
       38.60        64.01        12.16        21.24         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       17.72         1.81        15.42        16.27        11.80        44.38 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.15        15.32        15.58        13.48        12.23        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.54        38.99        17.62        37.05        22.68        76.01 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       35.24        29.56        17.82         6.21         3.85         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       17.88        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW 
       28.24        16.27        92.98       110.60         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L 
        6.77        56.48        27.06        75.39         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       64.08        58.72        47.84        20.22         2.89         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 
       59.38        60.16        67.20        56.35        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
        8.52        54.21        29.49         5.52        10.65 

  CNOT1 MUTATED CNOT1 WILD-TYPE 
           2.76            0.56 
  CNOT1 MUTATED CNOT1 WILD-TYPE 
          91.73          166.03 
  CNOT1 MUTATED CNOT1 WILD-TYPE 
          25.58           17.23 
[1] "2.8 - 91.7 (25.6)"  "0.6 - 166.0 (17.2)"
[1] "hr=" "3.3"
D62V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  CNOT1 MUTATED         0       11         6        4
  CNOT1 WILD-TYPE       2      111       129      130
D62V3, multiclass
           clus
vv          CNOT1 MUTATED CNOT1 WILD-TYPE
  STAGE I               0               2
  STAGE II             11             111
  STAGE III             6             129
  STAGE IV              4             130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  CNOT1 MUTATED          7  10   1
  CNOT1 WILD-TYPE      109 180  56
D62V4, multiclass
          clus
vv         CNOT1 MUTATED CNOT1 WILD-TYPE
  T0+T1+T2             7             109
  T3                  10             180
  T4                   1              56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CNOT1 MUTATED    14   1   3   0
  CNOT1 WILD-TYPE 211  45  72   8
D62V5, multiclass
    clus
vv   CNOT1 MUTATED CNOT1 WILD-TYPE
  N0            14             211
  N1             1              45
  N2             3              72
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                 cls
clus                0   1
  CNOT1 MUTATED     8   0
  CNOT1 WILD-TYPE 181  11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT1 MUTATED      8    0
  CNOT1 WILD-TYPE  181   11
   clus
vv  CNOT1 MUTATED CNOT1 WILD-TYPE
  0             8             181
  1             0              11
[1] 2 2
[1] FALSE
D62V7, binary
                 cls
clus                0   1
  CNOT1 MUTATED     3  18
  CNOT1 WILD-TYPE  99 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT1 MUTATED      3   18
  CNOT1 WILD-TYPE   99  275
        clus
vv       CNOT1 MUTATED CNOT1 WILD-TYPE
  FEMALE             3              99
  MALE              18             275
[1] 2 2
[1] FALSE
D62V8, binary
                 cls
clus                0   1
  CNOT1 MUTATED    21   0
  CNOT1 WILD-TYPE 329  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT1 MUTATED     21    0
  CNOT1 WILD-TYPE  329   20
     clus
vv    CNOT1 MUTATED CNOT1 WILD-TYPE
  NO             21             329
  YES             0              20
[1] 2 2
[1] FALSE
D62V9, continuous
D62V10, continuous
D62V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CNOT1 MUTATED       1                         0    19
  CNOT1 WILD-TYPE    38                        22   298
D62V12, multiclass
                           clus
vv                          CNOT1 MUTATED CNOT1 WILD-TYPE
  ASIAN                                 1              38
  BLACK OR AFRICAN AMERICAN             0              22
  WHITE                                19             298
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V13, binary
                 cls
clus                0   1
  CNOT1 MUTATED     3  17
  CNOT1 WILD-TYPE   5 338
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT1 MUTATED      3   17
  CNOT1 WILD-TYPE    5  338
                        clus
vv                       CNOT1 MUTATED CNOT1 WILD-TYPE
  HISPANIC OR LATINO                 3               5
  NOT HISPANIC OR LATINO            17             338
[1] 2 2
[1] FALSE

Clustering(63) Variable = PARD3 MUTATION ANALYSIS
D63V1, survival
                 sevent
clus2               0   1
  PARD3 MUTATED    14   8
  PARD3 WILD-TYPE 203 167
  PARD3 MUTATED PARD3 WILD-TYPE 
             22             370 
  PARD3 MUTATED PARD3 WILD-TYPE 
              8             167 
$`PARD3 MUTATED`
TCGA-DK-A3IU TCGA-DK-A6AW TCGA-DK-A6B6 TCGA-E7-A541 TCGA-GV-A3JZ TCGA-K4-A3WU 
       23.21        53.29        36.66        25.58        19.82         3.45 
TCGA-KQ-A41N TCGA-S5-A6DX TCGA-XF-A9ST TCGA-XF-A9T5 TCGA-CU-A3QU TCGA-DK-A2I4 
       52.73         1.84         4.21        66.64         5.19       142.78 
TCGA-G2-AA3C TCGA-GU-A42Q TCGA-GU-A767 TCGA-H4-A2HO TCGA-K4-A5RJ TCGA-SY-A9G5 
        6.94        11.31         4.73         1.51        17.72        38.99 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-XF-AAMG TCGA-ZF-A9R0 
       69.34        35.24       110.60        22.36 

$`PARD3 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      130.88        46.68        87.32         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 
       21.30         9.67        66.05        17.98        64.18        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       67.36        15.68        50.70        38.24        52.01       165.73 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
      166.03        13.64        13.64        56.15        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       15.35         0.92         1.22        33.04         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
       24.30        23.41        17.98        29.16        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       12.85        27.35         3.62        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
        5.69         8.25        18.08        58.92         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         3.06         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY 
        9.67        31.07        17.23        11.08        33.01        17.62 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
       70.32        21.40        19.13        17.75        24.92        10.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       32.78        32.98        20.28        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       22.72         9.01        25.02         2.76         9.14        27.68 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78N 
       50.56        35.97        46.98        14.24        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SV 
       51.32         3.22        15.98        34.45        14.93        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 
       11.90        21.04        26.27        18.90         2.24         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       13.74        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       94.29         3.48        88.87        34.06        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
        0.62        41.75        51.16        66.54        10.22        47.80 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
        2.50        17.42        40.08         7.33         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 
        4.67        17.56        36.43        28.41         1.94         2.93 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       23.01        12.79        12.56        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       13.08        29.79         1.84        21.86        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        17.95         7.79 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       15.02        13.58        18.81        19.00        15.35        12.03 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        38.83        29.72         5.36        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
       24.03        24.66        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       27.98         5.52        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       19.33         5.36        27.45         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.27        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
        7.23        20.12        66.02        29.36        20.71        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07         8.94        13.91        26.70         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
        3.12        20.98         2.20        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
       15.78         7.00        14.27        21.34        19.10         8.48 
TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
       36.49        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
        9.07        11.70         1.81        15.42        16.27        11.80 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       44.38         1.15        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.67        16.54        17.62        37.05        22.68        76.01 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         6.21         3.85         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       48.62        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       28.24        16.27        92.98         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 
       56.48        27.06        75.39         0.66        11.97        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       58.72        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        67.20        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  PARD3 MUTATED PARD3 WILD-TYPE 
           1.51            0.56 
  PARD3 MUTATED PARD3 WILD-TYPE 
         142.78          166.03 
  PARD3 MUTATED PARD3 WILD-TYPE 
         22.785          17.490 
[1] "1.5 - 142.8 (22.8)" "0.6 - 166.0 (17.5)"
[1] "hr=" "1.5"
D63V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PARD3 MUTATED         0        5        10        7
  PARD3 WILD-TYPE       2      117       125      127
D63V3, multiclass
           clus
vv          PARD3 MUTATED PARD3 WILD-TYPE
  STAGE I               0               2
  STAGE II              5             117
  STAGE III            10             125
  STAGE IV              7             127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  PARD3 MUTATED          5  10   6
  PARD3 WILD-TYPE      111 180  51
D63V4, multiclass
          clus
vv         PARD3 MUTATED PARD3 WILD-TYPE
  T0+T1+T2             5             111
  T3                  10             180
  T4                   6              51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PARD3 MUTATED    13   4   2   1
  PARD3 WILD-TYPE 212  42  73   7
D63V5, multiclass
    clus
vv   PARD3 MUTATED PARD3 WILD-TYPE
  N0            13             212
  N1             4              42
  N2             2              73
  N3             1               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"
D63V6, binary
                 cls
clus                0   1
  PARD3 MUTATED     9   0
  PARD3 WILD-TYPE 180  11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARD3 MUTATED      9    0
  PARD3 WILD-TYPE  180   11
   clus
vv  PARD3 MUTATED PARD3 WILD-TYPE
  0             9             180
  1             0              11
[1] 2 2
[1] FALSE
D63V7, binary
                 cls
clus                0   1
  PARD3 MUTATED     1  21
  PARD3 WILD-TYPE 101 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARD3 MUTATED      1   21
  PARD3 WILD-TYPE  101  272
        clus
vv       PARD3 MUTATED PARD3 WILD-TYPE
  FEMALE             1             101
  MALE              21             272
[1] 2 2
[1] FALSE
D63V8, binary
                 cls
clus                0   1
  PARD3 MUTATED    21   0
  PARD3 WILD-TYPE 329  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARD3 MUTATED     21    0
  PARD3 WILD-TYPE  329   20
     clus
vv    PARD3 MUTATED PARD3 WILD-TYPE
  NO             21             329
  YES             0              20
[1] 2 2
[1] FALSE
D63V9, continuous
D63V10, continuous
D63V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PARD3 MUTATED       0                         1    21
  PARD3 WILD-TYPE    39                        21   296
D63V12, multiclass
                           clus
vv                          PARD3 MUTATED PARD3 WILD-TYPE
  ASIAN                                 0              39
  BLACK OR AFRICAN AMERICAN             1              21
  WHITE                                21             296
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V13, binary
                 cls
clus                0   1
  PARD3 MUTATED     2  20
  PARD3 WILD-TYPE   6 335
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARD3 MUTATED      2   20
  PARD3 WILD-TYPE    6  335
                        clus
vv                       PARD3 MUTATED PARD3 WILD-TYPE
  HISPANIC OR LATINO                 2               6
  NOT HISPANIC OR LATINO            20             335
[1] 2 2
[1] FALSE

Clustering(64) Variable = EZR MUTATION ANALYSIS
D64V1, survival
               sevent
clus2             0   1
  EZR MUTATED    10   2
  EZR WILD-TYPE 207 173
  EZR MUTATED EZR WILD-TYPE 
           12           380 
  EZR MUTATED EZR WILD-TYPE 
            2           173 
$`EZR MUTATED`
TCGA-DK-A1AC TCGA-DK-A6AW TCGA-FD-A6TB TCGA-UY-A9PH TCGA-DK-A1AF TCGA-DK-A2I4 
      130.88        53.29        18.81        51.32        17.62       142.78 
TCGA-FD-A3N5 TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-XF-A9SI TCGA-XF-AAN5 TCGA-ZF-AA4X 
       22.52         8.48        19.40        79.66        75.39        67.20 

$`EZR WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 
       23.21         9.67        66.05        17.98        64.18        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       67.36        15.68        50.70        36.66        38.24        52.01 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
      165.73       166.03        13.64        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
        6.28        62.86         6.15        12.69        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        4.31         9.67        31.07        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       17.62        70.32        21.40        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       10.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        8.58        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A9SJ 
       46.98        14.24         1.84        33.14        86.83         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
       15.98        34.45        14.93         4.21        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       13.74        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       94.29         3.48        88.87        34.06        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
        0.62        41.75        51.16        66.54        10.22        47.80 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
        2.50        17.42        40.08         7.33         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 
        4.67        17.56        36.43        28.41         1.94         2.93 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       23.01        12.79        12.56        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       13.08         5.19        29.79         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
       18.41       112.44        16.14        15.62        17.95         7.79 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       15.02        13.58        18.81        19.00        15.35        12.03 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        38.83        29.72         5.36        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
       24.03        24.66        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 
        8.09        32.02        16.77         8.94        12.62        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
        5.52        25.74        22.98        14.96        20.91        19.33 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF 
        5.36        27.45         2.70         7.10        13.35         2.27 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC 
       10.85        12.66        10.65         8.94         3.25        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       61.94        48.00        15.95        26.93        59.31         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       20.12        66.02         6.94        29.36        20.71        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07         8.94        13.91        26.70         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        3.12        20.98         2.20        11.31        18.97         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05        15.78         4.73         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
       19.10        36.49         1.51        38.60        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       21.24         9.07        11.70        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       16.27        11.80        44.38         1.15        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       13.48        12.23        16.67        16.54        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       37.05        22.68        76.01        69.34        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         6.21         3.85         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       64.80        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       27.06         0.66        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       35.84        21.86        28.41        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       47.84        20.22         2.89         8.61        59.38        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        19.40         8.52        54.21        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  EZR MUTATED EZR WILD-TYPE 
         8.48          0.56 
  EZR MUTATED EZR WILD-TYPE 
       142.78        166.03 
  EZR MUTATED EZR WILD-TYPE 
       52.305        17.195 
[1] "8.5 - 142.8 (52.3)" "0.6 - 166.0 (17.2)"
[1] "hr=" "4.8"
D64V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  EZR MUTATED         0        6         4        2
  EZR WILD-TYPE       2      116       131      132
D64V3, multiclass
           clus
vv          EZR MUTATED EZR WILD-TYPE
  STAGE I             0             2
  STAGE II            6           116
  STAGE III           4           131
  STAGE IV            2           132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1+T2  T3  T4
  EZR MUTATED          5   5   0
  EZR WILD-TYPE      111 185  57
D64V4, multiclass
          clus
vv         EZR MUTATED EZR WILD-TYPE
  T0+T1+T2           5           111
  T3                 5           185
  T4                 0            57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  EZR MUTATED     8   0   1   0
  EZR WILD-TYPE 217  46  74   8
D64V5, multiclass
    clus
vv   EZR MUTATED EZR WILD-TYPE
  N0           8           217
  N1           0            46
  N2           1            74
  N3           0             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
               cls
clus              0   1
  EZR MUTATED     5   1
  EZR WILD-TYPE 184  10
[1] "tbl2"
               cls
clus            [,1] [,2]
  EZR MUTATED      5    1
  EZR WILD-TYPE  184   10
   clus
vv  EZR MUTATED EZR WILD-TYPE
  0           5           184
  1           1            10
[1] 2 2
[1] FALSE
D64V7, binary
               cls
clus              0   1
  EZR MUTATED     4   8
  EZR WILD-TYPE  98 285
[1] "tbl2"
               cls
clus            [,1] [,2]
  EZR MUTATED      4    8
  EZR WILD-TYPE   98  285
        clus
vv       EZR MUTATED EZR WILD-TYPE
  FEMALE           4            98
  MALE             8           285
[1] 2 2
[1] FALSE
D64V8, binary
               cls
clus              0   1
  EZR MUTATED    11   1
  EZR WILD-TYPE 339  19
[1] "tbl2"
               cls
clus            [,1] [,2]
  EZR MUTATED     11    1
  EZR WILD-TYPE  339   19
     clus
vv    EZR MUTATED EZR WILD-TYPE
  NO           11           339
  YES           1            19
[1] 2 2
[1] FALSE
D64V9, continuous
D64V10, continuous
D64V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EZR MUTATED       1                         2     9
  EZR WILD-TYPE    38                        20   308
D64V12, multiclass
                           clus
vv                          EZR MUTATED EZR WILD-TYPE
  ASIAN                               1            38
  BLACK OR AFRICAN AMERICAN           2            20
  WHITE                               9           308
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V13, binary
               cls
clus              0   1
  EZR MUTATED     0  11
  EZR WILD-TYPE   8 344
[1] "tbl2"
               cls
clus            [,1] [,2]
  EZR MUTATED      0   11
  EZR WILD-TYPE    8  344
                        clus
vv                       EZR MUTATED EZR WILD-TYPE
  HISPANIC OR LATINO               0             8
  NOT HISPANIC OR LATINO          11           344
[1] 2 2
[1] FALSE

Clustering(65) Variable = MOAP1 MUTATION ANALYSIS
D65V1, survival
                 sevent
clus2               0   1
  MOAP1 MUTATED     7   0
  MOAP1 WILD-TYPE 210 175
  MOAP1 MUTATED MOAP1 WILD-TYPE 
              7             385 
  MOAP1 MUTATED MOAP1 WILD-TYPE 
              0             175 
$`MOAP1 MUTATED`
TCGA-DK-A6AW TCGA-GC-A3YS TCGA-XF-A9T0 TCGA-CF-A27C TCGA-DK-AA6X TCGA-GD-A2C5 
       53.29        24.92        26.27        13.97        15.35        26.70 
TCGA-ZF-AA51 
       56.35 

$`MOAP1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      130.88        46.68        87.32         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       21.30        23.21         9.67        66.05        17.98        64.18 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       29.16        46.78        19.79        12.85        27.35         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.36         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       11.08        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       17.75        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        3.45         2.76         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       35.97        46.98        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       51.32         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       12.76        11.90        21.04        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.10        13.74        10.82        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       86.30        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       30.28        94.29         3.48        88.87        34.06        19.69 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       57.90        12.23        24.13        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       50.04         0.62        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       16.18         4.67        17.56        36.43        28.41         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG 
        2.93        23.01        12.79        12.56        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       13.08         5.19        29.79         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW 
        7.79       142.78         4.80        13.58         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       10.55       163.30        15.02        13.58        18.81        19.00 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       12.03        43.59        38.83        29.72         5.36        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70         0.56         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
        4.24        24.03        24.66        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       14.37         8.09        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
       20.91        19.33         5.36        27.45         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       13.35         2.27        10.85        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25        22.88        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       59.31         7.23        20.12        66.02         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 
       20.71        15.81        15.91        14.07         8.94        13.91 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
       38.60        64.01        12.16        21.24         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       17.72         1.81        15.42        16.27        11.80        44.38 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.15        15.32        15.58        13.48        12.23        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.54        38.99        17.62        37.05        22.68        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34        35.24        29.56        17.82         6.21         3.85 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32         6.77        56.48        27.06        75.39 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       21.86        28.41        13.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       20.22         2.89         8.61        59.38        60.16        67.20 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        19.40         8.52        54.21        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  MOAP1 MUTATED MOAP1 WILD-TYPE 
          13.97            0.56 
  MOAP1 MUTATED MOAP1 WILD-TYPE 
          56.35          166.03 
  MOAP1 MUTATED MOAP1 WILD-TYPE 
          26.27           17.62 
[1] "14.0 - 56.4 (26.3)" "0.6 - 166.0 (17.6)"
[1] "hr="     "9300000"
D65V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  MOAP1 MUTATED         0        3         2        2
  MOAP1 WILD-TYPE       2      119       133      132
D65V3, multiclass
           clus
vv          MOAP1 MUTATED MOAP1 WILD-TYPE
  STAGE I               0               2
  STAGE II              3             119
  STAGE III             2             133
  STAGE IV              2             132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  MOAP1 MUTATED          2   4   0
  MOAP1 WILD-TYPE      114 186  57
D65V4, multiclass
          clus
vv         MOAP1 MUTATED MOAP1 WILD-TYPE
  T0+T1+T2             2             114
  T3                   4             186
  T4                   0              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MOAP1 MUTATED     4   1   1   0
  MOAP1 WILD-TYPE 221  45  74   8
D65V5, multiclass
    clus
vv   MOAP1 MUTATED MOAP1 WILD-TYPE
  N0             4             221
  N1             1              45
  N2             1              74
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                 cls
clus                0   1
  MOAP1 MUTATED     4   0
  MOAP1 WILD-TYPE 185  11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOAP1 MUTATED      4    0
  MOAP1 WILD-TYPE  185   11
   clus
vv  MOAP1 MUTATED MOAP1 WILD-TYPE
  0             4             185
  1             0              11
[1] 2 2
[1] FALSE
D65V7, binary
                 cls
clus                0   1
  MOAP1 MUTATED     2   5
  MOAP1 WILD-TYPE 100 288
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOAP1 MUTATED      2    5
  MOAP1 WILD-TYPE  100  288
        clus
vv       MOAP1 MUTATED MOAP1 WILD-TYPE
  FEMALE             2             100
  MALE               5             288
[1] 2 2
[1] FALSE
D65V8, binary
                 cls
clus                0   1
  MOAP1 MUTATED     5   1
  MOAP1 WILD-TYPE 345  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOAP1 MUTATED      5    1
  MOAP1 WILD-TYPE  345   19
     clus
vv    MOAP1 MUTATED MOAP1 WILD-TYPE
  NO              5             345
  YES             1              19
[1] 2 2
[1] FALSE
D65V9, continuous
D65V10, continuous
D65V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MOAP1 MUTATED       1                         0     6
  MOAP1 WILD-TYPE    38                        22   311
D65V12, multiclass
                           clus
vv                          MOAP1 MUTATED MOAP1 WILD-TYPE
  ASIAN                                 1              38
  BLACK OR AFRICAN AMERICAN             0              22
  WHITE                                 6             311
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V13, binary
                 cls
clus                0   1
  MOAP1 MUTATED     0   7
  MOAP1 WILD-TYPE   8 348
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOAP1 MUTATED      0    7
  MOAP1 WILD-TYPE    8  348
                        clus
vv                       MOAP1 MUTATED MOAP1 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO             7             348
[1] 2 2
[1] FALSE

Clustering(66) Variable = SF3B1 MUTATION ANALYSIS
D66V1, survival
                 sevent
clus2               0   1
  SF3B1 MUTATED    14  10
  SF3B1 WILD-TYPE 203 165
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             24             368 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             10             165 
$`SF3B1 MUTATED`
TCGA-4Z-AA7Q TCGA-BL-A5ZZ TCGA-DK-A3X1 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A62P 
       16.77        12.39        66.05        15.35        25.58         6.28 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GV-A3QF TCGA-UY-A78N TCGA-XF-AAN3 TCGA-ZF-A9R4 
       17.62        21.40        20.28        86.83        86.30        30.28 
TCGA-ZF-AA4R TCGA-ZF-AA5P TCGA-BL-A0C8 TCGA-CU-A5W6 TCGA-DK-A1AE TCGA-DK-A2I4 
       34.06        12.23        40.08         1.84        16.14       142.78 
TCGA-DK-AA6P TCGA-FJ-A871 TCGA-G2-AA3F TCGA-GD-A3OQ TCGA-SY-A9G5 TCGA-UY-A9PD 
       15.02         8.94        29.36         3.12        38.99        17.82 

$`SF3B1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BT-A20N TCGA-BT-A20T 
      108.95        16.27        15.12        33.83        26.14        14.89 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
        8.35        20.48        25.94         9.96        28.70         8.98 
TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        2.04        18.58        12.92         4.90        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       13.58         2.14        19.00        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       87.32         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
        9.67        17.98        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       15.68        50.70        36.66        38.24        52.01       165.73 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
      166.03        13.64        13.64        56.15        11.18        20.32 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
        0.92         1.22        33.04         4.01        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       23.41        17.98        29.16        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       27.35         3.62        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        8.25        18.08        58.92        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
       12.69        12.36         3.06         4.31         9.67        31.07 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC 
       17.23        11.08        33.01        70.32        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK 
       24.92        10.92        32.78        32.98        19.82        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        8.58        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A9SJ 
       46.98        14.24         1.84        33.14        51.32         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
       15.98        34.45        14.93         4.21        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       13.74        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 
       91.73        98.99        44.32        30.94        61.45        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE 
        3.88         9.63        13.64        21.11        94.29         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       88.87        19.69        57.90        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65         8.35        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80         2.50        17.42         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       16.18         4.67        17.56        36.43        28.41         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
        2.93        23.01        12.79        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 
       11.87        13.08         5.19        29.79        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
       18.41       112.44        17.62        15.62        17.95         7.79 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       13.58        18.81        19.00        15.35        12.03        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         5.36        22.16         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
        0.56         0.66        26.96        26.24         4.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
       24.66        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
        5.52        25.74        22.98        14.96        20.91        19.33 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF 
        5.36        27.45         2.70         7.10        13.35         2.27 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
       10.85        12.66        10.65         3.25        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       48.00        15.95        26.93        59.31         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
       66.02         6.94        20.71        15.81        15.91        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 
        8.94        13.91        26.70         2.10        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31        18.97         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        7.00        14.27        21.34        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       11.80        44.38         1.15        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       12.23        16.67        16.54        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF 
       76.01        69.34        35.24        29.56         6.21         3.85 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32         6.77        56.48        27.06        75.39 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       21.86        28.41        13.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       20.22         2.89         8.61        59.38        60.16        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        19.40         8.52        54.21        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  SF3B1 MUTATED SF3B1 WILD-TYPE 
           1.84            0.56 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
         142.78          166.03 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
          19.05           17.59 
[1] "1.8 - 142.8 (19.1)" "0.6 - 166.0 (17.6)"
[1] "hr=" "1.2"
D66V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SF3B1 MUTATED         1        6         9        8
  SF3B1 WILD-TYPE       1      116       126      126
D66V3, multiclass
           clus
vv          SF3B1 MUTATED SF3B1 WILD-TYPE
  STAGE I               1               1
  STAGE II              6             116
  STAGE III             9             126
  STAGE IV              8             126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  SF3B1 MUTATED          7  10   5
  SF3B1 WILD-TYPE      109 180  52
D66V4, multiclass
          clus
vv         SF3B1 MUTATED SF3B1 WILD-TYPE
  T0+T1+T2             7             109
  T3                  10             180
  T4                   5              52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SF3B1 MUTATED    11   4   4   0
  SF3B1 WILD-TYPE 214  42  71   8
D66V5, multiclass
    clus
vv   SF3B1 MUTATED SF3B1 WILD-TYPE
  N0            11             214
  N1             4              42
  N2             4              71
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                 cls
clus                0   1
  SF3B1 MUTATED    12   0
  SF3B1 WILD-TYPE 177  11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B1 MUTATED     12    0
  SF3B1 WILD-TYPE  177   11
   clus
vv  SF3B1 MUTATED SF3B1 WILD-TYPE
  0            12             177
  1             0              11
[1] 2 2
[1] FALSE
D66V7, binary
                 cls
clus                0   1
  SF3B1 MUTATED     3  21
  SF3B1 WILD-TYPE  99 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B1 MUTATED      3   21
  SF3B1 WILD-TYPE   99  272
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  FEMALE             3              99
  MALE              21             272
[1] 2 2
[1] FALSE
D66V8, binary
                 cls
clus                0   1
  SF3B1 MUTATED    23   0
  SF3B1 WILD-TYPE 327  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B1 MUTATED     23    0
  SF3B1 WILD-TYPE  327   20
     clus
vv    SF3B1 MUTATED SF3B1 WILD-TYPE
  NO             23             327
  YES             0              20
[1] 2 2
[1] FALSE
D66V9, continuous
D66V10, continuous
D66V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SF3B1 MUTATED       1                         0    23
  SF3B1 WILD-TYPE    38                        22   294
D66V12, multiclass
                           clus
vv                          SF3B1 MUTATED SF3B1 WILD-TYPE
  ASIAN                                 1              38
  BLACK OR AFRICAN AMERICAN             0              22
  WHITE                                23             294
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V13, binary
                 cls
clus                0   1
  SF3B1 MUTATED     0  23
  SF3B1 WILD-TYPE   8 332
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B1 MUTATED      0   23
  SF3B1 WILD-TYPE    8  332
                        clus
vv                       SF3B1 MUTATED SF3B1 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            23             332
[1] 2 2
[1] FALSE

Clustering(67) Variable = RUNX1 MUTATION ANALYSIS
D67V1, survival
                 sevent
clus2               0   1
  RUNX1 MUTATED     5   8
  RUNX1 WILD-TYPE 212 167
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             13             379 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
              8             167 
$`RUNX1 MUTATED`
TCGA-DK-A1AC TCGA-DK-AA6W TCGA-FD-A43P TCGA-GC-A3YS TCGA-XF-A9ST TCGA-XF-A9T2 
      130.88        13.64        27.35        24.92         4.21        18.90 
TCGA-XF-A9T8 TCGA-XF-AAN7 TCGA-ZF-A9RC TCGA-E7-A85H TCGA-FD-A3B3 TCGA-UY-A78M 
       13.74        18.58        94.29        12.95        32.02        22.68 
TCGA-ZF-AA4N 
        2.89 

$`RUNX1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
       52.01       165.73       166.03        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       46.78        19.79        12.85         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       10.78         5.69         8.25        18.08        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
       62.86        18.81         6.15        12.69        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        4.31         9.67        31.07        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P 
       17.62        70.32        21.40        19.13        17.75        10.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       32.78        32.98        19.82        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       19.07        22.72         9.01        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        9.14        27.68        52.73        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ 
       14.24         1.84        33.14        86.83        51.32         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       15.98        34.45        14.93        12.76        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH 
       26.27         2.24        66.64         2.10        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63        71.57        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       30.94        61.45        86.30         3.88         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       21.11        30.28         3.48        88.87        34.06        19.69 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       57.90        12.23        24.13        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       50.04         0.62        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       16.18         4.67        17.56        36.43        28.41         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
        2.93        23.01        12.79        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.87        13.08         5.19        29.79         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       66.41        18.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       17.95         7.79       142.78         4.80        13.58         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       19.00        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        22.16         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
       26.96        26.24         4.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       14.07        14.37         8.09        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
       20.91        19.33         5.36        27.45         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       13.35         2.27        10.85        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25        22.88        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       59.31         7.23        20.12        66.02         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 
       20.71        15.81        15.91        14.07         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       26.70         2.10         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       18.97         7.63        20.05        15.78         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
       14.27        21.34        19.10         8.48        36.49         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
       19.40        38.60        64.01        12.16        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70        17.72         1.81        15.42        16.27        11.80 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       44.38         1.15        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O 
       16.67        16.54        38.99        17.62        37.05        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34        35.24        29.56        17.82         6.21         3.85 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32         6.77        56.48        27.06        75.39 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       21.86        28.41        13.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       20.22         8.61        59.38        60.16        67.20        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        19.40         8.52        54.21        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  RUNX1 MUTATED RUNX1 WILD-TYPE 
           2.89            0.56 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
         130.88          166.03 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
          18.90           17.62 
[1] "2.9 - 130.9 (18.9)" "0.6 - 166.0 (17.6)"
[1] "hr=" "1.2"
D67V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  RUNX1 MUTATED         0        3         7        3
  RUNX1 WILD-TYPE       2      119       128      131
D67V3, multiclass
           clus
vv          RUNX1 MUTATED RUNX1 WILD-TYPE
  STAGE I               0               2
  STAGE II              3             119
  STAGE III             7             128
  STAGE IV              3             131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  RUNX1 MUTATED          3   9   0
  RUNX1 WILD-TYPE      113 181  57
D67V4, multiclass
          clus
vv         RUNX1 MUTATED RUNX1 WILD-TYPE
  T0+T1+T2             3             113
  T3                   9             181
  T4                   0              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RUNX1 MUTATED     9   2   1   0
  RUNX1 WILD-TYPE 216  44  74   8
D67V5, multiclass
    clus
vv   RUNX1 MUTATED RUNX1 WILD-TYPE
  N0             9             216
  N1             2              44
  N2             1              74
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                 cls
clus                0   1
  RUNX1 MUTATED     3   0
  RUNX1 WILD-TYPE 186  11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED      3    0
  RUNX1 WILD-TYPE  186   11
   clus
vv  RUNX1 MUTATED RUNX1 WILD-TYPE
  0             3             186
  1             0              11
[1] 2 2
[1] FALSE
D67V7, binary
                 cls
clus                0   1
  RUNX1 MUTATED     2  11
  RUNX1 WILD-TYPE 100 282
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED      2   11
  RUNX1 WILD-TYPE  100  282
        clus
vv       RUNX1 MUTATED RUNX1 WILD-TYPE
  FEMALE             2             100
  MALE              11             282
[1] 2 2
[1] FALSE
D67V8, binary
                 cls
clus                0   1
  RUNX1 MUTATED    10   1
  RUNX1 WILD-TYPE 340  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED     10    1
  RUNX1 WILD-TYPE  340   19
     clus
vv    RUNX1 MUTATED RUNX1 WILD-TYPE
  NO             10             340
  YES             1              19
[1] 2 2
[1] FALSE
D67V9, continuous
D67V10, continuous
D67V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RUNX1 MUTATED       2                         1    10
  RUNX1 WILD-TYPE    37                        21   307
D67V12, multiclass
                           clus
vv                          RUNX1 MUTATED RUNX1 WILD-TYPE
  ASIAN                                 2              37
  BLACK OR AFRICAN AMERICAN             1              21
  WHITE                                10             307
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V13, binary
                 cls
clus                0   1
  RUNX1 MUTATED     0  12
  RUNX1 WILD-TYPE   8 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED      0   12
  RUNX1 WILD-TYPE    8  343
                        clus
vv                       RUNX1 MUTATED RUNX1 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            12             343
[1] 2 2
[1] FALSE

Clustering(68) Variable = MEGF8 MUTATION ANALYSIS
D68V1, survival
                 sevent
clus2               0   1
  MEGF8 MUTATED    13   7
  MEGF8 WILD-TYPE 204 168
  MEGF8 MUTATED MEGF8 WILD-TYPE 
             20             372 
  MEGF8 MUTATED MEGF8 WILD-TYPE 
              7             168 
$`MEGF8 MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-DK-A1AB TCGA-DK-A6AW TCGA-FD-A3SN TCGA-G2-A3VY 
       16.27        16.77        16.70        53.29        29.16        17.62 
TCGA-GV-A40G TCGA-XF-A9SJ TCGA-XF-A9T8 TCGA-ZF-AA53 TCGA-2F-A9KR TCGA-DK-A1AD 
       19.07         3.22        13.74        57.90       104.65       112.44 
TCGA-DK-AA6U TCGA-E7-A4IJ TCGA-E7-A85H TCGA-FJ-A3Z9 TCGA-GC-A3RC TCGA-MV-A51V 
       19.00        22.16        12.95        12.66        15.91        13.48 
TCGA-UY-A9PE TCGA-ZF-AA4V 
        6.21        59.38 

$`MEGF8 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
      108.95        15.12        33.83        12.39        26.14        14.89 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
        8.35        20.48        25.94         9.96        28.70         8.98 
TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        2.04        18.58        12.92         4.90        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 
       13.58         2.14        19.00       130.88        46.68        87.32 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       66.05        17.98        64.18        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S 
       50.70        36.66        38.24        52.01       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       13.64        13.64        56.15        11.18        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       25.58         0.92         1.22        33.04         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       24.30        23.41        17.98        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       27.35         3.62        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
        8.25        18.08        58.92         6.28        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.15        12.69        12.36         3.06         4.31         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3BM 
       31.07        17.23        11.08        33.01        70.32        21.40 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP 
       19.13        17.75        24.92        10.92        32.78        32.98 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND 
       19.82        20.28        27.35         8.58        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
       25.02         3.45         2.76         9.14        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       50.56        35.97        46.98        14.24         1.84        33.14 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       86.83        51.32        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       66.64         2.10        10.82        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       86.30        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       30.28        94.29         3.48        88.87        34.06        19.69 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N 
       12.23        24.13        11.97        94.88         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       16.83        17.16        34.98        27.62        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
       41.75        51.16        66.54        10.22        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       17.42        40.08         7.33         2.66         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       14.96         5.06         8.25        17.16        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       17.56        36.43        28.41         1.94         2.93        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       12.79        12.56        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       12.16        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.19        29.79         1.84        21.86        66.41        18.41 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       15.02        13.58        18.81        15.35        12.03        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       38.83        29.72         5.36         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       13.68        14.07        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3ZE 
        2.70         7.10        13.35         2.27        10.85        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        8.94         3.25        22.88        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       26.93        59.31         7.23        20.12        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 
       29.36        20.71        15.81        14.07         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       26.70         2.10         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       18.97         7.63        20.05        15.78         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
       14.27        21.34        19.10         8.48        36.49         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
       19.40        38.60        64.01        12.16        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70        17.72         1.81        15.42        16.27        11.80 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN 
       44.38         1.15        15.32        15.58        12.23        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.54        38.99        17.62        37.05        22.68        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HH 
       69.34        35.24        29.56        17.82         3.85         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
       17.88        48.62        64.80        79.66        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT 
       23.64        28.24        16.27        92.98       110.60         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC 
        8.32         6.77        56.48        27.06        75.39         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       11.97        22.36        25.41        31.20        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       28.41        13.41        64.08        58.72        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        2.89         8.61        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21        29.49         5.52        10.65 

  MEGF8 MUTATED MEGF8 WILD-TYPE 
           3.22            0.56 
  MEGF8 MUTATED MEGF8 WILD-TYPE 
         112.44          166.03 
  MEGF8 MUTATED MEGF8 WILD-TYPE 
         17.195          17.670 
[1] "3.2 - 112.4 (17.2)" "0.6 - 166.0 (17.7)"
[1] "hr=" "1.5"
D68V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  MEGF8 MUTATED         0        7         8        4
  MEGF8 WILD-TYPE       2      115       127      130
D68V3, multiclass
           clus
vv          MEGF8 MUTATED MEGF8 WILD-TYPE
  STAGE I               0               2
  STAGE II              7             115
  STAGE III             8             127
  STAGE IV              4             130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  MEGF8 MUTATED          6  10   1
  MEGF8 WILD-TYPE      110 180  56
D68V4, multiclass
          clus
vv         MEGF8 MUTATED MEGF8 WILD-TYPE
  T0+T1+T2             6             110
  T3                  10             180
  T4                   1              56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MEGF8 MUTATED    12   0   4   0
  MEGF8 WILD-TYPE 213  46  71   8
D68V5, multiclass
    clus
vv   MEGF8 MUTATED MEGF8 WILD-TYPE
  N0            12             213
  N1             0              46
  N2             4              71
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                 cls
clus                0   1
  MEGF8 MUTATED    14   0
  MEGF8 WILD-TYPE 175  11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF8 MUTATED     14    0
  MEGF8 WILD-TYPE  175   11
   clus
vv  MEGF8 MUTATED MEGF8 WILD-TYPE
  0            14             175
  1             0              11
[1] 2 2
[1] FALSE
D68V7, binary
                 cls
clus                0   1
  MEGF8 MUTATED     2  18
  MEGF8 WILD-TYPE 100 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF8 MUTATED      2   18
  MEGF8 WILD-TYPE  100  275
        clus
vv       MEGF8 MUTATED MEGF8 WILD-TYPE
  FEMALE             2             100
  MALE              18             275
[1] 2 2
[1] FALSE
D68V8, binary
                 cls
clus                0   1
  MEGF8 MUTATED    19   0
  MEGF8 WILD-TYPE 331  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF8 MUTATED     19    0
  MEGF8 WILD-TYPE  331   20
     clus
vv    MEGF8 MUTATED MEGF8 WILD-TYPE
  NO             19             331
  YES             0              20
[1] 2 2
[1] FALSE
D68V9, continuous
D68V10, continuous
D68V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MEGF8 MUTATED       3                         0    16
  MEGF8 WILD-TYPE    36                        22   301
D68V12, multiclass
                           clus
vv                          MEGF8 MUTATED MEGF8 WILD-TYPE
  ASIAN                                 3              36
  BLACK OR AFRICAN AMERICAN             0              22
  WHITE                                16             301
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V13, binary
                 cls
clus                0   1
  MEGF8 MUTATED     1  15
  MEGF8 WILD-TYPE   7 340
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF8 MUTATED      1   15
  MEGF8 WILD-TYPE    7  340
                        clus
vv                       MEGF8 MUTATED MEGF8 WILD-TYPE
  HISPANIC OR LATINO                 1               7
  NOT HISPANIC OR LATINO            15             340
[1] 2 2
[1] FALSE

Clustering(69) Variable = CASP8 MUTATION ANALYSIS
D69V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED    10   4
  CASP8 WILD-TYPE 207 171
  CASP8 MUTATED CASP8 WILD-TYPE 
             14             378 
  CASP8 MUTATED CASP8 WILD-TYPE 
              4             171 
$`CASP8 MUTATED`
TCGA-DK-A3IN TCGA-DK-A6AW TCGA-DK-A6B6 TCGA-DK-AA74 TCGA-GU-AATP TCGA-XF-A9T3 
        8.22        53.29        36.66        56.15        32.98         2.24 
TCGA-ZF-A9RC TCGA-BT-A20O TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-DK-A3WW TCGA-FD-A3N6 
       94.29        12.16        23.01        12.79        20.81        27.98 
TCGA-GU-A42Q TCGA-UY-A78K 
       11.31        17.62 

$`CASP8 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
      130.88        46.68        87.32        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 
       23.21         9.67        66.05        17.98        64.18        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       67.36        15.68        50.70        38.24        52.01       165.73 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
      166.03        13.64        13.64        11.18        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       25.58         0.92         1.22        33.04         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
       24.30        23.41        17.98        29.16        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       12.85        27.35         3.62        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
        5.69         8.25        18.08        58.92         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         3.06         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY 
        9.67        31.07        17.23        11.08        33.01        17.62 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
       70.32        21.40        19.13        17.75        24.92        10.92 
TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       32.78        19.82        20.28        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       22.72         9.01        25.02         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
       27.68        52.73        50.56        35.97        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK 
        1.84        33.14        86.83        51.32         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       34.45        14.93         4.21        12.76        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       26.27        18.90        66.64         2.10        13.74        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       11.31        54.90         7.63        71.57        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 
       44.32        30.94        61.45        86.30        18.58         3.88 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RE TCGA-ZF-A9RL 
        9.63        13.64        21.11        30.28         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       34.06        19.69        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       34.98        27.62        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       66.54        10.22        47.80         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74         6.58        13.15        19.04 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       17.88        19.50         5.06        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       17.16        16.18         4.67        17.56        36.43        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
        1.94         2.93        12.56        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       13.08         5.19        29.79         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WX 
        7.79       142.78         4.80        13.58         8.15        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
      163.30        15.02        13.58        18.81        19.00        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       12.03        43.59        38.83        29.72         5.36        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70         0.56         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
        4.24        24.03        24.66        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       14.37         8.09        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       22.52         5.52        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       19.33         5.36        27.45         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.27        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
        7.23        20.12        66.02         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91        14.07         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-A762 
        2.10         3.12        20.98         2.20        18.97         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05        15.78         4.73         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       19.10         8.48        36.49         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       64.01        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
        1.81        15.42        16.27        11.80        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       15.32        15.58        13.48        12.23        16.67        16.54 
TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       38.99        37.05        22.68        76.01        69.34        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         6.21         3.85         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       48.62        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW 
       28.24        16.27        92.98       110.60         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L 
        6.77        56.48        27.06        75.39         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       13.41        64.08        58.72        47.84        20.22         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21        29.49         5.52        10.65 

  CASP8 MUTATED CASP8 WILD-TYPE 
           2.24            0.56 
  CASP8 MUTATED CASP8 WILD-TYPE 
          94.29          166.03 
  CASP8 MUTATED CASP8 WILD-TYPE 
          21.91           17.59 
[1] "2.2 - 94.3 (21.9)"  "0.6 - 166.0 (17.6)"
[1] "hr=" "1.8"
D69V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  CASP8 MUTATED         0        3         8        3
  CASP8 WILD-TYPE       2      119       127      131
D69V3, multiclass
           clus
vv          CASP8 MUTATED CASP8 WILD-TYPE
  STAGE I               0               2
  STAGE II              3             119
  STAGE III             8             127
  STAGE IV              3             131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  CASP8 MUTATED          3   8   1
  CASP8 WILD-TYPE      113 182  56
D69V4, multiclass
          clus
vv         CASP8 MUTATED CASP8 WILD-TYPE
  T0+T1+T2             3             113
  T3                   8             182
  T4                   1              56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CASP8 MUTATED    10   0   3   0
  CASP8 WILD-TYPE 215  46  72   8
D69V5, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  N0            10             215
  N1             0              46
  N2             3              72
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                 cls
clus                0   1
  CASP8 MUTATED     7   0
  CASP8 WILD-TYPE 182  11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      7    0
  CASP8 WILD-TYPE  182   11
   clus
vv  CASP8 MUTATED CASP8 WILD-TYPE
  0             7             182
  1             0              11
[1] 2 2
[1] FALSE
D69V7, binary
                 cls
clus                0   1
  CASP8 MUTATED     3  11
  CASP8 WILD-TYPE  99 282
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      3   11
  CASP8 WILD-TYPE   99  282
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  FEMALE             3              99
  MALE              11             282
[1] 2 2
[1] FALSE
D69V8, binary
                 cls
clus                0   1
  CASP8 MUTATED    11   0
  CASP8 WILD-TYPE 339  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     11    0
  CASP8 WILD-TYPE  339   20
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO             11             339
  YES             0              20
[1] 2 2
[1] FALSE
D69V9, continuous
D69V10, continuous
D69V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CASP8 MUTATED       1                         1    11
  CASP8 WILD-TYPE    38                        21   306
D69V12, multiclass
                           clus
vv                          CASP8 MUTATED CASP8 WILD-TYPE
  ASIAN                                 1              38
  BLACK OR AFRICAN AMERICAN             1              21
  WHITE                                11             306
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V13, binary
                 cls
clus                0   1
  CASP8 MUTATED     0  13
  CASP8 WILD-TYPE   8 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      0   13
  CASP8 WILD-TYPE    8  342
                        clus
vv                       CASP8 MUTATED CASP8 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            13             342
[1] 2 2
[1] FALSE

Clustering(70) Variable = DAZAP1 MUTATION ANALYSIS
D70V1, survival
                  sevent
clus2                0   1
  DAZAP1 MUTATED     4   2
  DAZAP1 WILD-TYPE 213 173
  DAZAP1 MUTATED DAZAP1 WILD-TYPE 
               6              386 
  DAZAP1 MUTATED DAZAP1 WILD-TYPE 
               2              173 
$`DAZAP1 MUTATED`
TCGA-DK-A3IS TCGA-DK-A6B6 TCGA-ZF-A9R4 TCGA-E5-A4U1 TCGA-FJ-A3Z9 TCGA-XF-A9SX 
       50.27        36.66        30.28        38.83        12.66        23.64 

$`DAZAP1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
      130.88        46.68        87.32         8.22        17.72        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M 
       76.60        67.36        15.68        50.70        38.24        52.01 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
      165.73       166.03        13.64        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       33.01        17.62        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       24.92        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        3.45         2.76         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       35.97        46.98        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       51.32         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
        7.63        71.57        91.73        98.99        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       61.45        86.30        18.58         3.88         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       21.11        94.29         3.48        88.87        34.06        19.69 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       57.90        12.23        24.13        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       50.04         0.62        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       16.18         4.67        17.56        36.43        28.41         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
        2.93        23.01        12.79        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.87        13.08         5.19        29.79         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       66.41        18.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       17.95         7.79       142.78         4.80        13.58         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 
       19.00        15.35        12.03        43.59        29.72         5.36 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
       22.16         2.24        16.70         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN 
       26.24         4.24        24.03        24.66        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       12.62        22.52        27.98         5.52        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       14.96        20.91        19.33         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-FJ-A871 
        7.10        13.35         2.27        10.85        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25        22.88        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       59.31         7.23        20.12        66.02         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 
       20.71        15.81        15.91        14.07         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       26.70         2.10         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       18.97         7.63        20.05        15.78         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
       14.27        21.34        19.10         8.48        36.49         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
       19.40        38.60        64.01        12.16        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70        17.72         1.81        15.42        16.27        11.80 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       44.38         1.15        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        69.34        35.24        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        3.85         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
       66.41         5.98        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32         6.77        56.48        27.06        75.39 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       21.86        28.41        13.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       20.22         2.89         8.61        59.38        60.16        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        19.40         8.52        54.21        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  DAZAP1 MUTATED DAZAP1 WILD-TYPE 
           12.66             0.56 
  DAZAP1 MUTATED DAZAP1 WILD-TYPE 
           50.27           166.03 
  DAZAP1 MUTATED DAZAP1 WILD-TYPE 
           33.47            17.59 
[1] "12.7 - 50.3 (33.5)" "0.6 - 166.0 (17.6)"
[1] "hr=" "1.9"
D70V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  DAZAP1 MUTATED         0        4         0        1
  DAZAP1 WILD-TYPE       2      118       135      133
D70V3, multiclass
           clus
vv          DAZAP1 MUTATED DAZAP1 WILD-TYPE
  STAGE I                0                2
  STAGE II               4              118
  STAGE III              0              135
  STAGE IV               1              133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  DAZAP1 MUTATED          3   1   0
  DAZAP1 WILD-TYPE      113 189  57
D70V4, multiclass
          clus
vv         DAZAP1 MUTATED DAZAP1 WILD-TYPE
  T0+T1+T2              3              113
  T3                    1              189
  T4                    0               57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  DAZAP1 MUTATED     3   0   1   0
  DAZAP1 WILD-TYPE 222  46  74   8
D70V5, multiclass
    clus
vv   DAZAP1 MUTATED DAZAP1 WILD-TYPE
  N0              3              222
  N1              0               46
  N2              1               74
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                  cls
clus                 0   1
  DAZAP1 MUTATED     4   0
  DAZAP1 WILD-TYPE 185  11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DAZAP1 MUTATED      4    0
  DAZAP1 WILD-TYPE  185   11
   clus
vv  DAZAP1 MUTATED DAZAP1 WILD-TYPE
  0              4              185
  1              0               11
[1] 2 2
[1] FALSE
D70V7, binary
                  cls
clus                 0   1
  DAZAP1 MUTATED     1   5
  DAZAP1 WILD-TYPE 101 288
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DAZAP1 MUTATED      1    5
  DAZAP1 WILD-TYPE  101  288
        clus
vv       DAZAP1 MUTATED DAZAP1 WILD-TYPE
  FEMALE              1              101
  MALE                5              288
[1] 2 2
[1] FALSE
D70V8, binary
                  cls
clus                 0   1
  DAZAP1 MUTATED     6   0
  DAZAP1 WILD-TYPE 344  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DAZAP1 MUTATED      6    0
  DAZAP1 WILD-TYPE  344   20
     clus
vv    DAZAP1 MUTATED DAZAP1 WILD-TYPE
  NO               6              344
  YES              0               20
[1] 2 2
[1] FALSE
D70V9, continuous
D70V10, continuous
D70V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DAZAP1 MUTATED       0                         0     5
  DAZAP1 WILD-TYPE    39                        22   312
D70V12, multiclass
                           clus
vv                          DAZAP1 MUTATED DAZAP1 WILD-TYPE
  ASIAN                                  0               39
  BLACK OR AFRICAN AMERICAN              0               22
  WHITE                                  5              312
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V13, binary
                  cls
clus                 0   1
  DAZAP1 MUTATED     0   6
  DAZAP1 WILD-TYPE   8 349
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DAZAP1 MUTATED      0    6
  DAZAP1 WILD-TYPE    8  349
                        clus
vv                       DAZAP1 MUTATED DAZAP1 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO              6              349
[1] 2 2
[1] FALSE

Clustering(71) Variable = USP28 MUTATION ANALYSIS
D71V1, survival
                 sevent
clus2               0   1
  USP28 MUTATED     8   5
  USP28 WILD-TYPE 209 170
  USP28 MUTATED USP28 WILD-TYPE 
             13             379 
  USP28 MUTATED USP28 WILD-TYPE 
              5             170 
$`USP28 MUTATED`
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-GV-A3JZ TCGA-XF-AAN2 TCGA-ZF-A9R4 TCGA-2F-A9KO 
       13.64        56.15        19.82        61.45        30.28        24.13 
TCGA-4Z-AA7O TCGA-BT-A0YX TCGA-FD-A6TF TCGA-GV-A3JX TCGA-GV-A3QI TCGA-SY-A9G5 
       16.83        13.15         2.27        19.10        36.49        38.99 
TCGA-UY-A78M 
       22.68 

$`USP28 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      130.88        46.68        87.32         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       21.30        23.21         9.67        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       53.29        76.60        67.36        15.68        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA75 
       38.24        52.01       165.73       166.03        13.64        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       33.01        17.62        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A3QK 
       24.92        10.92        32.78        32.98        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        8.58        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       46.98        14.24         1.84        33.14        86.83        51.32 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
        3.22        15.98        34.45        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.10        13.74        10.82        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 
       71.57        91.73        98.99        44.32        30.94        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC 
       18.58         3.88         9.63        13.64        21.11        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.48        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7R 
       11.97        94.88       104.65         8.35        44.94        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       34.98        27.62        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       66.54        10.22        47.80         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O 
        7.33         2.66         6.74         6.58        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       17.88        19.50         5.06        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       17.16        16.18         4.67        17.56        36.43        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        1.94         2.93        23.01        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.10        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
        8.15        20.81        10.55       163.30        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       18.81        19.00        15.35        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        22.16         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 
       27.45         2.70         7.10        13.35        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65         8.94         3.25        22.88        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       15.95        26.93        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        29.36        20.71        15.81        15.91        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91        26.70         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        2.20        11.31        18.97         7.63        20.05        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-H4-A2HO 
        4.73         7.00        14.27        21.34         8.48         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
       19.40        38.60        64.01        12.16        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70        17.72         1.81        15.42        16.27        11.80 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       44.38         1.15        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A8OB 
       16.67        16.54        17.62        37.05        76.01        69.34 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       35.24        29.56        17.82         6.21         3.85         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
       17.88        48.62        64.80        79.66        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT 
       23.64        28.24        16.27        92.98       110.60         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC 
        8.32         6.77        56.48        27.06        75.39         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       11.97        22.36        25.41        31.20        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       28.41        13.41        64.08        58.72        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
        2.89         8.61        59.38        60.16        67.20        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        19.40         8.52        54.21        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  USP28 MUTATED USP28 WILD-TYPE 
           2.27            0.56 
  USP28 MUTATED USP28 WILD-TYPE 
          61.45          166.03 
  USP28 MUTATED USP28 WILD-TYPE 
          22.68           17.56 
[1] "2.3 - 61.5 (22.7)"  "0.6 - 166.0 (17.6)"
[1] "hr=" "1.4"
D71V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  USP28 MUTATED         0        4         5        4
  USP28 WILD-TYPE       2      118       130      130
D71V3, multiclass
           clus
vv          USP28 MUTATED USP28 WILD-TYPE
  STAGE I               0               2
  STAGE II              4             118
  STAGE III             5             130
  STAGE IV              4             130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  USP28 MUTATED          5   6   2
  USP28 WILD-TYPE      111 184  55
D71V4, multiclass
          clus
vv         USP28 MUTATED USP28 WILD-TYPE
  T0+T1+T2             5             111
  T3                   6             184
  T4                   2              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  USP28 MUTATED     8   1   2   1
  USP28 WILD-TYPE 217  45  73   7
D71V5, multiclass
    clus
vv   USP28 MUTATED USP28 WILD-TYPE
  N0             8             217
  N1             1              45
  N2             2              73
  N3             1               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"
D71V6, binary
                 cls
clus                0   1
  USP28 MUTATED     7   1
  USP28 WILD-TYPE 182  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      7    1
  USP28 WILD-TYPE  182   10
   clus
vv  USP28 MUTATED USP28 WILD-TYPE
  0             7             182
  1             1              10
[1] 2 2
[1] FALSE
D71V7, binary
                 cls
clus                0   1
  USP28 MUTATED     3  10
  USP28 WILD-TYPE  99 283
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      3   10
  USP28 WILD-TYPE   99  283
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  FEMALE             3              99
  MALE              10             283
[1] 2 2
[1] FALSE
D71V8, binary
                 cls
clus                0   1
  USP28 MUTATED    12   0
  USP28 WILD-TYPE 338  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED     12    0
  USP28 WILD-TYPE  338   20
     clus
vv    USP28 MUTATED USP28 WILD-TYPE
  NO             12             338
  YES             0              20
[1] 2 2
[1] FALSE
D71V9, continuous
D71V10, continuous
D71V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  USP28 MUTATED       1                         1    11
  USP28 WILD-TYPE    38                        21   306
D71V12, multiclass
                           clus
vv                          USP28 MUTATED USP28 WILD-TYPE
  ASIAN                                 1              38
  BLACK OR AFRICAN AMERICAN             1              21
  WHITE                                11             306
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V13, binary
                 cls
clus                0   1
  USP28 MUTATED     0  12
  USP28 WILD-TYPE   8 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      0   12
  USP28 WILD-TYPE    8  343
                        clus
vv                       USP28 MUTATED USP28 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            12             343
[1] 2 2
[1] FALSE

Clustering(72) Variable = SETD2 MUTATION ANALYSIS
D72V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED    14  13
  SETD2 WILD-TYPE 203 162
  SETD2 MUTATED SETD2 WILD-TYPE 
             27             365 
  SETD2 MUTATED SETD2 WILD-TYPE 
             13             162 
$`SETD2 MUTATED`
TCGA-4Z-AA84 TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A2I6 TCGA-DK-A3IU TCGA-DK-A6AW 
       15.12         2.14        16.70        87.32        23.21        53.29 
TCGA-DK-A6B6 TCGA-FD-A5C0 TCGA-G2-A3VY TCGA-XF-A9ST TCGA-XF-A9T8 TCGA-XF-AAML 
       36.66        18.08        17.62         4.21        13.74         7.63 
TCGA-ZF-A9RC TCGA-4Z-AA7R TCGA-4Z-AA86 TCGA-BT-A20R TCGA-CF-A1HR TCGA-DK-A1A3 
       94.29        17.16        10.22         5.06        12.79        21.86 
TCGA-DK-A1A7 TCGA-E7-A7XN TCGA-K4-A6MB TCGA-SY-A9G5 TCGA-UY-A9PF TCGA-ZF-A9R7 
       18.41        14.07        15.42        38.99         3.85        21.86 
TCGA-ZF-A9RD TCGA-ZF-AA4X TCGA-ZF-AA56 
       13.41        67.20         8.52 

$`SETD2 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        16.77        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IN 
       18.48        13.58        19.00       130.88        46.68         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
       17.72        50.27        21.30         9.67        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       64.18        76.60        67.36        15.68        50.70        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       29.16        46.78        19.79        12.85        27.35         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 
       26.73        53.88        10.78         5.69         8.25        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       33.01        70.32        21.40        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       10.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        8.58        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       46.98        14.24         1.84        33.14        86.83        51.32 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SW 
        3.22        15.98        34.45        14.93        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       10.82        11.31        54.90        71.57        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 
       44.32        30.94        61.45        86.30        18.58         3.88 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RE TCGA-ZF-A9RL 
        9.63        13.64        21.11        30.28         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       34.06        19.69        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S 
       94.88       104.65         8.35        44.94        16.83        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       19.50        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 
        4.67        17.56        36.43        28.41         1.94         2.93 
TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       23.01        12.56        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       12.16        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A1AE 
        5.19        29.79         1.84        66.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P 
       13.58         8.15        20.81        10.55       163.30        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       13.58        18.81        19.00        15.35        12.03        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         5.36        22.16         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
        0.56         0.66        26.96        26.24         4.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       24.66        13.68        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
       12.66        10.65         8.94         3.25        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       48.00        15.95        26.93        59.31         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       66.02         6.94        29.36        20.71        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07         8.94        13.91        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
       20.98         2.20        11.31        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       15.78         4.73         7.00        14.27        21.34        19.10 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.48        36.49         1.51        19.40        38.60        64.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       12.16        21.24         9.07        11.70        17.72         1.81 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       16.27        11.80        44.38         1.15        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L 
       13.48        12.23        16.67        16.54        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       22.68        76.01        69.34        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        6.21         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 
      110.60         2.96         8.32         6.77        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       75.39         0.66        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       35.84        28.41        64.08        58.72        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 
        2.89         8.61        59.38        60.16        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40        54.21        29.49         5.52        10.65 

  SETD2 MUTATED SETD2 WILD-TYPE 
           2.14            0.56 
  SETD2 MUTATED SETD2 WILD-TYPE 
          94.29          166.03 
  SETD2 MUTATED SETD2 WILD-TYPE 
          16.70           17.72 
[1] "2.1 - 94.3 (16.7)"  "0.6 - 166.0 (17.7)"
[1] "hr=" "1.2"
D72V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SETD2 MUTATED         0        8         7       12
  SETD2 WILD-TYPE       2      114       128      122
D72V3, multiclass
           clus
vv          SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I               0               2
  STAGE II              8             114
  STAGE III             7             128
  STAGE IV             12             122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  SETD2 MUTATED          6  14   4
  SETD2 WILD-TYPE      110 176  53
D72V4, multiclass
          clus
vv         SETD2 MUTATED SETD2 WILD-TYPE
  T0+T1+T2             6             110
  T3                  14             176
  T4                   4              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SETD2 MUTATED    12   4   7   0
  SETD2 WILD-TYPE 213  42  68   8
D72V5, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  N0            12             213
  N1             4              42
  N2             7              68
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                 cls
clus                0   1
  SETD2 MUTATED    15   1
  SETD2 WILD-TYPE 174  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     15    1
  SETD2 WILD-TYPE  174   10
   clus
vv  SETD2 MUTATED SETD2 WILD-TYPE
  0            15             174
  1             1              10
[1] 2 2
[1] FALSE
D72V7, binary
                 cls
clus                0   1
  SETD2 MUTATED     6  21
  SETD2 WILD-TYPE  96 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      6   21
  SETD2 WILD-TYPE   96  272
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE             6              96
  MALE              21             272
[1] 2 2
[1] FALSE
D72V8, binary
                 cls
clus                0   1
  SETD2 MUTATED    24   1
  SETD2 WILD-TYPE 326  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     24    1
  SETD2 WILD-TYPE  326   19
     clus
vv    SETD2 MUTATED SETD2 WILD-TYPE
  NO             24             326
  YES             1              19
[1] 2 2
[1] FALSE
D72V9, continuous
D72V10, continuous
D72V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SETD2 MUTATED       3                         2    22
  SETD2 WILD-TYPE    36                        20   295
D72V12, multiclass
                           clus
vv                          SETD2 MUTATED SETD2 WILD-TYPE
  ASIAN                                 3              36
  BLACK OR AFRICAN AMERICAN             2              20
  WHITE                                22             295
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V13, binary
                 cls
clus                0   1
  SETD2 MUTATED     0  24
  SETD2 WILD-TYPE   8 331
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      0   24
  SETD2 WILD-TYPE    8  331
                        clus
vv                       SETD2 MUTATED SETD2 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            24             331
[1] 2 2
[1] FALSE

Clustering(73) Variable = EME1 MUTATION ANALYSIS
D73V1, survival
                sevent
clus2              0   1
  EME1 MUTATED     3   2
  EME1 WILD-TYPE 214 173
  EME1 MUTATED EME1 WILD-TYPE 
             5            387 
  EME1 MUTATED EME1 WILD-TYPE 
             2            173 
$`EME1 MUTATED`
TCGA-2F-A9KT TCGA-DK-AA74 TCGA-S5-A6DX TCGA-G2-A3IB TCGA-ZF-A9R7 
      108.95        56.15         1.84         7.23        21.86 

$`EME1 WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
       16.27        16.77        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA75 
       52.01       165.73       166.03        13.64        13.64        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       33.01        17.62        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       24.92        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        3.45         2.76         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       35.97        46.98        14.24        33.14        86.83        51.32 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
        3.22        15.98        34.45        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.10        13.74        10.82        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       86.30        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       30.28        94.29         3.48        88.87        34.06        19.69 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       57.90        12.23        24.13        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       50.04         0.62        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       16.18         4.67        17.56        36.43        28.41         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
        2.93        23.01        12.79        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.87        13.08         5.19        29.79         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       66.41        18.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       17.95         7.79       142.78         4.80        13.58         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       19.00        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        22.16         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
       26.96        26.24         4.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.70         7.10        13.35         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65         8.94         3.25        22.88        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       15.95        26.93        59.31        20.12        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 
       29.36        20.71        15.81        15.91        14.07         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91        26.70         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31        18.97         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        7.00        14.27        21.34        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       11.80        44.38         1.15        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       12.23        16.67        16.54        38.99        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       22.68        76.01        69.34        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        6.21         3.85         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       79.66        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       31.20        35.84        28.41        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       47.84        20.22         2.89         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       67.20        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

  EME1 MUTATED EME1 WILD-TYPE 
          1.84           0.56 
  EME1 MUTATED EME1 WILD-TYPE 
        108.95         166.03 
  EME1 MUTATED EME1 WILD-TYPE 
         21.86          17.62 
[1] "1.8 - 109.0 (21.9)" "0.6 - 166.0 (17.6)"
[1] "hr=" "1.4"
D73V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  EME1 MUTATED         0        3         1        1
  EME1 WILD-TYPE       2      119       134      133
D73V3, multiclass
           clus
vv          EME1 MUTATED EME1 WILD-TYPE
  STAGE I              0              2
  STAGE II             3            119
  STAGE III            1            134
  STAGE IV             1            133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  EME1 MUTATED          1   1   1
  EME1 WILD-TYPE      115 189  56
D73V4, multiclass
          clus
vv         EME1 MUTATED EME1 WILD-TYPE
  T0+T1+T2            1            115
  T3                  1            189
  T4                  1             56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  EME1 MUTATED     2   0   1   0
  EME1 WILD-TYPE 223  46  74   8
D73V5, multiclass
    clus
vv   EME1 MUTATED EME1 WILD-TYPE
  N0            2            223
  N1            0             46
  N2            1             74
  N3            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                cls
clus               0   1
  EME1 MUTATED     3   0
  EME1 WILD-TYPE 186  11
[1] "tbl2"
                cls
clus             [,1] [,2]
  EME1 MUTATED      3    0
  EME1 WILD-TYPE  186   11
   clus
vv  EME1 MUTATED EME1 WILD-TYPE
  0            3            186
  1            0             11
[1] 2 2
[1] FALSE
D73V7, binary
                cls
clus               0   1
  EME1 MUTATED     1   4
  EME1 WILD-TYPE 101 289
[1] "tbl2"
                cls
clus             [,1] [,2]
  EME1 MUTATED      1    4
  EME1 WILD-TYPE  101  289
        clus
vv       EME1 MUTATED EME1 WILD-TYPE
  FEMALE            1            101
  MALE              4            289
[1] 2 2
[1] FALSE
D73V8, binary
                cls
clus               0   1
  EME1 MUTATED     5   0
  EME1 WILD-TYPE 345  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  EME1 MUTATED      5    0
  EME1 WILD-TYPE  345   20
     clus
vv    EME1 MUTATED EME1 WILD-TYPE
  NO             5            345
  YES            0             20
[1] 2 2
[1] FALSE
D73V9, continuous
[1] "Remove cluster labels:" "EME1 MUTATED"          
clus
  EME1 MUTATED EME1 WILD-TYPE 
             2            128 
    TCGA-DK-A2HX     TCGA-DK-A3IN     TCGA-DK-A3IV     TCGA-DK-A3X2 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-A6B2     TCGA-DK-A6B5     TCGA-DK-A6B6     TCGA-DK-AA6M 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-AA6R     TCGA-DK-AA6S     TCGA-DK-AA6W     TCGA-DK-AA75 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-E5-A4TZ     TCGA-E7-A541     TCGA-E7-A7DU     TCGA-E7-A7DV 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FT-A61P     TCGA-G2-A2ES     TCGA-G2-A3VY     TCGA-GC-A3BM 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GC-A3YS     TCGA-GV-A3JZ     TCGA-GV-A3QF     TCGA-GV-A3QK 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GV-A40E     TCGA-GV-A40G     TCGA-GV-A6ZA     TCGA-KQ-A41N 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-SY-A9G0     TCGA-UY-A78N     TCGA-XF-A9SJ     TCGA-XF-A9SK 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-A9SM     TCGA-XF-A9SP     TCGA-XF-A9ST     TCGA-XF-A9SV 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-A9SW     TCGA-XF-A9SY     TCGA-XF-A9T0     TCGA-XF-A9T2 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-A9T3     TCGA-XF-A9T5     TCGA-XF-A9T6     TCGA-XF-A9T8 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-AAMF     TCGA-XF-AAMH     TCGA-XF-AAMJ     TCGA-XF-AAML 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-AAMQ     TCGA-XF-AAMR     TCGA-XF-AAMY     TCGA-XF-AAMZ 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-AAN1     TCGA-XF-AAN2     TCGA-XF-AAN3     TCGA-XF-AAN7 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-AAN8     TCGA-YF-AA3M     TCGA-2F-A9KO     TCGA-2F-A9KP 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-2F-A9KQ     TCGA-2F-A9KR     TCGA-2F-A9KW     TCGA-CF-A1HS 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-CF-A27C     TCGA-CF-A3MF     TCGA-CF-A3MG     TCGA-CF-A3MH 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-CF-A3MI     TCGA-CF-A47S     TCGA-CF-A47T     TCGA-CF-A47V 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-CF-A47W     TCGA-CF-A47X     TCGA-CF-A47Y     TCGA-CF-A5U8 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-CF-A5UA     TCGA-CF-A7I0     TCGA-DK-A3WX     TCGA-DK-AA6P 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-AA6U     TCGA-DK-AA76     TCGA-E5-A2PC     TCGA-E5-A4U1 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-E7-A519     TCGA-E7-A6MD     TCGA-G2-A2EC     TCGA-G2-A2EF 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-G2-A2EJ     TCGA-G2-A2EK     TCGA-G2-A2EL     TCGA-G2-A2EO 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-G2-A3IE     TCGA-GC-A3I6     TCGA-GC-A3OO     TCGA-GC-A3RC 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GC-A3RD     TCGA-GC-A6I1     TCGA-GC-A6I3     TCGA-GD-A3OS 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GD-A6C6     TCGA-GV-A3JV     TCGA-GV-A3JW     TCGA-GV-A3JX 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GV-A3QH     TCGA-GV-A3QI     TCGA-SY-A9G5     TCGA-UY-A78L 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-UY-A78M     TCGA-XF-A8HH     TCGA-XF-A8HI     TCGA-XF-A9SG 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-A9SH     TCGA-XF-A9SI     TCGA-XF-A9SL     TCGA-XF-A9SU 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-A9SX     TCGA-XF-A9SZ     TCGA-XF-A9T4     TCGA-XF-AAME 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-AAMG     TCGA-XF-AAMT     TCGA-XF-AAMW     TCGA-XF-AAMX 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-AAN0     TCGA-XF-AAN4     TCGA-XF-AAN5     TCGA-YF-AA3L 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
D73V10, continuous
[1] "Remove cluster labels:" "EME1 MUTATED"          
clus
  EME1 MUTATED EME1 WILD-TYPE 
             2            213 
    TCGA-4Z-AA7M     TCGA-4Z-AA89     TCGA-BL-A5ZZ     TCGA-BT-A20N 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-BT-A42C     TCGA-C4-A0EZ     TCGA-CU-A0YN     TCGA-CU-A0YR 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-CU-A3KJ     TCGA-CU-A72E     TCGA-DK-A1A5     TCGA-DK-A1AA 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-A1AC     TCGA-DK-A2HX     TCGA-DK-A2I6     TCGA-DK-A3IN 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-A3IQ     TCGA-DK-A3IU     TCGA-DK-A3IV     TCGA-DK-A3X1 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-A3X2     TCGA-DK-A6AV     TCGA-DK-A6AW     TCGA-DK-A6B0 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-A6B2     TCGA-DK-A6B6     TCGA-DK-AA6L     TCGA-DK-AA6R 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-AA75     TCGA-E5-A4TZ     TCGA-FD-A3B6     TCGA-FD-A3B7 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A3NA     TCGA-FD-A3SJ     TCGA-FD-A3SM     TCGA-FD-A3SN 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A3SQ     TCGA-FD-A3SR     TCGA-FD-A3SS     TCGA-FD-A43P 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A43X     TCGA-FD-A5BT     TCGA-FD-A5BX     TCGA-FD-A5C0 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A6TB     TCGA-FD-A6TC     TCGA-FD-A6TE     TCGA-FD-A6TG 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A6TH     TCGA-FJ-A3ZF     TCGA-FT-A61P     TCGA-G2-A2ES 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-G2-AA3D     TCGA-GC-A3BM     TCGA-GC-A3RB     TCGA-GC-A3WC 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GC-A3YS     TCGA-GU-A42P     TCGA-GU-A763     TCGA-GU-AATP 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GV-A3JZ     TCGA-GV-A3QF     TCGA-GV-A3QG     TCGA-GV-A3QK 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GV-A40E     TCGA-GV-A40G     TCGA-HQ-A5ND     TCGA-K4-A3WS 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-KQ-A41N     TCGA-R3-A69X     TCGA-SY-A9G0     TCGA-UY-A78N 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-A9SJ     TCGA-XF-A9SK     TCGA-XF-A9SM     TCGA-XF-A9SP 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-A9ST     TCGA-XF-A9SV     TCGA-XF-A9SY     TCGA-XF-A9T3 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-A9T8     TCGA-XF-AAMF     TCGA-XF-AAMH     TCGA-XF-AAMQ 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-AAN1     TCGA-XF-AAN2     TCGA-XF-AAN7     TCGA-XF-AAN8 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-YF-AA3M     TCGA-ZF-A9R2     TCGA-ZF-A9RL     TCGA-ZF-AA5P 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-2F-A9KO     TCGA-2F-A9KP     TCGA-2F-A9KR     TCGA-5N-A9KI 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-5N-A9KM     TCGA-BL-A0C8     TCGA-BL-A13I     TCGA-BL-A13J 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-BL-A3JM     TCGA-BT-A20J     TCGA-BT-A2LA     TCGA-BT-A42B 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-BT-A42E     TCGA-C4-A0F0     TCGA-C4-A0F1     TCGA-C4-A0F6 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-CF-A3MH     TCGA-CF-A3MI     TCGA-CF-A47W     TCGA-CF-A47X 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-CF-A5UA     TCGA-CF-A9FH     TCGA-CU-A3QU     TCGA-CU-A3YL 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-CU-A5W6     TCGA-DK-A1A3     TCGA-DK-A1A6     TCGA-DK-A1AE 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-A3IL     TCGA-DK-A3IM     TCGA-DK-A3WX     TCGA-DK-AA6P 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-AA6T     TCGA-DK-AA6U     TCGA-DK-AA76     TCGA-E7-A4XJ 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-E7-A519     TCGA-E7-A5KF     TCGA-E7-A678     TCGA-E7-A6ME 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-E7-A6MF     TCGA-E7-A7PW     TCGA-E7-A7XN     TCGA-E7-A85H 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-E7-A97Q     TCGA-FD-A3B3     TCGA-FD-A3B4     TCGA-FD-A3B5 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A3B8     TCGA-FD-A3N5     TCGA-FD-A3N6     TCGA-FD-A3SO 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A3SP     TCGA-FD-A43N     TCGA-FD-A43S     TCGA-FD-A43U 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A5BU     TCGA-FD-A5BV     TCGA-FD-A62N     TCGA-FD-A6TK 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FJ-A3Z9     TCGA-FJ-A3ZE     TCGA-FJ-A871     TCGA-G2-A2EF 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-G2-A2EJ     TCGA-G2-A2EL     TCGA-G2-A3IE     TCGA-G2-AA3B 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-G2-AA3C     TCGA-G2-AA3F     TCGA-GD-A2C5     TCGA-GD-A3OQ 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GD-A3OS     TCGA-GD-A6C6     TCGA-GU-A42Q     TCGA-GU-A42R 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GU-A764     TCGA-GU-AATQ     TCGA-GV-A3JV     TCGA-GV-A3JX 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GV-A3QH     TCGA-GV-A3QI     TCGA-H4-A2HO     TCGA-H4-A2HQ 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-HQ-A5NE     TCGA-K4-A3WV     TCGA-K4-A5RH     TCGA-K4-A5RI 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-K4-A83P     TCGA-K4-AAQO     TCGA-KQ-A41R     TCGA-PQ-A6FI 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-PQ-A6FN     TCGA-UY-A8OB     TCGA-UY-A9PB     TCGA-UY-A9PE 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-UY-A9PF     TCGA-XF-A9SL     TCGA-XF-A9SU     TCGA-XF-A9SX 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-A9SZ     TCGA-XF-AAMT     TCGA-XF-AAN0     TCGA-XF-AAN4 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-AAN5     TCGA-YF-AA3L     TCGA-ZF-A9R0     TCGA-ZF-A9R3 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-ZF-A9R5     TCGA-ZF-A9R9     TCGA-ZF-A9RD     TCGA-ZF-A9RF 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-ZF-A9RM     TCGA-ZF-AA4U     TCGA-ZF-AA4V     TCGA-ZF-AA51 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-ZF-AA52     TCGA-ZF-AA58     TCGA-ZF-AA5H     TCGA-ZF-AA5N 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GU-AATO 
"EME1 WILD-TYPE" 
D73V11, continuous
[1] "Remove cluster labels:" "EME1 MUTATED"          
clus
  EME1 MUTATED EME1 WILD-TYPE 
             2            286 
    TCGA-4Z-AA84     TCGA-4Z-AA89     TCGA-BT-A20N     TCGA-BT-A20T 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-BT-A20W     TCGA-BT-A2LD     TCGA-BT-A3PJ     TCGA-BT-A3PK 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-BT-A42C     TCGA-CU-A0YN     TCGA-CU-A0YO     TCGA-CU-A0YR 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-CU-A3KJ     TCGA-CU-A72E     TCGA-DK-A1A5     TCGA-DK-A1AA 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-A1AB     TCGA-DK-A1AC     TCGA-DK-A2HX     TCGA-DK-A2I6 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-A3IN     TCGA-DK-A3IQ     TCGA-DK-A3IS     TCGA-DK-A3IT 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-A3IU     TCGA-DK-A3X1     TCGA-DK-A3X2     TCGA-DK-A6AV 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-A6AW     TCGA-DK-A6B0     TCGA-DK-A6B1     TCGA-DK-A6B2 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-A6B5     TCGA-DK-AA6L     TCGA-DK-AA6R     TCGA-DK-AA6S 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-AA71     TCGA-DK-AA77     TCGA-E5-A4TZ     TCGA-E7-A541 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-E7-A7DU     TCGA-E7-A7DV     TCGA-FD-A3B6     TCGA-FD-A3B7 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A3NA     TCGA-FD-A3SJ     TCGA-FD-A3SL     TCGA-FD-A3SM 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A3SN     TCGA-FD-A3SQ     TCGA-FD-A3SR     TCGA-FD-A3SS 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A43P     TCGA-FD-A43X     TCGA-FD-A5BR     TCGA-FD-A5BS 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A5BT     TCGA-FD-A5BX     TCGA-FD-A5BY     TCGA-FD-A5C0 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A5C1     TCGA-FD-A62P     TCGA-FD-A6TA     TCGA-FD-A6TB 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A6TC     TCGA-FD-A6TD     TCGA-FD-A6TE     TCGA-FD-A6TG 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A6TH     TCGA-FD-A6TI     TCGA-FJ-A3Z7     TCGA-FT-A61P 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-G2-AA3D     TCGA-GC-A3BM     TCGA-GC-A3RB     TCGA-GC-A3WC 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GC-A3YS     TCGA-GU-A42P     TCGA-GU-A763     TCGA-GU-AATP 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GV-A3JZ     TCGA-GV-A3QF     TCGA-GV-A3QG     TCGA-GV-A3QK 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GV-A40G     TCGA-HQ-A5ND     TCGA-K4-A3WS     TCGA-K4-A4AB 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-K4-A4AC     TCGA-K4-A54R     TCGA-KQ-A41N     TCGA-KQ-A41O 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-KQ-A41P     TCGA-KQ-A41Q     TCGA-R3-A69X     TCGA-SY-A9G0 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-UY-A78N     TCGA-XF-A9SJ     TCGA-XF-A9SK     TCGA-XF-A9SM 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-A9SP     TCGA-XF-A9ST     TCGA-XF-A9SV     TCGA-XF-A9SW 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-A9SY     TCGA-XF-A9T0     TCGA-XF-A9T2     TCGA-XF-A9T3 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-A9T5     TCGA-XF-A9T6     TCGA-XF-A9T8     TCGA-XF-AAMF 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-AAMH     TCGA-XF-AAMJ     TCGA-XF-AAML     TCGA-XF-AAMQ 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-AAMR     TCGA-XF-AAMY     TCGA-XF-AAMZ     TCGA-XF-AAN1 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-AAN2     TCGA-XF-AAN3     TCGA-XF-AAN7     TCGA-XF-AAN8 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-YC-A8S6     TCGA-ZF-A9R2     TCGA-ZF-A9RC     TCGA-ZF-AA4R 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-ZF-AA4T     TCGA-ZF-AA5P     TCGA-2F-A9KO     TCGA-2F-A9KP 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-2F-A9KQ     TCGA-2F-A9KR     TCGA-2F-A9KW     TCGA-4Z-AA7N 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-4Z-AA7O     TCGA-4Z-AA7R     TCGA-4Z-AA7S     TCGA-4Z-AA7W 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-4Z-AA7Y     TCGA-4Z-AA80     TCGA-4Z-AA81     TCGA-4Z-AA82 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-4Z-AA86     TCGA-4Z-AA87     TCGA-5N-A9KM     TCGA-BL-A0C8 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-BL-A13I     TCGA-BL-A13J     TCGA-BL-A3JM     TCGA-BT-A0S7 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-BT-A0YX     TCGA-BT-A20J     TCGA-BT-A20O     TCGA-BT-A20P 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-BT-A20Q     TCGA-BT-A20V     TCGA-BT-A20X     TCGA-BT-A2LA 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-BT-A2LB     TCGA-BT-A3PH     TCGA-BT-A42B     TCGA-BT-A42E 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-BT-A42F     TCGA-CU-A3QU     TCGA-CU-A3YL     TCGA-CU-A5W6 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-A1A3     TCGA-DK-A1A6     TCGA-DK-A1A7     TCGA-DK-A1AD 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-A1AE     TCGA-DK-A1AF     TCGA-DK-A1AG     TCGA-DK-A2I1 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-A2I2     TCGA-DK-A2I4     TCGA-DK-A3IK     TCGA-DK-A3IL 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-A3IM     TCGA-DK-A3WW     TCGA-DK-A3WX     TCGA-DK-A3WY 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-DK-AA6Q     TCGA-E5-A2PC     TCGA-E5-A4U1     TCGA-E7-A6MD 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-E7-A85H     TCGA-E7-A97Q     TCGA-FD-A3B3     TCGA-FD-A3B4 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A3B5     TCGA-FD-A3B8     TCGA-FD-A3N5     TCGA-FD-A3N6 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A3SO     TCGA-FD-A3SP     TCGA-FD-A43N     TCGA-FD-A43S 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A43U     TCGA-FD-A5BU     TCGA-FD-A5BV     TCGA-FD-A5BZ 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A62N     TCGA-FD-A62O     TCGA-FD-A62S     TCGA-FD-A6TF 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-FD-A6TK     TCGA-FJ-A3Z9     TCGA-FT-A3EE     TCGA-G2-AA3B 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-G2-AA3C     TCGA-G2-AA3F     TCGA-GC-A3I6     TCGA-GC-A3OO 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GC-A3RC     TCGA-GC-A3RD     TCGA-GC-A6I1     TCGA-GC-A6I3 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GD-A2C5     TCGA-GD-A3OP     TCGA-GD-A3OQ     TCGA-GD-A6C6 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GD-A76B     TCGA-GU-A42Q     TCGA-GU-A42R     TCGA-GU-A762 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GU-A764     TCGA-GU-A766     TCGA-GU-A767     TCGA-GU-AATQ 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-GV-A3JV     TCGA-GV-A3JX     TCGA-GV-A3QI     TCGA-H4-A2HO 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-HQ-A2OF     TCGA-HQ-A5NE     TCGA-K4-A3WV     TCGA-K4-A5RH 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-K4-A5RI     TCGA-K4-A5RJ     TCGA-K4-A6FZ     TCGA-K4-A6MB 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-K4-A83P     TCGA-KQ-A41R     TCGA-LC-A66R     TCGA-MV-A51V 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-PQ-A6FI     TCGA-PQ-A6FN     TCGA-S5-AA26     TCGA-SY-A9G5 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-UY-A78K     TCGA-UY-A78L     TCGA-UY-A78O     TCGA-XF-A8HH 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-A8HI     TCGA-XF-A9SG     TCGA-XF-A9SH     TCGA-XF-A9SI 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-A9SL     TCGA-XF-A9SU     TCGA-XF-A9SX     TCGA-XF-A9SZ 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-A9T4     TCGA-XF-AAME     TCGA-XF-AAMG     TCGA-XF-AAMT 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-AAMW     TCGA-XF-AAMX     TCGA-XF-AAN0     TCGA-XF-AAN4 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-XF-AAN5     TCGA-YF-AA3L     TCGA-ZF-A9R1     TCGA-ZF-A9R5 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-ZF-A9R9     TCGA-ZF-A9RD     TCGA-ZF-A9RG     TCGA-ZF-A9RM 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-ZF-AA4V     TCGA-ZF-AA4W     TCGA-ZF-AA56     TCGA-ZF-AA58 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" "EME1 WILD-TYPE" 
    TCGA-ZF-AA5H     TCGA-GU-AATO 
"EME1 WILD-TYPE" "EME1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EME1 MUTATED       0                         1     4
  EME1 WILD-TYPE    39                        21   313
D73V12, multiclass
                           clus
vv                          EME1 MUTATED EME1 WILD-TYPE
  ASIAN                                0             39
  BLACK OR AFRICAN AMERICAN            1             21
  WHITE                                4            313
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V13, binary
                cls
clus               0   1
  EME1 MUTATED     0   5
  EME1 WILD-TYPE   8 350
[1] "tbl2"
                cls
clus             [,1] [,2]
  EME1 MUTATED      0    5
  EME1 WILD-TYPE    8  350
                        clus
vv                       EME1 MUTATED EME1 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO            5            350
[1] 2 2
[1] FALSE

Clustering(74) Variable = ADC MUTATION ANALYSIS
D74V1, survival
               sevent
clus2             0   1
  ADC MUTATED     3   2
  ADC WILD-TYPE 214 173
  ADC MUTATED ADC WILD-TYPE 
            5           387 
  ADC MUTATED ADC WILD-TYPE 
            2           173 
$`ADC MUTATED`
TCGA-2F-A9KT TCGA-XF-A9SW TCGA-4Z-AA87 TCGA-G2-A3IE TCGA-ZF-A9R7 
      108.95        11.90        47.80        20.12        21.86 

$`ADC WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
       16.27        16.77        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       29.16        46.78        19.79        12.85        27.35         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.36         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       11.08        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       17.75        24.92        10.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       20.28        27.35         8.58        19.07        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
       25.02         3.45         2.76         9.14        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       50.56        35.97        46.98        14.24         1.84        33.14 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       86.83        51.32         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
        4.21        12.76        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
        7.63        71.57        91.73        98.99        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       61.45        86.30        18.58         3.88         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
       21.11        30.28        94.29         3.48        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       19.69        57.90        12.23        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65         8.35        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       16.18         4.67        17.56        36.43        28.41         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
        2.93        23.01        12.79        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.87        13.08         5.19        29.79         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       66.41        18.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       17.95         7.79       142.78         4.80        13.58         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       19.00        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        22.16         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
       26.96        26.24         4.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.70         7.10        13.35         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65         8.94         3.25        22.88        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3B TCGA-G2-AA3C 
       15.95        26.93        59.31         7.23        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 
       29.36        20.71        15.81        15.91        14.07         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91        26.70         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31        18.97         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        7.00        14.27        21.34        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       11.80        44.38         1.15        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       12.23        16.67        16.54        38.99        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       22.68        76.01        69.34        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        6.21         3.85         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       79.66        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       31.20        35.84        28.41        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       47.84        20.22         2.89         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       67.20        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

  ADC MUTATED ADC WILD-TYPE 
        11.90          0.56 
  ADC MUTATED ADC WILD-TYPE 
       108.95        166.03 
  ADC MUTATED ADC WILD-TYPE 
        21.86         17.62 
[1] "11.9 - 109.0 (21.9)" "0.6 - 166.0 (17.6)" 
[1] "hr=" "1.6"
D74V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  ADC MUTATED         0        3         1        1
  ADC WILD-TYPE       2      119       134      133
D74V3, multiclass
           clus
vv          ADC MUTATED ADC WILD-TYPE
  STAGE I             0             2
  STAGE II            3           119
  STAGE III           1           134
  STAGE IV            1           133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1+T2  T3  T4
  ADC MUTATED          1   1   1
  ADC WILD-TYPE      115 189  56
D74V4, multiclass
          clus
vv         ADC MUTATED ADC WILD-TYPE
  T0+T1+T2           1           115
  T3                 1           189
  T4                 1            56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  ADC MUTATED     2   0   1   0
  ADC WILD-TYPE 223  46  74   8
D74V5, multiclass
    clus
vv   ADC MUTATED ADC WILD-TYPE
  N0           2           223
  N1           0            46
  N2           1            74
  N3           0             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
               cls
clus              0   1
  ADC MUTATED     3   0
  ADC WILD-TYPE 186  11
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADC MUTATED      3    0
  ADC WILD-TYPE  186   11
   clus
vv  ADC MUTATED ADC WILD-TYPE
  0           3           186
  1           0            11
[1] 2 2
[1] FALSE
D74V7, binary
               cls
clus              0   1
  ADC MUTATED     1   4
  ADC WILD-TYPE 101 289
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADC MUTATED      1    4
  ADC WILD-TYPE  101  289
        clus
vv       ADC MUTATED ADC WILD-TYPE
  FEMALE           1           101
  MALE             4           289
[1] 2 2
[1] FALSE
D74V8, binary
               cls
clus              0   1
  ADC MUTATED     5   0
  ADC WILD-TYPE 345  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADC MUTATED      5    0
  ADC WILD-TYPE  345   20
     clus
vv    ADC MUTATED ADC WILD-TYPE
  NO            5           345
  YES           0            20
[1] 2 2
[1] FALSE
D74V9, continuous
D74V10, continuous
[1] "Remove cluster labels:" "ADC MUTATED"           
clus
  ADC MUTATED ADC WILD-TYPE 
            1           214 
   TCGA-4Z-AA7M    TCGA-4Z-AA89    TCGA-BL-A5ZZ    TCGA-BT-A20N    TCGA-BT-A42C 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-C4-A0EZ    TCGA-CU-A0YN    TCGA-CU-A0YR    TCGA-CU-A3KJ    TCGA-CU-A72E 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-DK-A1A5    TCGA-DK-A1AA    TCGA-DK-A1AC    TCGA-DK-A2HX    TCGA-DK-A2I6 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-DK-A3IN    TCGA-DK-A3IQ    TCGA-DK-A3IU    TCGA-DK-A3IV    TCGA-DK-A3X1 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-DK-A3X2    TCGA-DK-A6AV    TCGA-DK-A6AW    TCGA-DK-A6B0    TCGA-DK-A6B2 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-DK-A6B6    TCGA-DK-AA6L    TCGA-DK-AA6R    TCGA-DK-AA74    TCGA-DK-AA75 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-E5-A4TZ    TCGA-FD-A3B6    TCGA-FD-A3B7    TCGA-FD-A3NA    TCGA-FD-A3SJ 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-FD-A3SM    TCGA-FD-A3SN    TCGA-FD-A3SQ    TCGA-FD-A3SR    TCGA-FD-A3SS 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-FD-A43P    TCGA-FD-A43X    TCGA-FD-A5BT    TCGA-FD-A5BX    TCGA-FD-A5C0 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-FD-A6TB    TCGA-FD-A6TC    TCGA-FD-A6TE    TCGA-FD-A6TG    TCGA-FD-A6TH 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-FJ-A3ZF    TCGA-FT-A61P    TCGA-G2-A2ES    TCGA-G2-AA3D    TCGA-GC-A3BM 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-GC-A3RB    TCGA-GC-A3WC    TCGA-GC-A3YS    TCGA-GU-A42P    TCGA-GU-A763 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-GU-AATP    TCGA-GV-A3JZ    TCGA-GV-A3QF    TCGA-GV-A3QG    TCGA-GV-A3QK 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-GV-A40E    TCGA-GV-A40G    TCGA-HQ-A5ND    TCGA-K4-A3WS    TCGA-KQ-A41N 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-R3-A69X    TCGA-S5-A6DX    TCGA-SY-A9G0    TCGA-UY-A78N    TCGA-XF-A9SJ 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-XF-A9SK    TCGA-XF-A9SM    TCGA-XF-A9SP    TCGA-XF-A9ST    TCGA-XF-A9SV 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-XF-A9SY    TCGA-XF-A9T3    TCGA-XF-A9T8    TCGA-XF-AAMF    TCGA-XF-AAMH 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-XF-AAMQ    TCGA-XF-AAN1    TCGA-XF-AAN2    TCGA-XF-AAN7    TCGA-XF-AAN8 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-YF-AA3M    TCGA-ZF-A9R2    TCGA-ZF-A9RL    TCGA-ZF-AA5P    TCGA-2F-A9KO 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-2F-A9KP    TCGA-2F-A9KR    TCGA-5N-A9KI    TCGA-5N-A9KM    TCGA-BL-A0C8 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-BL-A13I    TCGA-BL-A13J    TCGA-BL-A3JM    TCGA-BT-A20J    TCGA-BT-A2LA 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-BT-A42B    TCGA-BT-A42E    TCGA-C4-A0F0    TCGA-C4-A0F1    TCGA-C4-A0F6 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-CF-A3MH    TCGA-CF-A3MI    TCGA-CF-A47W    TCGA-CF-A47X    TCGA-CF-A5UA 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-CF-A9FH    TCGA-CU-A3QU    TCGA-CU-A3YL    TCGA-CU-A5W6    TCGA-DK-A1A3 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-DK-A1A6    TCGA-DK-A1AE    TCGA-DK-A3IL    TCGA-DK-A3IM    TCGA-DK-A3WX 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-DK-AA6P    TCGA-DK-AA6T    TCGA-DK-AA6U    TCGA-DK-AA76    TCGA-E7-A4XJ 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-E7-A519    TCGA-E7-A5KF    TCGA-E7-A678    TCGA-E7-A6ME    TCGA-E7-A6MF 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-E7-A7PW    TCGA-E7-A7XN    TCGA-E7-A85H    TCGA-E7-A97Q    TCGA-FD-A3B3 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-FD-A3B4    TCGA-FD-A3B5    TCGA-FD-A3B8    TCGA-FD-A3N5    TCGA-FD-A3N6 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-FD-A3SO    TCGA-FD-A3SP    TCGA-FD-A43N    TCGA-FD-A43S    TCGA-FD-A43U 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-FD-A5BU    TCGA-FD-A5BV    TCGA-FD-A62N    TCGA-FD-A6TK    TCGA-FJ-A3Z9 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-FJ-A3ZE    TCGA-FJ-A871    TCGA-G2-A2EF    TCGA-G2-A2EJ    TCGA-G2-A2EL 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-G2-AA3B    TCGA-G2-AA3C    TCGA-G2-AA3F    TCGA-GD-A2C5    TCGA-GD-A3OQ 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-GD-A3OS    TCGA-GD-A6C6    TCGA-GU-A42Q    TCGA-GU-A42R    TCGA-GU-A764 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-GU-AATQ    TCGA-GV-A3JV    TCGA-GV-A3JX    TCGA-GV-A3QH    TCGA-GV-A3QI 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-H4-A2HO    TCGA-H4-A2HQ    TCGA-HQ-A5NE    TCGA-K4-A3WV    TCGA-K4-A5RH 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-K4-A5RI    TCGA-K4-A83P    TCGA-K4-AAQO    TCGA-KQ-A41R    TCGA-PQ-A6FI 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-PQ-A6FN    TCGA-UY-A8OB    TCGA-UY-A9PB    TCGA-UY-A9PE    TCGA-UY-A9PF 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-XF-A9SL    TCGA-XF-A9SU    TCGA-XF-A9SX    TCGA-XF-A9SZ    TCGA-XF-AAMT 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-XF-AAN0    TCGA-XF-AAN4    TCGA-XF-AAN5    TCGA-YF-AA3L    TCGA-ZF-A9R0 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-ZF-A9R3    TCGA-ZF-A9R5    TCGA-ZF-A9R9    TCGA-ZF-A9RD    TCGA-ZF-A9RF 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-ZF-A9RM    TCGA-ZF-AA4U    TCGA-ZF-AA4V    TCGA-ZF-AA51    TCGA-ZF-AA52 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-ZF-AA58    TCGA-ZF-AA5H    TCGA-ZF-AA5N    TCGA-GU-AATO 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
D74V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ADC MUTATED       0                         1     4
  ADC WILD-TYPE    39                        21   313
D74V12, multiclass
                           clus
vv                          ADC MUTATED ADC WILD-TYPE
  ASIAN                               0            39
  BLACK OR AFRICAN AMERICAN           1            21
  WHITE                               4           313
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V13, binary
               cls
clus              0   1
  ADC MUTATED     0   4
  ADC WILD-TYPE   8 351
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADC MUTATED      0    4
  ADC WILD-TYPE    8  351
                        clus
vv                       ADC MUTATED ADC WILD-TYPE
  HISPANIC OR LATINO               0             8
  NOT HISPANIC OR LATINO           4           351
[1] 2 2
[1] FALSE

Clustering(75) Variable = CNOT3 MUTATION ANALYSIS
D75V1, survival
                 sevent
clus2               0   1
  CNOT3 MUTATED     3   7
  CNOT3 WILD-TYPE 214 168
  CNOT3 MUTATED CNOT3 WILD-TYPE 
             10             382 
  CNOT3 MUTATED CNOT3 WILD-TYPE 
              7             168 
$`CNOT3 MUTATED`
TCGA-DK-A1AC TCGA-FD-A3SM TCGA-S5-A6DX TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-BT-A0YX 
      130.88        17.98         1.84        41.75        10.22        13.15 
TCGA-E7-A7XN TCGA-E7-A97P TCGA-FD-A3SO TCGA-GC-A3RC 
       14.07        14.37         5.52        15.91 

$`CNOT3 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN 
       33.04         4.01        60.66        24.30        23.41        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       33.01        17.62        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       24.92        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        3.45         2.76         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       35.97        46.98        14.24        33.14        86.83        51.32 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
        3.22        15.98        34.45        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.10        13.74        10.82        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       86.30        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       30.28        94.29         3.48        88.87        34.06        19.69 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       57.90        12.23        24.13        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-5N-A9KI 
       50.04         0.62        51.16        66.54        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       17.42        40.08         7.33         2.66         6.74         6.58 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       19.04        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
        5.06         8.25        17.16        16.18         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR 
       36.43        28.41         1.94         2.93        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.56        13.97        12.59        12.13        13.08        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU 
       13.12        12.00        12.10        11.87        13.08         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       29.79         1.84        21.86        66.41        18.41       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       15.02        13.58        18.81        19.00        15.35        12.03 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        38.83        29.72         5.36        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 
       24.03        24.66        13.68        12.95         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SP 
       16.77         8.94        12.62        22.52        27.98        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.70         7.10        13.35         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65         8.94         3.25        22.88        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       15.95        26.93        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A6I1 
        6.94        29.36        20.71        15.81        14.07         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91        26.70         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31        18.97         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        7.00        14.27        21.34        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       11.80        44.38         1.15        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       12.23        16.67        16.54        38.99        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       22.68        76.01        69.34        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        6.21         3.85         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       79.66        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       58.72        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        67.20        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  CNOT3 MUTATED CNOT3 WILD-TYPE 
           1.84            0.56 
  CNOT3 MUTATED CNOT3 WILD-TYPE 
         130.88          166.03 
  CNOT3 MUTATED CNOT3 WILD-TYPE 
          14.22           17.72 
[1] "1.8 - 130.9 (14.2)" "0.6 - 166.0 (17.7)"
[1] "hr=" "1.8"
D75V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  CNOT3 MUTATED         0        3         3        4
  CNOT3 WILD-TYPE       2      119       132      130
D75V3, multiclass
           clus
vv          CNOT3 MUTATED CNOT3 WILD-TYPE
  STAGE I               0               2
  STAGE II              3             119
  STAGE III             3             132
  STAGE IV              4             130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  CNOT3 MUTATED          3   6   1
  CNOT3 WILD-TYPE      113 184  56
D75V4, multiclass
          clus
vv         CNOT3 MUTATED CNOT3 WILD-TYPE
  T0+T1+T2             3             113
  T3                   6             184
  T4                   1              56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CNOT3 MUTATED     5   2   2   0
  CNOT3 WILD-TYPE 220  44  73   8
D75V5, multiclass
    clus
vv   CNOT3 MUTATED CNOT3 WILD-TYPE
  N0             5             220
  N1             2              44
  N2             2              73
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                 cls
clus                0   1
  CNOT3 MUTATED     7   1
  CNOT3 WILD-TYPE 182  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT3 MUTATED      7    1
  CNOT3 WILD-TYPE  182   10
   clus
vv  CNOT3 MUTATED CNOT3 WILD-TYPE
  0             7             182
  1             1              10
[1] 2 2
[1] FALSE
D75V7, binary
                 cls
clus                0   1
  CNOT3 MUTATED     1   9
  CNOT3 WILD-TYPE 101 284
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT3 MUTATED      1    9
  CNOT3 WILD-TYPE  101  284
        clus
vv       CNOT3 MUTATED CNOT3 WILD-TYPE
  FEMALE             1             101
  MALE               9             284
[1] 2 2
[1] FALSE
D75V8, binary
                 cls
clus                0   1
  CNOT3 MUTATED    10   0
  CNOT3 WILD-TYPE 340  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT3 MUTATED     10    0
  CNOT3 WILD-TYPE  340   20
     clus
vv    CNOT3 MUTATED CNOT3 WILD-TYPE
  NO             10             340
  YES             0              20
[1] 2 2
[1] FALSE
D75V9, continuous
[1] "Remove cluster labels:" "CNOT3 MUTATED"         
clus
  CNOT3 MUTATED CNOT3 WILD-TYPE 
              1             129 
     TCGA-2F-A9KT      TCGA-DK-A2HX      TCGA-DK-A3IN      TCGA-DK-A3IV 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-DK-A3X2      TCGA-DK-A6B2      TCGA-DK-A6B5      TCGA-DK-A6B6 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-DK-AA6M      TCGA-DK-AA6R      TCGA-DK-AA6S      TCGA-DK-AA6W 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-DK-AA75      TCGA-E5-A4TZ      TCGA-E7-A541      TCGA-E7-A7DU 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-E7-A7DV      TCGA-FT-A61P      TCGA-G2-A2ES      TCGA-G2-A3VY 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-GC-A3BM      TCGA-GC-A3YS      TCGA-GV-A3JZ      TCGA-GV-A3QF 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-GV-A3QK      TCGA-GV-A40E      TCGA-GV-A40G      TCGA-GV-A6ZA 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-KQ-A41N      TCGA-SY-A9G0      TCGA-UY-A78N      TCGA-XF-A9SJ 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-A9SK      TCGA-XF-A9SM      TCGA-XF-A9SP      TCGA-XF-A9ST 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-A9SV      TCGA-XF-A9SW      TCGA-XF-A9SY      TCGA-XF-A9T0 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-A9T2      TCGA-XF-A9T3      TCGA-XF-A9T5      TCGA-XF-A9T6 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-A9T8      TCGA-XF-AAMF      TCGA-XF-AAMH      TCGA-XF-AAMJ 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-AAML      TCGA-XF-AAMQ      TCGA-XF-AAMR      TCGA-XF-AAMY 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-AAMZ      TCGA-XF-AAN1      TCGA-XF-AAN2      TCGA-XF-AAN3 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-AAN7      TCGA-XF-AAN8      TCGA-YF-AA3M      TCGA-2F-A9KO 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-2F-A9KP      TCGA-2F-A9KQ      TCGA-2F-A9KR      TCGA-2F-A9KW 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-CF-A1HS      TCGA-CF-A27C      TCGA-CF-A3MF      TCGA-CF-A3MG 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-CF-A3MH      TCGA-CF-A3MI      TCGA-CF-A47S      TCGA-CF-A47T 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-CF-A47V      TCGA-CF-A47W      TCGA-CF-A47X      TCGA-CF-A47Y 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-CF-A5U8      TCGA-CF-A5UA      TCGA-CF-A7I0      TCGA-DK-A3WX 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-DK-AA6P      TCGA-DK-AA6U      TCGA-DK-AA76      TCGA-E5-A2PC 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-E5-A4U1      TCGA-E7-A519      TCGA-E7-A6MD      TCGA-G2-A2EC 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-G2-A2EF      TCGA-G2-A2EJ      TCGA-G2-A2EK      TCGA-G2-A2EL 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-G2-A2EO      TCGA-G2-A3IB      TCGA-G2-A3IE      TCGA-GC-A3I6 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-GC-A3OO      TCGA-GC-A3RD      TCGA-GC-A6I1      TCGA-GC-A6I3 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-GD-A3OS      TCGA-GD-A6C6      TCGA-GV-A3JV      TCGA-GV-A3JW 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-GV-A3JX      TCGA-GV-A3QH      TCGA-GV-A3QI      TCGA-SY-A9G5 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-UY-A78L      TCGA-UY-A78M      TCGA-XF-A8HH      TCGA-XF-A8HI 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-A9SG      TCGA-XF-A9SH      TCGA-XF-A9SI      TCGA-XF-A9SL 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-A9SU      TCGA-XF-A9SX      TCGA-XF-A9SZ      TCGA-XF-A9T4 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-AAME      TCGA-XF-AAMG      TCGA-XF-AAMT      TCGA-XF-AAMW 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-AAMX      TCGA-XF-AAN0      TCGA-XF-AAN4      TCGA-XF-AAN5 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-YF-AA3L 
"CNOT3 WILD-TYPE" 
D75V10, continuous
D75V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CNOT3 MUTATED       2                         1     7
  CNOT3 WILD-TYPE    37                        21   310
D75V12, multiclass
                           clus
vv                          CNOT3 MUTATED CNOT3 WILD-TYPE
  ASIAN                                 2              37
  BLACK OR AFRICAN AMERICAN             1              21
  WHITE                                 7             310
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V13, binary
                 cls
clus                0   1
  CNOT3 MUTATED     0   7
  CNOT3 WILD-TYPE   8 348
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT3 MUTATED      0    7
  CNOT3 WILD-TYPE    8  348
                        clus
vv                       CNOT3 MUTATED CNOT3 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO             7             348
[1] 2 2
[1] FALSE

Clustering(76) Variable = SSH3 MUTATION ANALYSIS
D76V1, survival
                sevent
clus2              0   1
  SSH3 MUTATED    11   4
  SSH3 WILD-TYPE 206 171
  SSH3 MUTATED SSH3 WILD-TYPE 
            15            377 
  SSH3 MUTATED SSH3 WILD-TYPE 
             4            171 
$`SSH3 MUTATED`
TCGA-2F-A9KT TCGA-DK-A2I6 TCGA-DK-A6AW TCGA-DK-AA77 TCGA-FD-A3SS TCGA-S5-A6DX 
      108.95        87.32        53.29        20.32        12.85         1.84 
TCGA-ZF-A9RC TCGA-4Z-AA7O TCGA-4Z-AA7Y TCGA-C4-A0F6 TCGA-CU-A5W6 TCGA-DK-A1AG 
       94.29        16.83        50.04        23.01         1.84        15.62 
TCGA-E7-A85H TCGA-XF-A9SH TCGA-ZF-A9R7 
       12.95        64.80        21.86 

$`SSH3 WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
       16.27        16.77        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        8.98         2.04        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       46.68         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 
        9.67        66.05        17.98        64.18        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       15.68        50.70        36.66        38.24        52.01       165.73 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A4TZ 
      166.03        13.64        13.64        56.15        11.18        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       25.58         0.92         1.22        33.04         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
       24.30        23.41        17.98        29.16        46.78        19.79 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       27.35         3.62        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
        8.25        18.08        58.92         6.28        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.15        12.69        12.36         3.06         4.31         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D 
       31.07        17.23        11.08        33.01        17.62        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 
       21.40        19.13        17.75        24.92        10.92        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       32.98        19.82        20.28        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       22.72         9.01        25.02         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
       27.68        52.73        50.56        35.97        46.98        14.24 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
       33.14        86.83        51.32         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       14.93         4.21        12.76        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       18.90         2.24        66.64         2.10        13.74        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       11.31        54.90         7.63        71.57        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 
       44.32        30.94        61.45        86.30        18.58         3.88 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RE TCGA-ZF-A9RL 
        9.63        13.64        21.11        30.28         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       34.06        19.69        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA7S 
       94.88       104.65         8.35        44.94        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       27.62         0.62        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       16.18         4.67        17.56        36.43        28.41         1.94 
TCGA-C4-A0F1 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
        2.93        12.79        12.56        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       13.08         5.19        29.79        21.86        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
      112.44        16.14        17.62        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       15.02        13.58        18.81        19.00        15.35        12.03 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        38.83        29.72         5.36        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A97P TCGA-E7-A97Q 
       24.03        24.66        13.68        14.07        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
        5.52        25.74        22.98        14.96        20.91        19.33 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF 
        5.36        27.45         2.70         7.10        13.35         2.27 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC 
       10.85        12.66        10.65         8.94         3.25        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       61.94        48.00        15.95        26.93        59.31         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       20.12        66.02         6.94        29.36        20.71        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07         8.94        13.91        26.70         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        3.12        20.98         2.20        11.31        18.97         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05        15.78         4.73         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       19.10         8.48        36.49         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       64.01        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
        1.81        15.42        16.27        11.80        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       15.32        15.58        13.48        12.23        16.67        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       38.99        17.62        37.05        22.68        76.01        69.34 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       35.24        29.56        17.82         6.21         3.85         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       17.88        48.62        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW 
       28.24        16.27        92.98       110.60         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L 
        6.77        56.48        27.06        75.39         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       22.36        25.41        31.20        35.84        28.41        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       64.08        58.72        47.84        20.22         2.89         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 
       59.38        60.16        67.20        56.35        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
        8.52        54.21        29.49         5.52        10.65 

  SSH3 MUTATED SSH3 WILD-TYPE 
          1.84           0.56 
  SSH3 MUTATED SSH3 WILD-TYPE 
        108.95         166.03 
  SSH3 MUTATED SSH3 WILD-TYPE 
         21.86          17.62 
[1] "1.8 - 109.0 (21.9)" "0.6 - 166.0 (17.6)"
[1] "hr=" "2.3"
D76V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  SSH3 MUTATED         0        7         5        3
  SSH3 WILD-TYPE       2      115       130      131
D76V3, multiclass
           clus
vv          SSH3 MUTATED SSH3 WILD-TYPE
  STAGE I              0              2
  STAGE II             7            115
  STAGE III            5            130
  STAGE IV             3            131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  SSH3 MUTATED          7   4   3
  SSH3 WILD-TYPE      109 186  54
D76V4, multiclass
          clus
vv         SSH3 MUTATED SSH3 WILD-TYPE
  T0+T1+T2            7            109
  T3                  4            186
  T4                  3             54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  SSH3 MUTATED    11   1   1   1
  SSH3 WILD-TYPE 214  45  74   7
D76V5, multiclass
    clus
vv   SSH3 MUTATED SSH3 WILD-TYPE
  N0           11            214
  N1            1             45
  N2            1             74
  N3            1              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"
D76V6, binary
                cls
clus               0   1
  SSH3 MUTATED    12   0
  SSH3 WILD-TYPE 177  11
[1] "tbl2"
                cls
clus             [,1] [,2]
  SSH3 MUTATED     12    0
  SSH3 WILD-TYPE  177   11
   clus
vv  SSH3 MUTATED SSH3 WILD-TYPE
  0           12            177
  1            0             11
[1] 2 2
[1] FALSE
D76V7, binary
                cls
clus               0   1
  SSH3 MUTATED     3  12
  SSH3 WILD-TYPE  99 281
[1] "tbl2"
                cls
clus             [,1] [,2]
  SSH3 MUTATED      3   12
  SSH3 WILD-TYPE   99  281
        clus
vv       SSH3 MUTATED SSH3 WILD-TYPE
  FEMALE            3             99
  MALE             12            281
[1] 2 2
[1] FALSE
D76V8, binary
                cls
clus               0   1
  SSH3 MUTATED    14   0
  SSH3 WILD-TYPE 336  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  SSH3 MUTATED     14    0
  SSH3 WILD-TYPE  336   20
     clus
vv    SSH3 MUTATED SSH3 WILD-TYPE
  NO            14            336
  YES            0             20
[1] 2 2
[1] FALSE
D76V9, continuous
[1] "Remove cluster labels:" "SSH3 MUTATED"          
clus
  SSH3 MUTATED SSH3 WILD-TYPE 
             2            128 
    TCGA-DK-A2HX     TCGA-DK-A3IN     TCGA-DK-A3IV     TCGA-DK-A3X2 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-DK-A6B2     TCGA-DK-A6B5     TCGA-DK-A6B6     TCGA-DK-AA6M 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-DK-AA6R     TCGA-DK-AA6S     TCGA-DK-AA6W     TCGA-DK-AA75 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-E5-A4TZ     TCGA-E7-A541     TCGA-E7-A7DU     TCGA-E7-A7DV 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-FT-A61P     TCGA-G2-A2ES     TCGA-G2-A3VY     TCGA-GC-A3BM 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-GC-A3YS     TCGA-GV-A3JZ     TCGA-GV-A3QF     TCGA-GV-A3QK 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-GV-A40E     TCGA-GV-A40G     TCGA-GV-A6ZA     TCGA-KQ-A41N 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-SY-A9G0     TCGA-UY-A78N     TCGA-XF-A9SJ     TCGA-XF-A9SK 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-A9SM     TCGA-XF-A9SP     TCGA-XF-A9ST     TCGA-XF-A9SV 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-A9SW     TCGA-XF-A9SY     TCGA-XF-A9T0     TCGA-XF-A9T2 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-A9T3     TCGA-XF-A9T5     TCGA-XF-A9T6     TCGA-XF-A9T8 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-AAMF     TCGA-XF-AAMH     TCGA-XF-AAMJ     TCGA-XF-AAML 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-AAMQ     TCGA-XF-AAMR     TCGA-XF-AAMY     TCGA-XF-AAMZ 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-AAN1     TCGA-XF-AAN2     TCGA-XF-AAN3     TCGA-XF-AAN7 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-AAN8     TCGA-YF-AA3M     TCGA-2F-A9KO     TCGA-2F-A9KP 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-2F-A9KQ     TCGA-2F-A9KR     TCGA-2F-A9KW     TCGA-CF-A1HS 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-CF-A27C     TCGA-CF-A3MF     TCGA-CF-A3MG     TCGA-CF-A3MH 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-CF-A3MI     TCGA-CF-A47S     TCGA-CF-A47T     TCGA-CF-A47V 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-CF-A47W     TCGA-CF-A47X     TCGA-CF-A47Y     TCGA-CF-A5U8 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-CF-A5UA     TCGA-CF-A7I0     TCGA-DK-A3WX     TCGA-DK-AA6P 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-DK-AA6U     TCGA-DK-AA76     TCGA-E5-A2PC     TCGA-E5-A4U1 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-E7-A519     TCGA-E7-A6MD     TCGA-G2-A2EC     TCGA-G2-A2EF 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-G2-A2EJ     TCGA-G2-A2EK     TCGA-G2-A2EL     TCGA-G2-A2EO 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-G2-A3IB     TCGA-G2-A3IE     TCGA-GC-A3I6     TCGA-GC-A3OO 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-GC-A3RC     TCGA-GC-A3RD     TCGA-GC-A6I1     TCGA-GC-A6I3 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-GD-A3OS     TCGA-GD-A6C6     TCGA-GV-A3JV     TCGA-GV-A3JW 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-GV-A3JX     TCGA-GV-A3QH     TCGA-GV-A3QI     TCGA-SY-A9G5 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-UY-A78L     TCGA-UY-A78M     TCGA-XF-A8HH     TCGA-XF-A8HI 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-A9SG     TCGA-XF-A9SI     TCGA-XF-A9SL     TCGA-XF-A9SU 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-A9SX     TCGA-XF-A9SZ     TCGA-XF-A9T4     TCGA-XF-AAME 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-AAMG     TCGA-XF-AAMT     TCGA-XF-AAMW     TCGA-XF-AAMX 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-AAN0     TCGA-XF-AAN4     TCGA-XF-AAN5     TCGA-YF-AA3L 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
D76V10, continuous
D76V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SSH3 MUTATED       2                         1    11
  SSH3 WILD-TYPE    37                        21   306
D76V12, multiclass
                           clus
vv                          SSH3 MUTATED SSH3 WILD-TYPE
  ASIAN                                2             37
  BLACK OR AFRICAN AMERICAN            1             21
  WHITE                               11            306
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V13, binary
                cls
clus               0   1
  SSH3 MUTATED     0  12
  SSH3 WILD-TYPE   8 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  SSH3 MUTATED      0   12
  SSH3 WILD-TYPE    8  343
                        clus
vv                       SSH3 MUTATED SSH3 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           12            343
[1] 2 2
[1] FALSE

Clustering(77) Variable = AHR MUTATION ANALYSIS
D77V1, survival
               sevent
clus2             0   1
  AHR MUTATED    14   8
  AHR WILD-TYPE 203 167
  AHR MUTATED AHR WILD-TYPE 
           22           370 
  AHR MUTATED AHR WILD-TYPE 
            8           167 
$`AHR MUTATED`
TCGA-DK-A1AB TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-AA75 TCGA-E7-A7DU 
       16.70        23.21        66.05        64.18        11.18         0.92 
TCGA-FD-A6TA TCGA-K4-A54R TCGA-UY-A9PH TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-4Z-AA80 
       62.86        27.68        51.32        44.32        61.45         0.62 
TCGA-C4-A0F0 TCGA-CF-A47Y TCGA-DK-AA76 TCGA-FJ-A3ZE TCGA-GD-A3OP TCGA-KQ-A41R 
        1.94        12.26        12.03        10.65         2.10        44.38 
TCGA-LT-A5Z6 TCGA-S5-AA26 TCGA-UY-A8OB TCGA-XF-A9SL 
       15.58        16.54        69.34        66.41 

$`AHR WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC 
       15.12        18.48        13.58         2.14        19.00       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
        9.67        17.98        53.29        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S 
       50.70        36.66        38.24        52.01       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 
       13.64        13.64        56.15        20.32        15.35        25.58 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        1.22        33.04         4.01        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       17.98        29.16        46.78        19.79        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
        3.62        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       18.08        58.92         6.28        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.36         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       11.08        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       17.75        24.92        10.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       20.28        27.35         8.58        19.07        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41N TCGA-KQ-A41O 
       25.02         3.45         2.76         9.14        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       35.97        46.98        14.24         1.84        33.14        86.83 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
        3.22        15.98        34.45        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.10        13.74        10.82        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN7 
       71.57        91.73        98.99        30.94        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
        3.88         9.63        13.64        21.11        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.48        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 
       16.83        17.16        34.98        27.62        50.04        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM 
       51.16        66.54        10.22        47.80         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       19.04        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
        5.06         8.25        17.16        16.18         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       36.43        28.41         2.93        23.01        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.10        12.62        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.10        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
        8.15        20.81        10.55       163.30        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       18.81        19.00        15.35        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        22.16         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
       26.96        26.24         4.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.70         7.10        13.35         2.27        10.85        12.66 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        8.94         3.25        22.88        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       26.93        59.31         7.23        20.12        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 
       29.36        20.71        15.81        15.91        14.07         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       13.91        26.70         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       18.97         7.63        20.05        15.78         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
       14.27        21.34        19.10         8.48        36.49         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
       19.40        38.60        64.01        12.16        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70        17.72         1.81        15.42        16.27        11.80 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 
        1.15        15.32        13.48        12.23        16.67        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A9PA TCGA-UY-A9PB 
       17.62        37.05        22.68        76.01        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         6.21         3.85         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       64.80        79.66         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       58.72        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        67.20        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  AHR MUTATED AHR WILD-TYPE 
         0.62          0.56 
  AHR MUTATED AHR WILD-TYPE 
        69.34        166.03 
  AHR MUTATED AHR WILD-TYPE 
       19.955        17.620 
[1] "0.6 - 69.3 (20.0)"  "0.6 - 166.0 (17.6)"
[1] "hr=" "1.4"
D77V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  AHR MUTATED         0       11         4        7
  AHR WILD-TYPE       2      111       131      127
D77V3, multiclass
           clus
vv          AHR MUTATED AHR WILD-TYPE
  STAGE I             0             2
  STAGE II           11           111
  STAGE III           4           131
  STAGE IV            7           127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1+T2  T3  T4
  AHR MUTATED          9   8   2
  AHR WILD-TYPE      107 182  55
D77V4, multiclass
          clus
vv         AHR MUTATED AHR WILD-TYPE
  T0+T1+T2           9           107
  T3                 8           182
  T4                 2            55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  AHR MUTATED    14   1   5   1
  AHR WILD-TYPE 211  45  70   7
D77V5, multiclass
    clus
vv   AHR MUTATED AHR WILD-TYPE
  N0          14           211
  N1           1            45
  N2           5            70
  N3           1             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"
D77V6, binary
               cls
clus              0   1
  AHR MUTATED    10   1
  AHR WILD-TYPE 179  10
[1] "tbl2"
               cls
clus            [,1] [,2]
  AHR MUTATED     10    1
  AHR WILD-TYPE  179   10
   clus
vv  AHR MUTATED AHR WILD-TYPE
  0          10           179
  1           1            10
[1] 2 2
[1] FALSE
D77V7, binary
               cls
clus              0   1
  AHR MUTATED     7  15
  AHR WILD-TYPE  95 278
[1] "tbl2"
               cls
clus            [,1] [,2]
  AHR MUTATED      7   15
  AHR WILD-TYPE   95  278
        clus
vv       AHR MUTATED AHR WILD-TYPE
  FEMALE           7            95
  MALE            15           278
[1] 2 2
[1] FALSE
D77V8, binary
               cls
clus              0   1
  AHR MUTATED    19   1
  AHR WILD-TYPE 331  19
[1] "tbl2"
               cls
clus            [,1] [,2]
  AHR MUTATED     19    1
  AHR WILD-TYPE  331   19
     clus
vv    AHR MUTATED AHR WILD-TYPE
  NO           19           331
  YES           1            19
[1] 2 2
[1] FALSE
D77V9, continuous
D77V10, continuous
D77V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AHR MUTATED       2                         1    18
  AHR WILD-TYPE    37                        21   299
D77V12, multiclass
                           clus
vv                          AHR MUTATED AHR WILD-TYPE
  ASIAN                               2            37
  BLACK OR AFRICAN AMERICAN           1            21
  WHITE                              18           299
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V13, binary
               cls
clus              0   1
  AHR MUTATED     1  19
  AHR WILD-TYPE   7 336
[1] "tbl2"
               cls
clus            [,1] [,2]
  AHR MUTATED      1   19
  AHR WILD-TYPE    7  336
                        clus
vv                       AHR MUTATED AHR WILD-TYPE
  HISPANIC OR LATINO               1             7
  NOT HISPANIC OR LATINO          19           336
[1] 2 2
[1] FALSE

Clustering(78) Variable = EIF4A2 MUTATION ANALYSIS
D78V1, survival
                  sevent
clus2                0   1
  EIF4A2 MUTATED     6   5
  EIF4A2 WILD-TYPE 211 170
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
              11              381 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
               5              170 
$`EIF4A2 MUTATED`
TCGA-C4-A0F7 TCGA-DK-A3IN TCGA-DK-A6AW TCGA-DK-A6B6 TCGA-FD-A3SL TCGA-XF-AAN3 
        2.04         8.22        53.29        36.66        23.41        86.30 
TCGA-2F-A9KR TCGA-4Z-AA81 TCGA-K4-A5RH TCGA-LT-A5Z6 TCGA-ZF-A9RF 
      104.65        41.75         9.07        15.58        64.08 

$`EIF4A2 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       28.70         8.98        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       46.68        87.32        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 
        9.67        66.05        17.98        64.18        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S 
       15.68        50.70        38.24        52.01       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       13.64        13.64        56.15        11.18        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       25.58         0.92         1.22        33.04         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       24.30        17.98        29.16        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       27.35         3.62        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
        8.25        18.08        58.92         6.28        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.15        12.69        12.36         3.06         4.31         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D 
       31.07        17.23        11.08        33.01        17.62        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 
       21.40        19.13        17.75        24.92        10.92        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       32.98        19.82        20.28        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       22.72         9.01        25.02         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
       27.68        52.73        50.56        35.97        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK 
        1.84        33.14        86.83        51.32         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       34.45        14.93         4.21        12.76        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        66.64         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-XF-AAN8 
       98.99        44.32        30.94        61.45        18.58         3.88 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE 
        9.63        13.64        21.11        30.28        94.29         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO 
       88.87        34.06        19.69        57.90        12.23        24.13 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       11.97        94.88         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 
       34.98        27.62        50.04         0.62        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       10.22        47.80         2.50        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        2.66         6.74         6.58        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       17.88        19.50         5.06        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       17.16        16.18         4.67        17.56        36.43        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        1.94         2.93        23.01        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.10        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
        8.15        20.81        10.55       163.30        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       18.81        19.00        15.35        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        22.16         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
       12.66        10.65         8.94         3.25        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       48.00        15.95        26.93        59.31         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       66.02         6.94        29.36        20.71        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07         8.94        13.91        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
       20.98         2.20        11.31        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       15.78         4.73         7.00        14.27        21.34        19.10 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.48        36.49         1.51        19.40        38.60        64.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       12.16        21.24        11.70        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V 
       16.27        11.80        44.38         1.15        15.32        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       12.23        16.67        16.54        38.99        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       22.68        76.01        69.34        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        6.21         3.85         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       79.66        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG 
       31.20        35.84        21.86        28.41        13.41        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       47.84        20.22         2.89         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       67.20        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
            2.04             0.56 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
          104.65           166.03 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
           36.66            17.62 
[1] "2.0 - 104.7 (36.7)" "0.6 - 166.0 (17.6)"
[1] "hr=" "1.4"
D78V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  EIF4A2 MUTATED         0        5         3        3
  EIF4A2 WILD-TYPE       2      117       132      131
D78V3, multiclass
           clus
vv          EIF4A2 MUTATED EIF4A2 WILD-TYPE
  STAGE I                0                2
  STAGE II               5              117
  STAGE III              3              132
  STAGE IV               3              131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  EIF4A2 MUTATED          3   3   3
  EIF4A2 WILD-TYPE      113 187  54
D78V4, multiclass
          clus
vv         EIF4A2 MUTATED EIF4A2 WILD-TYPE
  T0+T1+T2              3              113
  T3                    3              187
  T4                    3               54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  EIF4A2 MUTATED     5   0   3   0
  EIF4A2 WILD-TYPE 220  46  72   8
D78V5, multiclass
    clus
vv   EIF4A2 MUTATED EIF4A2 WILD-TYPE
  N0              5              220
  N1              0               46
  N2              3               72
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                  cls
clus                 0   1
  EIF4A2 MUTATED     6   1
  EIF4A2 WILD-TYPE 183  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4A2 MUTATED      6    1
  EIF4A2 WILD-TYPE  183   10
   clus
vv  EIF4A2 MUTATED EIF4A2 WILD-TYPE
  0              6              183
  1              1               10
[1] 2 2
[1] FALSE
D78V7, binary
                  cls
clus                 0   1
  EIF4A2 MUTATED     1  10
  EIF4A2 WILD-TYPE 101 283
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4A2 MUTATED      1   10
  EIF4A2 WILD-TYPE  101  283
        clus
vv       EIF4A2 MUTATED EIF4A2 WILD-TYPE
  FEMALE              1              101
  MALE               10              283
[1] 2 2
[1] FALSE
D78V8, binary
                  cls
clus                 0   1
  EIF4A2 MUTATED    10   0
  EIF4A2 WILD-TYPE 340  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4A2 MUTATED     10    0
  EIF4A2 WILD-TYPE  340   20
     clus
vv    EIF4A2 MUTATED EIF4A2 WILD-TYPE
  NO              10              340
  YES              0               20
[1] 2 2
[1] FALSE
D78V9, continuous
D78V10, continuous
D78V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EIF4A2 MUTATED       0                         0     9
  EIF4A2 WILD-TYPE    39                        22   308
D78V12, multiclass
                           clus
vv                          EIF4A2 MUTATED EIF4A2 WILD-TYPE
  ASIAN                                  0               39
  BLACK OR AFRICAN AMERICAN              0               22
  WHITE                                  9              308
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V13, binary
                  cls
clus                 0   1
  EIF4A2 MUTATED     0   8
  EIF4A2 WILD-TYPE   8 347
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4A2 MUTATED      0    8
  EIF4A2 WILD-TYPE    8  347
                        clus
vv                       EIF4A2 MUTATED EIF4A2 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO              8              347
[1] 2 2
[1] FALSE

Clustering(79) Variable = EPHA2 MUTATION ANALYSIS
D79V1, survival
                 sevent
clus2               0   1
  EPHA2 MUTATED    11   8
  EPHA2 WILD-TYPE 206 167
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             19             373 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
              8             167 
$`EPHA2 MUTATED`
TCGA-DK-A2I6 TCGA-DK-A3X1 TCGA-DK-AA6L TCGA-FD-A5BX TCGA-KQ-A41O TCGA-XF-A9T6 
       87.32        66.05        38.24         5.69        50.56         2.10 
TCGA-XF-AAMH TCGA-4Z-AA7Y TCGA-5N-A9KM TCGA-BT-A2LB TCGA-BT-A42B TCGA-DK-A1A7 
       11.31        50.04        17.42        16.18        17.56        18.41 
TCGA-E7-A7XN TCGA-FD-A3N5 TCGA-GC-A6I3 TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-KQ-A41R 
       14.07        22.52        13.91         8.48        19.40        44.38 
TCGA-XF-AAN5 
       75.39 

$`EPHA2 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
      130.88        46.68         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       23.21         9.67        17.98        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6R 
       67.36        15.68        50.70        36.66        52.01       165.73 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
      166.03        13.64        13.64        56.15        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       15.35        25.58         0.92         1.22        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
       60.66        24.30        23.41        17.98        29.16        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       19.79        12.85        27.35         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
       10.78         8.25        18.08        58.92         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         3.06         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY 
        9.67        31.07        17.23        11.08        33.01        17.62 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
       70.32        21.40        19.13        17.75        24.92        10.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       32.78        32.98        19.82        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       19.07        22.72         9.01        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
        9.14        27.68        52.73        35.97        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK 
        1.84        33.14        86.83        51.32         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       34.45        14.93         4.21        12.76        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMF 
       26.27        18.90         2.24        66.64        13.74        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63        71.57        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       30.94        61.45        86.30        18.58         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL 
       13.64        21.11        30.28        94.29         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       34.06        19.69        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       34.98        27.62         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80         2.50        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A3PH TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
        4.67        36.43        28.41         1.94         2.93        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       12.79        12.56        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       12.16        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AD 
        5.19        29.79         1.84        21.86        66.41       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       15.02        13.58        18.81        19.00        15.35        12.03 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        38.83        29.72         5.36        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
       24.03        24.66        13.68        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO 
       32.02        16.77         8.94        12.62        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
       12.66        10.65         8.94         3.25        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       48.00        15.95        26.93        59.31         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       66.02         6.94        29.36        20.71        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       14.07         8.94        26.70         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        2.20        11.31        18.97         7.63        20.05        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI 
        4.73         7.00        14.27        21.34        19.10        36.49 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
        1.51        38.60        64.01        12.16        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70        17.72         1.81        15.42        16.27        11.80 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.15        15.32        15.58        13.48        12.23        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.54        38.99        17.62        37.05        22.68        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34        35.24        29.56        17.82         6.21         3.85 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-YC-A9TC 
        2.96         8.32         6.77        56.48        27.06         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       11.97        22.36        25.41        31.20        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       28.41        13.41        64.08        58.72        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
        2.89         8.61        59.38        60.16        67.20        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        19.40         8.52        54.21        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  EPHA2 MUTATED EPHA2 WILD-TYPE 
           2.10            0.56 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
          87.32          166.03 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
          18.41           17.62 
[1] "2.1 - 87.3 (18.4)"  "0.6 - 166.0 (17.6)"
[1] "hr=" "1.2"
D79V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  EPHA2 MUTATED         0        4         6        9
  EPHA2 WILD-TYPE       2      118       129      125
D79V3, multiclass
           clus
vv          EPHA2 MUTATED EPHA2 WILD-TYPE
  STAGE I               0               2
  STAGE II              4             118
  STAGE III             6             129
  STAGE IV              9             125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  EPHA2 MUTATED          4  12   1
  EPHA2 WILD-TYPE      112 178  56
D79V4, multiclass
          clus
vv         EPHA2 MUTATED EPHA2 WILD-TYPE
  T0+T1+T2             4             112
  T3                  12             178
  T4                   1              56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EPHA2 MUTATED     9   7   1   0
  EPHA2 WILD-TYPE 216  39  74   8
D79V5, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  N0             9             216
  N1             7              39
  N2             1              74
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                 cls
clus                0   1
  EPHA2 MUTATED     7   1
  EPHA2 WILD-TYPE 182  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      7    1
  EPHA2 WILD-TYPE  182   10
   clus
vv  EPHA2 MUTATED EPHA2 WILD-TYPE
  0             7             182
  1             1              10
[1] 2 2
[1] FALSE
D79V7, binary
                 cls
clus                0   1
  EPHA2 MUTATED     9  10
  EPHA2 WILD-TYPE  93 283
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      9   10
  EPHA2 WILD-TYPE   93  283
        clus
vv       EPHA2 MUTATED EPHA2 WILD-TYPE
  FEMALE             9              93
  MALE              10             283
[1] 2 2
[1] FALSE
D79V8, binary
                 cls
clus                0   1
  EPHA2 MUTATED    18   0
  EPHA2 WILD-TYPE 332  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED     18    0
  EPHA2 WILD-TYPE  332   20
     clus
vv    EPHA2 MUTATED EPHA2 WILD-TYPE
  NO             18             332
  YES             0              20
[1] 2 2
[1] FALSE
D79V9, continuous
D79V10, continuous
D79V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPHA2 MUTATED       1                         3    14
  EPHA2 WILD-TYPE    38                        19   303
D79V12, multiclass
                           clus
vv                          EPHA2 MUTATED EPHA2 WILD-TYPE
  ASIAN                                 1              38
  BLACK OR AFRICAN AMERICAN             3              19
  WHITE                                14             303
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V13, binary
                 cls
clus                0   1
  EPHA2 MUTATED     0  17
  EPHA2 WILD-TYPE   8 338
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      0   17
  EPHA2 WILD-TYPE    8  338
                        clus
vv                       EPHA2 MUTATED EPHA2 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            17             338
[1] 2 2
[1] FALSE

Clustering(80) Variable = OGDH MUTATION ANALYSIS
D80V1, survival
                sevent
clus2              0   1
  OGDH MUTATED    13   6
  OGDH WILD-TYPE 204 169
  OGDH MUTATED OGDH WILD-TYPE 
            19            373 
  OGDH MUTATED OGDH WILD-TYPE 
             6            169 
$`OGDH MUTATED`
TCGA-BT-A42C TCGA-CU-A0YR TCGA-DK-A3IS TCGA-DK-AA6S TCGA-FD-A62P TCGA-GV-A40E 
       28.70        15.12        50.27       166.03         6.28         8.58 
TCGA-S5-A6DX TCGA-UY-A78N TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-ZF-A9RC TCGA-4Z-AA7W 
        1.84        86.83        21.04         2.24        94.29        27.62 
TCGA-BT-A0YX TCGA-DK-AA6U TCGA-K4-A5RH TCGA-K4-A83P TCGA-MV-A51V TCGA-UY-A9PA 
       13.15        19.00         9.07        16.27        13.48        35.24 
TCGA-XF-A9SG 
       48.62 

$`OGDH WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ 
        8.98         2.04        18.58        12.92         4.90        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       13.58         2.14        19.00        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       87.32         8.22        17.72        21.30        23.21         9.67 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       66.05        17.98        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       15.68        50.70        36.66        38.24        52.01       165.73 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       13.64        13.64        56.15        11.18        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       25.58         0.92         1.22        33.04         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
       24.30        23.41        17.98        29.16        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       12.85        27.35         3.62        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB 
        5.69         8.25        18.08        58.92        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.15        12.69        12.36         3.06         4.31         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D 
       31.07        17.23        11.08        33.01        17.62        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 
       21.40        19.13        17.75        24.92        10.92        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA 
       32.98        19.82        20.28        27.35        19.07        22.72 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        9.01        25.02         3.45         2.76         9.14        27.68 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 
       52.73        50.56        35.97        46.98        14.24        33.14 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       51.32         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 
       12.76        11.90        26.27        18.90        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       13.74        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.48        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 
       16.83        17.16        34.98        50.04         0.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM 
       51.16        66.54        10.22        47.80         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J 
       40.08         7.33         2.66         6.74         6.58        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50         5.06        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        8.25        17.16        16.18         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         1.94         2.93        23.01        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.00        12.10        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        1.84        21.86        66.41        18.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P 
       13.58         8.15        20.81        10.55       163.30        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       13.58        18.81        15.35        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        22.16         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
       12.66        10.65         8.94         3.25        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       48.00        15.95        26.93        59.31         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       66.02         6.94        29.36        20.71        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07         8.94        13.91        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
       20.98         2.20        11.31        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       15.78         4.73         7.00        14.27        21.34        19.10 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.48        36.49         1.51        19.40        38.60        64.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       12.16        21.24        11.70        17.72         1.81        15.42 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI 
       11.80        44.38         1.15        15.32        15.58        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       76.01        69.34        29.56        17.82         6.21         3.85 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
        1.87        17.88        64.80        79.66        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT 
       23.64        28.24        16.27        92.98       110.60         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC 
        8.32         6.77        56.48        27.06        75.39         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       11.97        22.36        25.41        31.20        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       28.41        13.41        64.08        58.72        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
        2.89         8.61        59.38        60.16        67.20        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        19.40         8.52        54.21        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  OGDH MUTATED OGDH WILD-TYPE 
          1.84           0.56 
  OGDH MUTATED OGDH WILD-TYPE 
        166.03         165.73 
  OGDH MUTATED OGDH WILD-TYPE 
         19.00          17.62 
[1] "1.8 - 166.0 (19.0)" "0.6 - 165.7 (17.6)"
[1] "hr=" "1.6"
D80V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  OGDH MUTATED         0        7         6        6
  OGDH WILD-TYPE       2      115       129      128
D80V3, multiclass
           clus
vv          OGDH MUTATED OGDH WILD-TYPE
  STAGE I              0              2
  STAGE II             7            115
  STAGE III            6            129
  STAGE IV             6            128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  OGDH MUTATED          6   8   2
  OGDH WILD-TYPE      110 182  55
D80V4, multiclass
          clus
vv         OGDH MUTATED OGDH WILD-TYPE
  T0+T1+T2            6            110
  T3                  8            182
  T4                  2             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  OGDH MUTATED    12   2   4   0
  OGDH WILD-TYPE 213  44  71   8
D80V5, multiclass
    clus
vv   OGDH MUTATED OGDH WILD-TYPE
  N0           12            213
  N1            2             44
  N2            4             71
  N3            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                cls
clus               0   1
  OGDH MUTATED     8   0
  OGDH WILD-TYPE 181  11
[1] "tbl2"
                cls
clus             [,1] [,2]
  OGDH MUTATED      8    0
  OGDH WILD-TYPE  181   11
   clus
vv  OGDH MUTATED OGDH WILD-TYPE
  0            8            181
  1            0             11
[1] 2 2
[1] FALSE
D80V7, binary
                cls
clus               0   1
  OGDH MUTATED     3  16
  OGDH WILD-TYPE  99 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  OGDH MUTATED      3   16
  OGDH WILD-TYPE   99  277
        clus
vv       OGDH MUTATED OGDH WILD-TYPE
  FEMALE            3             99
  MALE             16            277
[1] 2 2
[1] FALSE
D80V8, binary
                cls
clus               0   1
  OGDH MUTATED    17   1
  OGDH WILD-TYPE 333  19
[1] "tbl2"
                cls
clus             [,1] [,2]
  OGDH MUTATED     17    1
  OGDH WILD-TYPE  333   19
     clus
vv    OGDH MUTATED OGDH WILD-TYPE
  NO            17            333
  YES            1             19
[1] 2 2
[1] FALSE
D80V9, continuous
D80V10, continuous
D80V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OGDH MUTATED       0                         0    18
  OGDH WILD-TYPE    39                        22   299
D80V12, multiclass
                           clus
vv                          OGDH MUTATED OGDH WILD-TYPE
  ASIAN                                0             39
  BLACK OR AFRICAN AMERICAN            0             22
  WHITE                               18            299
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V13, binary
                cls
clus               0   1
  OGDH MUTATED     1  17
  OGDH WILD-TYPE   7 338
[1] "tbl2"
                cls
clus             [,1] [,2]
  OGDH MUTATED      1   17
  OGDH WILD-TYPE    7  338
                        clus
vv                       OGDH MUTATED OGDH WILD-TYPE
  HISPANIC OR LATINO                1              7
  NOT HISPANIC OR LATINO           17            338
[1] 2 2
[1] FALSE

Clustering(81) Variable = POU3F1 MUTATION ANALYSIS
D81V1, survival
                  sevent
clus2                0   1
  POU3F1 MUTATED     1   2
  POU3F1 WILD-TYPE 216 173
  POU3F1 MUTATED POU3F1 WILD-TYPE 
               3              389 
  POU3F1 MUTATED POU3F1 WILD-TYPE 
               2              173 
$`POU3F1 MUTATED`
TCGA-FD-A6TH TCGA-E5-A2PC TCGA-GU-AATO 
        4.31        43.59        10.65 

$`POU3F1 WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       28.70         8.98         2.04        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      130.88        46.68        87.32         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       21.30        23.21         9.67        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       53.29        76.60        67.36        15.68        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       38.24        52.01       165.73       166.03        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU 
       56.15        11.18        20.32        15.35        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        1.22        33.04         4.01        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       17.98        29.16        46.78        19.79        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
        3.62        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
       18.08        58.92         6.28        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.69        12.36         3.06         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       11.08        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       17.75        24.92        10.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       20.28        27.35         8.58        19.07        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
       25.02         3.45         2.76         9.14        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       50.56        35.97        46.98        14.24         1.84        33.14 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       86.83        51.32         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
        4.21        12.76        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
        2.24        66.64         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63        71.57        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       30.94        61.45        86.30        18.58         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL 
       13.64        21.11        30.28        94.29         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       34.06        19.69        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       34.98        27.62        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       66.54        10.22        47.80         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50         5.06        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        8.25        17.16        16.18         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         1.94         2.93        23.01        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.00        12.10        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        1.84        21.86        66.41        18.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P 
       13.58         8.15        20.81        10.55       163.30        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 
       13.58        18.81        19.00        15.35        12.03        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        22.16         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
       12.66        10.65         8.94         3.25        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       48.00        15.95        26.93        59.31         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       66.02         6.94        29.36        20.71        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07         8.94        13.91        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
       20.98         2.20        11.31        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       15.78         4.73         7.00        14.27        21.34        19.10 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.48        36.49         1.51        19.40        38.60        64.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       12.16        21.24         9.07        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       15.42        16.27        11.80        44.38         1.15        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       15.58        13.48        12.23        16.67        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       17.62        37.05        22.68        76.01        69.34        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         6.21         3.85         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       48.62        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW 
       28.24        16.27        92.98       110.60         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L 
        6.77        56.48        27.06        75.39         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       13.41        64.08        58.72        47.84        20.22         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       19.40         8.52        54.21        29.49         5.52 

  POU3F1 MUTATED POU3F1 WILD-TYPE 
            4.31             0.56 
  POU3F1 MUTATED POU3F1 WILD-TYPE 
           43.59           166.03 
  POU3F1 MUTATED POU3F1 WILD-TYPE 
           10.65            17.62 
[1] "4.3 - 43.6 (10.7)"  "0.6 - 166.0 (17.6)"
[1] "hr=" "2"  
D81V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  POU3F1 MUTATED         0        0         0        3
  POU3F1 WILD-TYPE       2      122       135      131
D81V3, multiclass
           clus
vv          POU3F1 MUTATED POU3F1 WILD-TYPE
  STAGE I                0                2
  STAGE II               0              122
  STAGE III              0              135
  STAGE IV               3              131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  POU3F1 MUTATED          1   1   1
  POU3F1 WILD-TYPE      115 189  56
D81V4, multiclass
          clus
vv         POU3F1 MUTATED POU3F1 WILD-TYPE
  T0+T1+T2              1              115
  T3                    1              189
  T4                    1               56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  POU3F1 MUTATED     0   1   2   0
  POU3F1 WILD-TYPE 225  45  73   8
D81V5, multiclass
    clus
vv   POU3F1 MUTATED POU3F1 WILD-TYPE
  N0              0              225
  N1              1               45
  N2              2               73
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                  cls
clus                 0   1
  POU3F1 MUTATED     0   0
  POU3F1 WILD-TYPE 189  11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POU3F1 MUTATED      0    0
  POU3F1 WILD-TYPE  189   11
D81V7, binary
                  cls
clus                 0   1
  POU3F1 MUTATED     1   2
  POU3F1 WILD-TYPE 101 291
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POU3F1 MUTATED      1    2
  POU3F1 WILD-TYPE  101  291
        clus
vv       POU3F1 MUTATED POU3F1 WILD-TYPE
  FEMALE              1              101
  MALE                2              291
[1] 2 2
[1] FALSE
D81V8, binary
                  cls
clus                 0   1
  POU3F1 MUTATED     3   0
  POU3F1 WILD-TYPE 347  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POU3F1 MUTATED      3    0
  POU3F1 WILD-TYPE  347   20
     clus
vv    POU3F1 MUTATED POU3F1 WILD-TYPE
  NO               3              347
  YES              0               20
[1] 2 2
[1] FALSE
D81V9, continuous
[1] "Remove cluster labels:" "POU3F1 MUTATED"        
clus
  POU3F1 MUTATED POU3F1 WILD-TYPE 
               1              129 
      TCGA-2F-A9KT       TCGA-DK-A2HX       TCGA-DK-A3IN       TCGA-DK-A3IV 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-A3X2       TCGA-DK-A6B2       TCGA-DK-A6B5       TCGA-DK-A6B6 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-AA6M       TCGA-DK-AA6R       TCGA-DK-AA6S       TCGA-DK-AA6W 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-AA75       TCGA-E5-A4TZ       TCGA-E7-A541       TCGA-E7-A7DU 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-E7-A7DV       TCGA-FT-A61P       TCGA-G2-A2ES       TCGA-G2-A3VY 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GC-A3BM       TCGA-GC-A3YS       TCGA-GV-A3JZ       TCGA-GV-A3QF 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GV-A3QK       TCGA-GV-A40E       TCGA-GV-A40G       TCGA-GV-A6ZA 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-KQ-A41N       TCGA-SY-A9G0       TCGA-UY-A78N       TCGA-XF-A9SJ 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-A9SK       TCGA-XF-A9SM       TCGA-XF-A9SP       TCGA-XF-A9ST 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-A9SV       TCGA-XF-A9SW       TCGA-XF-A9SY       TCGA-XF-A9T0 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-A9T2       TCGA-XF-A9T3       TCGA-XF-A9T5       TCGA-XF-A9T6 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-A9T8       TCGA-XF-AAMF       TCGA-XF-AAMH       TCGA-XF-AAMJ 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-AAML       TCGA-XF-AAMQ       TCGA-XF-AAMR       TCGA-XF-AAMY 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-AAMZ       TCGA-XF-AAN1       TCGA-XF-AAN2       TCGA-XF-AAN3 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-AAN7       TCGA-XF-AAN8       TCGA-YF-AA3M       TCGA-2F-A9KO 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-2F-A9KP       TCGA-2F-A9KQ       TCGA-2F-A9KR       TCGA-2F-A9KW 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-CF-A1HS       TCGA-CF-A27C       TCGA-CF-A3MF       TCGA-CF-A3MG 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-CF-A3MH       TCGA-CF-A3MI       TCGA-CF-A47S       TCGA-CF-A47T 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-CF-A47V       TCGA-CF-A47W       TCGA-CF-A47X       TCGA-CF-A47Y 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-CF-A5U8       TCGA-CF-A5UA       TCGA-CF-A7I0       TCGA-DK-A3WX 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-AA6P       TCGA-DK-AA6U       TCGA-DK-AA76       TCGA-E5-A4U1 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-E7-A519       TCGA-E7-A6MD       TCGA-G2-A2EC       TCGA-G2-A2EF 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-G2-A2EJ       TCGA-G2-A2EK       TCGA-G2-A2EL       TCGA-G2-A2EO 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-G2-A3IB       TCGA-G2-A3IE       TCGA-GC-A3I6       TCGA-GC-A3OO 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GC-A3RC       TCGA-GC-A3RD       TCGA-GC-A6I1       TCGA-GC-A6I3 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GD-A3OS       TCGA-GD-A6C6       TCGA-GV-A3JV       TCGA-GV-A3JW 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GV-A3JX       TCGA-GV-A3QH       TCGA-GV-A3QI       TCGA-SY-A9G5 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-UY-A78L       TCGA-UY-A78M       TCGA-XF-A8HH       TCGA-XF-A8HI 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-A9SG       TCGA-XF-A9SH       TCGA-XF-A9SI       TCGA-XF-A9SL 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-A9SU       TCGA-XF-A9SX       TCGA-XF-A9SZ       TCGA-XF-A9T4 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-AAME       TCGA-XF-AAMG       TCGA-XF-AAMT       TCGA-XF-AAMW 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-AAMX       TCGA-XF-AAN0       TCGA-XF-AAN4       TCGA-XF-AAN5 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-YF-AA3L 
"POU3F1 WILD-TYPE" 
D81V10, continuous
[1] "Remove cluster labels:" "POU3F1 MUTATED"        
clus
  POU3F1 MUTATED POU3F1 WILD-TYPE 
               2              213 
      TCGA-4Z-AA7M       TCGA-4Z-AA89       TCGA-BL-A5ZZ       TCGA-BT-A20N 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-BT-A42C       TCGA-C4-A0EZ       TCGA-CU-A0YN       TCGA-CU-A0YR 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-CU-A3KJ       TCGA-CU-A72E       TCGA-DK-A1A5       TCGA-DK-A1AA 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-A1AC       TCGA-DK-A2HX       TCGA-DK-A2I6       TCGA-DK-A3IN 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-A3IQ       TCGA-DK-A3IU       TCGA-DK-A3IV       TCGA-DK-A3X1 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-A3X2       TCGA-DK-A6AV       TCGA-DK-A6AW       TCGA-DK-A6B0 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-A6B2       TCGA-DK-A6B6       TCGA-DK-AA6L       TCGA-DK-AA6R 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-AA74       TCGA-DK-AA75       TCGA-E5-A4TZ       TCGA-FD-A3B6 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FD-A3B7       TCGA-FD-A3NA       TCGA-FD-A3SJ       TCGA-FD-A3SM 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FD-A3SN       TCGA-FD-A3SQ       TCGA-FD-A3SR       TCGA-FD-A3SS 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FD-A43P       TCGA-FD-A43X       TCGA-FD-A5BT       TCGA-FD-A5BX 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FD-A5C0       TCGA-FD-A6TB       TCGA-FD-A6TC       TCGA-FD-A6TE 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FD-A6TG       TCGA-FJ-A3ZF       TCGA-FT-A61P       TCGA-G2-A2ES 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-G2-AA3D       TCGA-GC-A3BM       TCGA-GC-A3RB       TCGA-GC-A3WC 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GC-A3YS       TCGA-GU-A42P       TCGA-GU-A763       TCGA-GU-AATP 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QG       TCGA-GV-A3QK 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GV-A40E       TCGA-GV-A40G       TCGA-HQ-A5ND       TCGA-K4-A3WS 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-KQ-A41N       TCGA-R3-A69X       TCGA-S5-A6DX       TCGA-SY-A9G0 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-UY-A78N       TCGA-XF-A9SJ       TCGA-XF-A9SK       TCGA-XF-A9SM 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-A9SP       TCGA-XF-A9ST       TCGA-XF-A9SV       TCGA-XF-A9SY 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-A9T3       TCGA-XF-A9T8       TCGA-XF-AAMF       TCGA-XF-AAMH 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-AAMQ       TCGA-XF-AAN1       TCGA-XF-AAN2       TCGA-XF-AAN7 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-AAN8       TCGA-YF-AA3M       TCGA-ZF-A9R2       TCGA-ZF-A9RL 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-ZF-AA5P       TCGA-2F-A9KO       TCGA-2F-A9KP       TCGA-2F-A9KR 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-5N-A9KI       TCGA-5N-A9KM       TCGA-BL-A0C8       TCGA-BL-A13I 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-BL-A13J       TCGA-BL-A3JM       TCGA-BT-A20J       TCGA-BT-A2LA 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-BT-A42B       TCGA-BT-A42E       TCGA-C4-A0F0       TCGA-C4-A0F1 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-C4-A0F6       TCGA-CF-A3MH       TCGA-CF-A3MI       TCGA-CF-A47W 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-CF-A47X       TCGA-CF-A5UA       TCGA-CF-A9FH       TCGA-CU-A3QU 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-CU-A3YL       TCGA-CU-A5W6       TCGA-DK-A1A3       TCGA-DK-A1A6 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-A1AE       TCGA-DK-A3IL       TCGA-DK-A3IM       TCGA-DK-A3WX 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-AA6P       TCGA-DK-AA6T       TCGA-DK-AA6U       TCGA-DK-AA76 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-E7-A4XJ       TCGA-E7-A519       TCGA-E7-A5KF       TCGA-E7-A678 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-E7-A6ME       TCGA-E7-A6MF       TCGA-E7-A7PW       TCGA-E7-A7XN 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-E7-A85H       TCGA-E7-A97Q       TCGA-FD-A3B3       TCGA-FD-A3B4 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FD-A3B5       TCGA-FD-A3B8       TCGA-FD-A3N5       TCGA-FD-A3N6 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FD-A3SO       TCGA-FD-A3SP       TCGA-FD-A43N       TCGA-FD-A43S 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FD-A43U       TCGA-FD-A5BU       TCGA-FD-A5BV       TCGA-FD-A62N 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FD-A6TK       TCGA-FJ-A3Z9       TCGA-FJ-A3ZE       TCGA-FJ-A871 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-G2-A2EF       TCGA-G2-A2EJ       TCGA-G2-A2EL       TCGA-G2-A3IE 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-G2-AA3B       TCGA-G2-AA3C       TCGA-G2-AA3F       TCGA-GD-A2C5 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GD-A3OQ       TCGA-GD-A3OS       TCGA-GD-A6C6       TCGA-GU-A42Q 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GU-A42R       TCGA-GU-A764       TCGA-GU-AATQ       TCGA-GV-A3JV 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GV-A3JX       TCGA-GV-A3QH       TCGA-GV-A3QI       TCGA-H4-A2HO 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-H4-A2HQ       TCGA-HQ-A5NE       TCGA-K4-A3WV       TCGA-K4-A5RH 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-K4-A5RI       TCGA-K4-A83P       TCGA-K4-AAQO       TCGA-KQ-A41R 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-PQ-A6FI       TCGA-PQ-A6FN       TCGA-UY-A8OB       TCGA-UY-A9PB 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-UY-A9PE       TCGA-UY-A9PF       TCGA-XF-A9SL       TCGA-XF-A9SU 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-A9SX       TCGA-XF-A9SZ       TCGA-XF-AAMT       TCGA-XF-AAN0 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-AAN4       TCGA-XF-AAN5       TCGA-YF-AA3L       TCGA-ZF-A9R0 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-ZF-A9R3       TCGA-ZF-A9R5       TCGA-ZF-A9R9       TCGA-ZF-A9RD 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-ZF-A9RF       TCGA-ZF-A9RM       TCGA-ZF-AA4U       TCGA-ZF-AA4V 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-ZF-AA51       TCGA-ZF-AA52       TCGA-ZF-AA58       TCGA-ZF-AA5H 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-ZF-AA5N 
"POU3F1 WILD-TYPE" 
D81V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  POU3F1 MUTATED       0                         0     3
  POU3F1 WILD-TYPE    39                        22   314
D81V12, multiclass
                           clus
vv                          POU3F1 MUTATED POU3F1 WILD-TYPE
  ASIAN                                  0               39
  BLACK OR AFRICAN AMERICAN              0               22
  WHITE                                  3              314
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V13, binary
                  cls
clus                 0   1
  POU3F1 MUTATED     0   3
  POU3F1 WILD-TYPE   8 352
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POU3F1 MUTATED      0    3
  POU3F1 WILD-TYPE    8  352
                        clus
vv                       POU3F1 MUTATED POU3F1 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO              3              352
[1] 2 2
[1] FALSE
