[1] "ofn"        "-oTHNSC-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/HNSC-TP/22506490/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/22815324/transformed.cor.cli.txt"

nPatients in clinical file=528, in cluster file=511, common to both=511
[1]  62 511
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           364            147 
  TP53 MUTATED TP53 WILD-TYPE 
           364            147 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
             112              399 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
             112              399 
[1] "NSD1 MUTATION ANALYSIS"
[1] 3
  NSD1 MUTATED NSD1 WILD-TYPE 
            62            449 
  NSD1 MUTATED NSD1 WILD-TYPE 
            62            449 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
             54             457 
  CASP8 MUTATED CASP8 WILD-TYPE 
             54             457 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            81            430 
  MLL2 MUTATED MLL2 WILD-TYPE 
            81            430 
[1] "TGFBR2 MUTATION ANALYSIS"
[1] 3
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              24              487 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              24              487 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
             24             487 
  HLA-B MUTATED HLA-B WILD-TYPE 
             24             487 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             33             478 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             33             478 
[1] "NOTCH1 MUTATION ANALYSIS"
[1] 3
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              90              421 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              90              421 
[1] "FAT1 MUTATION ANALYSIS"
[1] 3
  FAT1 MUTATED FAT1 WILD-TYPE 
           112            399 
  FAT1 MUTATED FAT1 WILD-TYPE 
           112            399 
[1] "JUB MUTATION ANALYSIS"
[1] 3
  JUB MUTATED JUB WILD-TYPE 
           34           477 
  JUB MUTATED JUB WILD-TYPE 
           34           477 
[1] "ZNF750 MUTATION ANALYSIS"
[1] 3
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              21              490 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              21              490 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              27              484 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              27              484 
[1] "HLA-A MUTATION ANALYSIS"
[1] 3
  HLA-A MUTATED HLA-A WILD-TYPE 
             22             489 
  HLA-A MUTATED HLA-A WILD-TYPE 
             22             489 
[1] "EPHA2 MUTATION ANALYSIS"
[1] 3
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             24             487 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             24             487 
[1] "RAC1 MUTATION ANALYSIS"
[1] 3
  RAC1 MUTATED RAC1 WILD-TYPE 
            15            496 
  RAC1 MUTATED RAC1 WILD-TYPE 
            15            496 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            31            480 
  HRAS MUTATED HRAS WILD-TYPE 
            31            480 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
             38             473 
  EP300 MUTATED EP300 WILD-TYPE 
             38             473 
[1] "OR6C65 MUTATION ANALYSIS"
[1] 3
  OR6C65 MUTATED OR6C65 WILD-TYPE 
              16              495 
  OR6C65 MUTATED OR6C65 WILD-TYPE 
              16              495 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              94              417 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              94              417 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            14            497 
  PTEN MUTATED PTEN WILD-TYPE 
            14            497 
[1] "RASA1 MUTATION ANALYSIS"
[1] 3
  RASA1 MUTATED RASA1 WILD-TYPE 
             18             493 
  RASA1 MUTATED RASA1 WILD-TYPE 
             18             493 
[1] "MAPK1 MUTATION ANALYSIS"
[1] 3
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             502 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             502 
[1] "NUDT11 MUTATION ANALYSIS"
[1] 3
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               9              502 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               9              502 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
             17             494 
  KDM6A MUTATED KDM6A WILD-TYPE 
             17             494 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           17           494 
  RB1 MUTATED RB1 WILD-TYPE 
           17           494 
[1] "KEAP1 MUTATION ANALYSIS"
[1] 3
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             489 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             489 
[1] "KRT17 MUTATION ANALYSIS"
[1] 3
  KRT17 MUTATED KRT17 WILD-TYPE 
              6             505 
  KRT17 MUTATED KRT17 WILD-TYPE 
              6             505 
[1] "RHOA MUTATION ANALYSIS"
[1] 3
  RHOA MUTATED RHOA WILD-TYPE 
            10            501 
  RHOA MUTATED RHOA WILD-TYPE 
            10            501 
[1] "PTPN14 MUTATION ANALYSIS"
[1] 3
  PTPN14 MUTATED PTPN14 WILD-TYPE 
              16              495 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
              16              495 
[1] "KRTAP5-5 MUTATION ANALYSIS"
[1] 3
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 4                507 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 4                507 
[1] "ZNF623 MUTATION ANALYSIS"
[1] 3
  ZNF623 MUTATED ZNF623 WILD-TYPE 
              12              499 
  ZNF623 MUTATED ZNF623 WILD-TYPE 
              12              499 
[1] "TIGD4 MUTATION ANALYSIS"
[1] 3
  TIGD4 MUTATED TIGD4 WILD-TYPE 
              7             504 
  TIGD4 MUTATED TIGD4 WILD-TYPE 
              7             504 
[1] "NAP1L2 MUTATION ANALYSIS"
[1] 3
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               7              504 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               7              504 
[1] "CUL3 MUTATION ANALYSIS"
[1] 3
  CUL3 MUTATED CUL3 WILD-TYPE 
            16            495 
  CUL3 MUTATED CUL3 WILD-TYPE 
            16            495 
[1] "CREBBP MUTATION ANALYSIS"
[1] 3
  CREBBP MUTATED CREBBP WILD-TYPE 
              34              477 
  CREBBP MUTATED CREBBP WILD-TYPE 
              34              477 
[1] "VEZF1 MUTATION ANALYSIS"
[1] 3
  VEZF1 MUTATED VEZF1 WILD-TYPE 
              8             503 
  VEZF1 MUTATED VEZF1 WILD-TYPE 
              8             503 
[1] "MLL4 MUTATION ANALYSIS"
[1] 3
  MLL4 MUTATED MLL4 WILD-TYPE 
            19            492 
  MLL4 MUTATED MLL4 WILD-TYPE 
            19            492 
[1] "IRS4 MUTATION ANALYSIS"
[1] 3
  IRS4 MUTATED IRS4 WILD-TYPE 
            17            494 
  IRS4 MUTATED IRS4 WILD-TYPE 
            17            494 
[1] "HUWE1 MUTATION ANALYSIS"
[1] 3
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             46             465 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             46             465 
[1] "THSD7A MUTATION ANALYSIS"
[1] 3
  THSD7A MUTATED THSD7A WILD-TYPE 
              32              479 
  THSD7A MUTATED THSD7A WILD-TYPE 
              32              479 
[1] "C3ORF59 MUTATION ANALYSIS"
[1] 3
  C3ORF59 MUTATED C3ORF59 WILD-TYPE 
               10               501 
  C3ORF59 MUTATED C3ORF59 WILD-TYPE 
               10               501 
[1] "DYSF MUTATION ANALYSIS"
[1] 3
  DYSF MUTATED DYSF WILD-TYPE 
            20            491 
  DYSF MUTATED DYSF WILD-TYPE 
            20            491 
[1] "ZNF233 MUTATION ANALYSIS"
[1] 3
  ZNF233 MUTATED ZNF233 WILD-TYPE 
               9              502 
  ZNF233 MUTATED ZNF233 WILD-TYPE 
               9              502 
[1] "KIAA1267 MUTATION ANALYSIS"
[1] 3
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                11                500 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                11                500 
[1] "ASXL1 MUTATION ANALYSIS"
[1] 3
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             16             495 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             16             495 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             13             498 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             13             498 
[1] "GAGE2A MUTATION ANALYSIS"
[1] 3
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               4              507 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               4              507 
[1] "EMG1 MUTATION ANALYSIS"
[1] 3
  EMG1 MUTATED EMG1 WILD-TYPE 
             3            508 
  EMG1 MUTATED EMG1 WILD-TYPE 
             3            508 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               8              503 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               8              503 
[1] "KRTAP5-7 MUTATION ANALYSIS"
[1] 3
  KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE 
                 5                506 
  KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE 
                 5                506 
[1] "SLC9A6 MUTATION ANALYSIS"
[1] 3
  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
               5              506 
  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
               5              506 
[1] "ELF4 MUTATION ANALYSIS"
[1] 3
  ELF4 MUTATED ELF4 WILD-TYPE 
             7            504 
  ELF4 MUTATED ELF4 WILD-TYPE 
             7            504 
[1] "CTCF MUTATION ANALYSIS"
[1] 3
  CTCF MUTATED CTCF WILD-TYPE 
            15            496 
  CTCF MUTATED CTCF WILD-TYPE 
            15            496 
[1] "HNRNPL MUTATION ANALYSIS"
[1] 3
  HNRNPL MUTATED HNRNPL WILD-TYPE 
              11              500 
  HNRNPL MUTATED HNRNPL WILD-TYPE 
              11              500 
[1] "ZFP36L2 MUTATION ANALYSIS"
[1] 3
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                8               503 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                8               503 
[1] "MYH9 MUTATION ANALYSIS"
[1] 3
  MYH9 MUTATED MYH9 WILD-TYPE 
            21            490 
  MYH9 MUTATED MYH9 WILD-TYPE 
            21            490 
[1] "NOTCH2 MUTATION ANALYSIS"
[1] 3
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
              21              490 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
              21              490 
[1] "NCOR1 MUTATION ANALYSIS"
[1] 3
  NCOR1 MUTATED NCOR1 WILD-TYPE 
             17             494 
  NCOR1 MUTATED NCOR1 WILD-TYPE 
             17             494 
[1] "AK5 MUTATION ANALYSIS"
[1] 3
  AK5 MUTATED AK5 WILD-TYPE 
           13           498 
  AK5 MUTATED AK5 WILD-TYPE 
           13           498 
[1] "SPTY2D1 MUTATION ANALYSIS"
[1] 3
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
               10               501 
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
               10               501 
[1] "PIWIL2 MUTATION ANALYSIS"
[1] 3
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
               8              503 
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
               8              503 
[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] "HISTOLOGICAL_TYPE"                   
[15] "NUMBER_PACK_YEARS_SMOKED"            
[16] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 511 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=203,	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=274,	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=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=8,	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=22,	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=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=85,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	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 511 columns, 1 survival variables, and 13 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"             "HISTOLOGICAL_TYPE"            
 [9] "NUMBER_PACK_YEARS_SMOKED"      "YEAR_OF_TOBACCO_SMOKING_ONSET"
[11] "NUMBER_OF_LYMPH_NODES"         "RACE"                         
[13] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=60, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=6, 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  46 137  99 172 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   47   137    99   172 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  46 137  99 172 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   47   137    99   172 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
175  67 168   7 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
175  67 168   7 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
175  67 168   7 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
175  67 168   7 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=85, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=59, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=18, binary=FALSE, numeric=TRUE
RACE, nv=4, 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   191 172
  TP53 WILD-TYPE  98  48
  TP53 MUTATED TP53 WILD-TYPE 
           363            146 
  TP53 MUTATED TP53 WILD-TYPE 
           172             48 
$`TP53 MUTATED`
TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 
        9.30        20.48        30.18        25.71        51.29         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V3 
        9.24        52.08        11.08        35.05        32.48        24.39 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 
       32.88        70.13        11.61         6.02         0.36        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D 
       30.94        14.04        21.11        12.66        22.85        48.03 
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
        3.35        15.19        13.64         9.07        23.74        42.35 
TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       17.10        65.59        15.52        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
        4.01        41.85        29.42        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP 
        5.69        14.47         2.27        11.05        20.48        16.41 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7870 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ 
        9.14         4.41        66.28        20.52        10.55        27.19 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
        8.81         6.28        55.86        38.04         4.67        56.68 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       12.89        32.81        52.14        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       14.33        45.83        27.58        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
        8.58        12.39        71.31         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 
       11.84        11.57         8.52        52.08        50.07        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       48.00        23.90        47.44        28.04        19.07        34.13 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
        6.74        10.45        32.22        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T 
       11.74        35.01        25.41        17.29        29.72         7.40 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CQ-5326 TCGA-CQ-5329 
       31.69        12.39         4.41        12.07         2.93        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 
       62.37        45.99        10.42         4.24        41.19        15.75 
TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 
       32.38        66.28        46.95        56.58        13.25        14.99 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 
       38.76        64.87        53.52        41.88        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CR-6474 
       23.24        29.36        33.60        29.49        12.46        18.54 
TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       16.90        11.64        22.78         9.27        47.18        39.16 
TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 
       40.93         3.45         3.09        24.95         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 
        9.17        34.06        19.92        17.13        47.01        27.06 
TCGA-CR-7390 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       49.58        32.65        44.25        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       35.41        29.95       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5966 
       76.24        19.20        17.95       107.51        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       13.35        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       54.74        62.43        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       20.52        26.43        11.24       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6956 
       42.38        15.09        30.08         6.08        53.95         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
        8.42        28.34         4.14        64.83       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 
       18.81        12.66         7.99         5.26         1.84        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7236 
       12.92        21.80        71.21        10.75        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       89.65        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 
        4.96        11.87        47.97         2.10        18.41        35.54 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
        9.67         0.46        22.85        25.08        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       34.09       100.57        14.89        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7446 TCGA-CV-7568 
        7.17       153.86        16.64         6.38        35.93        30.48 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X 
       21.01       169.38       180.16        35.47        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
        7.07        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CV-A6K2 
       28.01         3.62        21.24        23.47        22.52        10.42 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        51.12        13.25        25.41         9.60        23.05 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       16.14        11.44        24.95        25.32        17.72        12.36 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 
        7.63        24.95        13.94        12.10        23.34        58.45 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       33.86        18.02        37.58        37.18        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
       20.25         3.02        18.94        24.95         0.46        17.85 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 
       20.25        12.43        15.16        15.06        33.76        28.47 
TCGA-HD-7831 TCGA-HD-8224 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E 
       21.93        14.66        13.84         3.65        15.95        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       11.84        37.41        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A7BN TCGA-MZ-A7D7 
       19.04        15.48        10.75        14.37        15.42        17.98 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       15.78        71.74        47.01        19.00        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        2.04        29.00        16.01        13.15        21.07        21.21 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC 
        7.30        21.47         9.34        12.72        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       12.89         5.62        14.76        12.20        17.82        15.32 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-T3-A92M TCGA-UF-A718 TCGA-UF-A719 
        8.32        12.72        15.91        13.71        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD 
        2.83        49.51        49.45        44.65        74.47        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-WA-A7GZ TCGA-KU-A66T 
       32.65        20.55        18.15 

$`TP53 WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-A6V1 TCGA-CQ-5323 
       37.28        68.48         3.55        28.11        19.82        48.20 
TCGA-CQ-7068 TCGA-CR-6472 TCGA-DQ-7593 TCGA-UF-A7JV TCGA-BA-5149 TCGA-BA-5153 
       43.04        34.52        40.24         2.96        26.50        57.93 
TCGA-BA-5556 TCGA-BA-A4IH TCGA-BA-A6DF TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 
       23.84        20.45         7.82        13.38         6.15       105.90 
TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-8596 TCGA-BB-A6UM TCGA-C9-A480 TCGA-CN-4730 
        4.80        18.38        71.05        12.92        12.69        26.86 
TCGA-CN-4734 TCGA-CN-4741 TCGA-CN-5361 TCGA-CN-5369 TCGA-CN-5374 TCGA-CN-A499 
       55.56        73.61        69.70        12.49        56.94        23.57 
TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       21.21        22.32        16.57         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5333 TCGA-CQ-6227 
       19.53        52.37        21.50        54.58        11.21         4.24 
TCGA-CQ-7071 TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       43.10        14.14        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       37.87        26.27        58.42        50.01        39.52        36.99 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 
       11.90        10.22        11.34         7.69        12.46        15.75 
TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7373 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7389 
       47.34        35.84        29.23        26.17        32.78        12.89 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7395 TCGA-CR-7404 TCGA-CV-5441 TCGA-CV-5442 
       30.02        46.85        30.58        48.39        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6938 TCGA-CV-6939 
       91.53        23.05        21.07         9.60         4.73        21.90 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6961 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7250 
       65.82        10.98         2.50         9.01       130.88        95.34 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7425 TCGA-CV-7427 
       49.71        57.47       210.97        89.33        56.48       156.49 
TCGA-CV-7429 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A6JO 
        3.52        22.19        27.98       159.65         1.05         6.48 
TCGA-CV-A6K0 TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-A6EK TCGA-D6-A6EN 
       19.92        10.55         2.53        18.67        28.77        22.59 
TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-7591 TCGA-DQ-7596 TCGA-F7-A50J TCGA-F7-A622 
       12.79        37.25        20.45        41.59        31.13        11.80 
TCGA-H7-7774 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8314 TCGA-HD-A4C1 
       13.38        20.94        25.74        27.48        22.03         0.36 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61I TCGA-KU-A6H7 
        4.27         6.90        38.53        14.50         0.07        19.27 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI 
        7.96        30.05         1.84        12.62         6.25         7.13 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T6 
       16.08        29.92        51.25        10.85        36.82        12.99 
TCGA-QK-A6IF TCGA-QK-A6V9 TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
       23.15        27.39        16.96         6.87         7.10        32.45 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A7JC TCGA-UP-A6WW 
        3.12        13.55        13.25        20.35        17.95        17.03 
TCGA-WA-A7H4 TCGA-KU-A66S 
       14.56        13.35 

  TP53 MUTATED TP53 WILD-TYPE 
          0.07           0.07 
  TP53 MUTATED TP53 WILD-TYPE 
        180.16         210.97 
  TP53 MUTATED TP53 WILD-TYPE 
        20.520         21.965 
[1] "0.1 - 180.2 (20.5)" "0.1 - 211.0 (22.0)"
[1] "hr=" "1.6"
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  TP53 MUTATED        17       50        58       194         9         1
  TP53 WILD-TYPE       8       25        22        59         2         0
D1V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I             17              8
  STAGE II            50             25
  STAGE III           58             22
  STAGE IVA          194             59
  STAGE IVB            9              2
  STAGE IVC            1              0
[1] 6 2
[1] 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      30  91  79 135
  TP53 WILD-TYPE    17  46  20  37
D1V4, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T0+T1           30             17
  T2              91             46
  T3              79             20
  T4             135             37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TP53 MUTATED   125  50 130   5
  TP53 WILD-TYPE  50  17  38   2
D1V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0          125             50
  N1           50             17
  N2          130             38
  N3            5              2
[1] 4 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   140   1
  TP53 WILD-TYPE  51   0
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    140    1
  TP53 WILD-TYPE   51    0
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0          140             51
  1            1              0
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus               0   1
  TP53 MUTATED    99 265
  TP53 WILD-TYPE  39 108
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     99  265
  TP53 WILD-TYPE   39  108
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           99             39
  MALE            265            108
[1] 2 2
[1] FALSE
D1V8, binary
                cls
clus               0   1
  TP53 MUTATED   106 212
  TP53 WILD-TYPE  51  81
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    106  212
  TP53 WILD-TYPE   51   81
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO           106             51
  YES          212             81
[1] 2 2
[1] FALSE
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA
  TP53 MUTATED                                   360
  TP53 WILD-TYPE                                 140
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  TP53 MUTATED                                                   3
  TP53 WILD-TYPE                                                 7
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  TP53 MUTATED                                                           1
  TP53 WILD-TYPE                                                         0
D1V9, multiclass
                                                           clus
vv                                                          TP53 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                360
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT            1
                                                           clus
vv                                                          TP53 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  140
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
D1V11, continuous
D1V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  2     7
  TP53 WILD-TYPE                                0     3
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                          38   303
  TP53 WILD-TYPE                         9   134
D1V13, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            2              0
  ASIAN                                       7              3
  BLACK OR AFRICAN AMERICAN                  38              9
  WHITE                                     303            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"
D1V14, binary
                cls
clus               0   1
  TP53 MUTATED    22 314
  TP53 WILD-TYPE   3 135
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     22  314
  TP53 WILD-TYPE    3  135
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO               22              3
  NOT HISPANIC OR LATINO          314            135
[1] 2 2
[1] FALSE

Clustering(2) Variable = CDKN2A MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2                0   1
  CDKN2A MUTATED    60  51
  CDKN2A WILD-TYPE 229 169
  CDKN2A MUTATED CDKN2A WILD-TYPE 
             111              398 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              51              169 
$`CDKN2A MUTATED`
TCGA-BA-4075 TCGA-BA-5557 TCGA-CN-6021 TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-7063 
        9.30        20.48         9.07        32.48        24.39        70.13 
TCGA-DQ-5629 TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5558 TCGA-BA-6872 TCGA-BA-6873 
       30.94         9.07        42.35        65.59        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DG TCGA-BB-A5HY 
       41.85        29.42        11.54         5.69         2.27        10.55 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-5359 
       12.69        55.86        32.81        12.99        14.33        12.39 
TCGA-CN-5360 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6019 
       71.31         8.52        52.08        48.00        23.90        34.13 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A640 TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5331 
       17.42        11.74         4.41         2.93        62.37        45.99 
TCGA-CQ-6220 TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-A4C6 TCGA-CQ-A4CD TCGA-CR-5247 
       32.38        56.58        38.76        44.48        33.60        11.77 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7370 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7386 
       22.78        15.75         3.45        34.06        19.92        47.01 
TCGA-CR-7394 TCGA-CV-5432 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-5976 
       44.25       129.21       107.51        80.12        86.83        48.59 
TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
       60.49        54.74        62.43        11.24       140.78        19.79 
TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7101 
       30.08        53.95         8.42         4.14       172.67         5.26 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7254 TCGA-CV-7255 
       71.21        10.75        31.36        26.20        47.97         2.10 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-7568 TCGA-CV-A45O 
        9.67         0.46        14.89        84.49        30.48        27.98 
TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A45Z TCGA-CV-A465 TCGA-CV-A6JD 
       21.01       180.16        45.96        48.20         7.07         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6825 TCGA-D6-A6EM 
       35.34         6.38        13.25        25.41        16.14         7.63 
TCGA-D6-A6EN TCGA-D6-A74Q TCGA-F7-A50I TCGA-F7-A61S TCGA-H7-8501 TCGA-HD-8224 
       22.59        23.34         3.02        18.94        15.16        14.66 
TCGA-HD-A633 TCGA-IQ-A6SH TCGA-MT-A67A TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T3 
       13.84        15.48        30.05        71.74        47.01        18.97 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A8ZB 
       21.07        21.21         7.30         9.34        12.72        17.82 
TCGA-RS-A6TO TCGA-UF-A7J9 TCGA-UF-A7JO 
       12.72        44.65        20.75 

$`CDKN2A WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
       37.28        68.48         3.55        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-A6V1 
       51.29         9.24        52.08        11.08        35.05        19.82 
TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       48.20        32.88        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
        0.36        34.36        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-6868 
       26.50        23.74        57.93        17.10        23.84        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE 
       21.17        14.83        20.45        27.95         7.10        14.47 
TCGA-BA-A6DF TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
        7.82        11.05        13.38        20.48        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 
      105.90         9.14         4.80         4.41        18.38        66.28 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       71.05        20.52        27.19        12.92         8.81         6.28 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4733 
       38.04         4.67        56.68        12.89        26.86        52.14 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       55.56        57.11        20.55        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5361 TCGA-CN-5363 
       13.05        42.02        46.32         8.58        69.70         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5374 
       16.21        11.54        11.84        11.57        12.49        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6020 
       50.07        30.67        47.44        28.04        19.07         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A498 
       10.45        32.22        38.89         3.68        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       23.57        17.29        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       22.32        12.39        16.57        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
       20.88        19.53        52.37        21.50        54.58        70.45 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6222 
       10.42        11.21         4.24        41.19        15.75        66.28 
TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 
       46.95        13.25         4.24        14.99        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE 
       41.88        43.10        77.56        23.24        29.36        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
       14.14        12.46        31.23        84.23        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
       26.27        58.42        50.01        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       16.90        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       12.46         9.27        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
       35.84         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 
        9.17        26.17        17.13        32.78        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7395 TCGA-CR-7397 
       49.58        30.02        46.85        32.65        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 
       17.16       108.95        76.24        19.20        17.95        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5978 
       76.50        91.53        17.92        13.35        23.05         7.07 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       43.23        21.07         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6945 
        5.46        20.52         4.73        21.90        26.43        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       42.38        15.09         6.08        65.82        10.98         7.13 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
       28.34         2.50        64.83       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        7.99         9.01         1.84        52.31        12.92        21.80 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7247 
      130.88        77.16         4.73        89.65        36.00        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7261 TCGA-CV-7263 
       17.13        95.34         4.96        11.87        49.71        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7415 TCGA-CV-7416 
       57.47        35.54       210.97        89.33        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 
       25.94         0.07        34.09       100.57        56.48       156.49 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 
        3.52        16.27        19.76         7.17       153.86        16.64 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45U 
        6.38        22.19        35.93       169.38       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        1.05         6.51        88.87        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       56.61        15.25        29.79         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6826 
       18.84        51.12         9.60        23.05         2.53        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 
       24.95        13.94        12.10        12.79        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 
       33.86        18.02        20.45        37.58        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W 
       32.71        21.63        20.25        31.13        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8502 
       17.85        11.80        20.25        12.43        13.38        15.06 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       20.94        33.76        28.47        25.74        21.93        27.48 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 
       22.03         0.36         4.27         3.65         6.90        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A6H7 
       33.57         5.29        13.68        13.84        19.04        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       10.75        14.37         7.96         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
       51.25        10.85        36.82        19.00        75.55         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A6IF TCGA-QK-A6IH 
       29.00        12.99        16.01        13.15        23.15        21.47 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       27.39        21.07        19.73        12.89         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       12.20        15.32         8.32        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ 
        7.10        32.45        13.71         3.12        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       20.35        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       74.47        17.95        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       13.94        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            0.46             0.07 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
          180.16           210.97 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
          22.590           20.535 
[1] "0.5 - 180.2 (22.6)" "0.1 - 211.0 (20.5)"
[1] "hr=" "1"  
D2V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  CDKN2A MUTATED         7       12        25        52         1         0
  CDKN2A WILD-TYPE      18       63        55       201        10         1
D2V3, multiclass
           clus
vv          CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE I                7               18
  STAGE II              12               63
  STAGE III             25               55
  STAGE IVA             52              201
  STAGE IVB              1               10
  STAGE IVC              0                1
[1] 6 2
[1] 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      11  26  23  39
  CDKN2A WILD-TYPE    36 111  76 133
D2V4, multiclass
       clus
vv      CDKN2A MUTATED CDKN2A WILD-TYPE
  T0+T1             11               36
  T2                26              111
  T3                23               76
  T4                39              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                N0  N1  N2  N3
  CDKN2A MUTATED    38  17  31   0
  CDKN2A WILD-TYPE 137  50 137   7
D2V5, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  N0             38              137
  N1             17               50
  N2             31              137
  N3              0                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"
D2V6, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    40   0
  CDKN2A WILD-TYPE 151   1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     40    0
  CDKN2A WILD-TYPE  151    1
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0             40              151
  1              0                1
[1] 2 2
[1] FALSE
D2V7, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    31  81
  CDKN2A WILD-TYPE 107 292
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     31   81
  CDKN2A WILD-TYPE  107  292
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE             31              107
  MALE               81              292
[1] 2 2
[1] FALSE
D2V8, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    31  66
  CDKN2A WILD-TYPE 126 227
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     31   66
  CDKN2A WILD-TYPE  126  227
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO              31              126
  YES             66              227
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  CDKN2A MUTATED                                   112
  CDKN2A WILD-TYPE                                 388
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  CDKN2A MUTATED                                                   0
  CDKN2A WILD-TYPE                                                10
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  CDKN2A MUTATED                                                           0
  CDKN2A WILD-TYPE                                                         1
D2V9, multiclass
                                                           clus
vv                                                          CDKN2A MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  112
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          CDKN2A WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    388
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, continuous
D2V11, continuous
D2V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDKN2A MUTATED                                  0     3
  CDKN2A WILD-TYPE                                2     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED                           7   100
  CDKN2A WILD-TYPE                        40   337
D2V13, multiclass
                                  clus
vv                                 CDKN2A MUTATED CDKN2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         3                7
  BLACK OR AFRICAN AMERICAN                     7               40
  WHITE                                       100              337
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     7 101
  CDKN2A WILD-TYPE  18 348
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      7  101
  CDKN2A WILD-TYPE   18  348
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  7               18
  NOT HISPANIC OR LATINO            101              348
[1] 2 2
[1] FALSE

Clustering(3) Variable = NSD1 MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  NSD1 MUTATED    43  19
  NSD1 WILD-TYPE 246 201
  NSD1 MUTATED NSD1 WILD-TYPE 
            62            447 
  NSD1 MUTATED NSD1 WILD-TYPE 
            19            201 
$`NSD1 MUTATED`
TCGA-CN-4727 TCGA-CN-A6V3 TCGA-H7-A6C5 TCGA-UF-A71D TCGA-BA-5555 TCGA-BA-6869 
       51.29        24.39        21.11        48.03        17.10        21.17 
TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BB-7870 TCGA-BB-A5HZ TCGA-CN-4730 
       29.42        14.47        20.48        66.28        27.19        26.86 
TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-A497 TCGA-CN-A63T TCGA-CN-A63U 
       45.83        46.32        71.31        35.01         7.40        31.69 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-7072 TCGA-CR-5247 TCGA-CR-6481 TCGA-CR-7364 
       12.39        12.07        77.56        11.77        10.22        47.18 
TCGA-CR-7385 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5441 TCGA-CV-6441 
       32.78        30.58         5.13        29.95        94.88         9.60 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7242 
       11.24       140.78         7.13        28.34         2.50        36.00 
TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7427 TCGA-CV-7440 TCGA-CV-7568 
       26.20        95.34        11.87       156.49        22.19        30.48 
TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A468 TCGA-CV-A6JU TCGA-D6-8569 TCGA-D6-A6EO 
       48.20        67.86        15.25         3.62        25.32        24.95 
TCGA-D6-A74Q TCGA-F7-7848 TCGA-F7-A623 TCGA-P3-A5QF TCGA-P3-A6T6 TCGA-P3-A6T8 
       23.34        37.18        20.25        10.85        12.99        13.15 
TCGA-QK-A6VB TCGA-QK-A8Z8 TCGA-QK-AA3J TCGA-TN-A7HL TCGA-UF-A719 TCGA-UF-A71B 
       21.07         5.62        15.32        20.35        54.67        49.51 
TCGA-UF-A7JF TCGA-KU-A66S 
       55.43        13.35 

$`NSD1 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       30.18        25.71         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       35.05        32.48        19.82        48.20        32.88        70.13 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 
       43.04        11.61        34.52         6.02         0.36        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A7JV 
       30.94        14.04        40.24        12.66        22.85         2.96 
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
        3.35        15.19        13.64         9.07        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 
       42.35        57.93        23.84        65.59        15.52        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
       12.62         4.01        41.85        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        7.10         5.69         7.82         2.27        11.05        13.38 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.80         4.41 
TCGA-BB-4228 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A6UM TCGA-BB-A6UO 
       18.38        71.05        20.52        10.55        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
        6.28        12.69        55.86        38.04         4.67        56.68 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
       12.89        32.81        52.14        55.56        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       20.55        14.33        27.58        73.61        13.05        42.02 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
        8.58        12.39        69.70         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.84        11.57        12.49         8.52        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
       19.07        34.13         6.74        10.45        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
        3.68        17.42        11.74        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 
       29.72        21.21        22.32        16.57         4.41         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       23.44        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 
        4.24        41.19        15.75        32.38        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       56.58        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       53.52        41.88        43.10        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 
       36.99        18.54        16.90        11.90        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 
        7.69        12.46        22.78        15.75         9.27        39.16 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
       47.34        40.93        35.84         3.45         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       29.23         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       26.17        17.13        47.01        27.06        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7399 
       30.02        46.85        32.65        44.25        24.79         5.95 
TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       35.41        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 
       76.24        19.20        17.95       107.51        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       60.49         7.07        43.23        54.74        21.07        62.43 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       90.12         2.14         9.70         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       21.90        26.43        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6959 
       30.08         6.08        53.95        65.82        10.98         8.42 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        4.14        64.83       172.67       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7254 
       89.65        31.36        18.97        17.13         4.96        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 
        2.10        49.71        18.41        57.47        35.54       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 
       89.33         9.67         0.46        22.85        25.08        25.94 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7429 
        0.07        34.09       100.57        14.89        56.48         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 
       16.27        84.49        19.76         7.17       153.86        16.64 
TCGA-CV-7438 TCGA-CV-7446 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
        6.38        35.93        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A6JD TCGA-CV-A6JE 
       60.43         0.76        56.61         7.07         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ 
        6.38        29.79         6.48        28.01        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       11.44        18.67        24.95        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 
        7.63        22.59        13.94        12.10        12.79        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 
       37.25        33.86        18.02        20.45        37.58        41.59 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 
       24.95         0.46        17.85        11.80        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       21.93        27.48        14.66        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65         6.90        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       71.74        51.25        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 
       18.97         2.04        29.00        16.01        21.07        21.21 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       23.15         7.30        21.47         9.34        12.72        27.39 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K 
       19.73        12.89        14.76        12.20        17.82         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.72        16.96         6.87        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A71A 
       13.71         3.12        13.55        13.25        64.80         2.83 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
       49.45        44.65        74.47        17.95        24.30        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       18.05        13.94        20.75        22.36        32.65        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66T 
       20.55        14.56        18.15 

  NSD1 MUTATED NSD1 WILD-TYPE 
          2.50           0.07 
  NSD1 MUTATED NSD1 WILD-TYPE 
        156.49         210.97 
  NSD1 MUTATED NSD1 WILD-TYPE 
        25.135         20.480 
[1] "2.5 - 156.5 (25.1)" "0.1 - 211.0 (20.5)"
[1] "hr=" "1.6"
D3V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  NSD1 MUTATED         1       13         9        30         1         1
  NSD1 WILD-TYPE      24       62        71       223        10         0
D3V3, multiclass
           clus
vv          NSD1 MUTATED NSD1 WILD-TYPE
  STAGE I              1             24
  STAGE II            13             62
  STAGE III            9             71
  STAGE IVA           30            223
  STAGE IVB            1             10
  STAGE IVC            1              0
[1] 6 2
[1] 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
  NSD1 MUTATED       7  12  13  25
  NSD1 WILD-TYPE    40 125  86 147
D3V4, multiclass
       clus
vv      NSD1 MUTATED NSD1 WILD-TYPE
  T0+T1            7             40
  T2              12            125
  T3              13             86
  T4              25            147
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  NSD1 MUTATED    31   7  13   0
  NSD1 WILD-TYPE 144  60 155   7
D3V5, multiclass
    clus
vv   NSD1 MUTATED NSD1 WILD-TYPE
  N0           31            144
  N1            7             60
  N2           13            155
  N3            0              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
  NSD1 MUTATED    26   1
  NSD1 WILD-TYPE 165   0
[1] "tbl2"
                cls
clus             [,1] [,2]
  NSD1 MUTATED     26    1
  NSD1 WILD-TYPE  165    0
   clus
vv  NSD1 MUTATED NSD1 WILD-TYPE
  0           26            165
  1            1              0
[1] 2 2
[1] FALSE
D3V7, binary
                cls
clus               0   1
  NSD1 MUTATED    12  50
  NSD1 WILD-TYPE 126 323
[1] "tbl2"
                cls
clus             [,1] [,2]
  NSD1 MUTATED     12   50
  NSD1 WILD-TYPE  126  323
        clus
vv       NSD1 MUTATED NSD1 WILD-TYPE
  FEMALE           12            126
  MALE             50            323
[1] 2 2
[1] FALSE
D3V8, binary
                cls
clus               0   1
  NSD1 MUTATED    20  37
  NSD1 WILD-TYPE 137 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  NSD1 MUTATED     20   37
  NSD1 WILD-TYPE  137  256
     clus
vv    NSD1 MUTATED NSD1 WILD-TYPE
  NO            20            137
  YES           37            256
[1] 2 2
[1] FALSE
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA
  NSD1 MUTATED                                    60
  NSD1 WILD-TYPE                                 440
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  NSD1 MUTATED                                                   2
  NSD1 WILD-TYPE                                                 8
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  NSD1 MUTATED                                                           0
  NSD1 WILD-TYPE                                                         1
D3V9, multiclass
                                                           clus
vv                                                          NSD1 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                 60
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT            0
                                                           clus
vv                                                          NSD1 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  440
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, continuous
D3V11, continuous
D3V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NSD1 MUTATED                                  0     0
  NSD1 WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NSD1 MUTATED                           6    53
  NSD1 WILD-TYPE                        41   384
D3V13, multiclass
                                  clus
vv                                 NSD1 MUTATED NSD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   6             41
  WHITE                                      53            384
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                cls
clus               0   1
  NSD1 MUTATED     5  52
  NSD1 WILD-TYPE  20 397
[1] "tbl2"
                cls
clus             [,1] [,2]
  NSD1 MUTATED      5   52
  NSD1 WILD-TYPE   20  397
                        clus
vv                       NSD1 MUTATED NSD1 WILD-TYPE
  HISPANIC OR LATINO                5             20
  NOT HISPANIC OR LATINO           52            397
[1] 2 2
[1] FALSE

Clustering(4) Variable = CASP8 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED    28  26
  CASP8 WILD-TYPE 261 194
  CASP8 MUTATED CASP8 WILD-TYPE 
             54             455 
  CASP8 MUTATED CASP8 WILD-TYPE 
             26             194 
$`CASP8 MUTATED`
TCGA-CQ-7068 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-6873 TCGA-CN-4734 TCGA-CN-5369 
       43.04        23.74        23.84         4.01        55.56        12.49 
TCGA-CN-A642 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
        2.70        52.37        54.58        45.99        11.21         4.24 
TCGA-CQ-6220 TCGA-CQ-7071 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7394 TCGA-CR-7395 
       32.38        43.10        34.06        26.17        44.25        30.58 
TCGA-CR-7402 TCGA-CV-5966 TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6943 TCGA-CV-6953 
       29.95        17.92        62.43         4.73        19.79        53.95 
TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7252 TCGA-CV-7413 TCGA-CV-7425 TCGA-CV-A45O 
       18.81         7.99         4.96         9.67        56.48        27.98 
TCGA-CV-A45P TCGA-CV-A45V TCGA-CV-A463 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM 
       21.01         1.05         0.76        15.25         5.98         6.38 
TCGA-CV-A6JO TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-A6EK TCGA-D6-A6EN TCGA-F7-A624 
        6.48        10.42        10.55        28.77        22.59        12.43 
TCGA-H7-8501 TCGA-HD-A4C1 TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A6T2 TCGA-QK-A64Z 
       15.16         0.36         1.84        12.62        75.55        21.07 
TCGA-QK-A6IG TCGA-QK-A6VB TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-UF-A7JO 
        7.30        21.07        12.72         6.87        32.45        20.75 

$`CASP8 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       32.88        70.13        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 
        9.07        26.50        42.35        57.93        17.10        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
       15.52        21.17        14.83        12.62        41.85        29.42 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       20.45        27.95        11.54         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
        7.82         2.27        11.05        13.38        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15       105.90         9.14         4.80         4.41        18.38 
TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       66.28        71.05        20.52        10.55        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        8.81         6.28        12.69        55.86        38.04         4.67 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       56.68        12.89        26.86        32.81        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        42.02        46.32         8.58        12.39        71.31 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       69.70         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        8.52        52.08        56.94        50.07        30.67        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       23.90        47.44        28.04        19.07        34.13         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       10.45        32.22        38.89         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        31.69        22.32        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5325 TCGA-CQ-5326 
       12.07        23.44        20.88        19.53        21.50         2.93 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6222 
       70.45        62.37        10.42        41.19        15.75        66.28 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       64.87        53.52        41.88        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       15.75         9.27        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       31.96         9.17        19.92        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 
       24.79         5.13         5.95        35.41        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       17.16       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 
      107.51        94.88        76.50        91.53        80.12        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       54.74        21.07         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
        5.46        20.52        21.90        26.43        11.24       140.78 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6954 
       12.03        42.38        15.09        30.08         6.08        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       10.98         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 
       64.83       172.67       111.16        12.66         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        1.84        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 
       26.20        18.97        17.13        95.34        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 
        2.10        49.71        18.41        57.47        35.54       210.97 
TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
       89.33         0.46        22.85        25.08        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 
       34.09       100.57        14.89       156.49         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       84.49        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
       22.19        35.93        30.48       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
       35.47        45.96         6.51        88.87        48.20        60.43 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JT 
       67.86        56.61         7.07        35.34        29.79        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7086 
        3.62        21.24        23.47        19.92        22.52        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       16.14        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       12.36         7.63        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 
       23.34        58.45        37.25        33.86        18.02        20.45 
TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       37.58        41.59        37.18        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       11.80        20.25        13.38        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         3.65         6.90        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        37.71        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67G TCGA-MT-A7BN 
       10.75        14.37         7.96        30.05         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 
       51.25        10.85        36.82        47.01        19.00        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A652 
        2.04        29.00        12.99        16.01        13.15        21.21 
TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC 
       23.15        21.47         9.34        12.72        27.39        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       12.89         5.62        14.76        12.20        17.82        15.32 
TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T3-A92M TCGA-T3-A92N 
        8.32        16.96        15.91         7.10        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT 
       55.43        29.46        18.05        13.94        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       17.03        20.55        14.56        13.35        18.15 

  CASP8 MUTATED CASP8 WILD-TYPE 
           0.36            0.07 
  CASP8 MUTATED CASP8 WILD-TYPE 
          75.55          210.97 
  CASP8 MUTATED CASP8 WILD-TYPE 
          19.30           21.11 
[1] "0.4 - 75.5 (19.3)"  "0.1 - 211.0 (21.1)"
[1] "hr=" "1.5"
D4V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  CASP8 MUTATED         2       11        10        24         1         0
  CASP8 WILD-TYPE      23       64        70       229        10         1
D4V3, multiclass
           clus
vv          CASP8 MUTATED CASP8 WILD-TYPE
  STAGE I               2              23
  STAGE II             11              64
  STAGE III            10              70
  STAGE IVA            24             229
  STAGE IVB             1              10
  STAGE IVC             0               1
[1] 6 2
[1] 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       2  17  10  20
  CASP8 WILD-TYPE    45 120  89 152
D4V4, multiclass
       clus
vv      CASP8 MUTATED CASP8 WILD-TYPE
  T0+T1             2              45
  T2               17             120
  T3               10              89
  T4               20             152
[1] 4 2
[1] TRUE
[1] "dimension of 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    24   6  10   1
  CASP8 WILD-TYPE 151  61 158   6
D4V5, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  N0            24             151
  N1             6              61
  N2            10             158
  N3             1               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"
D4V6, binary
                 cls
clus                0   1
  CASP8 MUTATED    22   0
  CASP8 WILD-TYPE 169   1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     22    0
  CASP8 WILD-TYPE  169    1
   clus
vv  CASP8 MUTATED CASP8 WILD-TYPE
  0            22             169
  1             0               1
[1] 2 2
[1] FALSE
D4V7, binary
                 cls
clus                0   1
  CASP8 MUTATED    26  28
  CASP8 WILD-TYPE 112 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     26   28
  CASP8 WILD-TYPE  112  345
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  FEMALE            26             112
  MALE              28             345
[1] 2 2
[1] FALSE
D4V8, binary
                 cls
clus                0   1
  CASP8 MUTATED    23  27
  CASP8 WILD-TYPE 134 266
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     23   27
  CASP8 WILD-TYPE  134  266
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO             23             134
  YES            27             266
[1] 2 2
[1] FALSE
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA
  CASP8 MUTATED                                    54
  CASP8 WILD-TYPE                                 446
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  CASP8 MUTATED                                                   0
  CASP8 WILD-TYPE                                                10
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  CASP8 MUTATED                                                           0
  CASP8 WILD-TYPE                                                         1
D4V9, multiclass
                                                           clus
vv                                                          CASP8 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  54
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             0
                                                           clus
vv                                                          CASP8 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   446
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, continuous
D4V11, continuous
D4V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASP8 MUTATED                                  0     1
  CASP8 WILD-TYPE                                2     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CASP8 MUTATED                           2    49
  CASP8 WILD-TYPE                        45   388
D4V13, multiclass
                                  clus
vv                                 CASP8 MUTATED CASP8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              45
  WHITE                                       49             388
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
                 cls
clus                0   1
  CASP8 MUTATED     4  48
  CASP8 WILD-TYPE  21 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      4   48
  CASP8 WILD-TYPE   21  401
                        clus
vv                       CASP8 MUTATED CASP8 WILD-TYPE
  HISPANIC OR LATINO                 4              21
  NOT HISPANIC OR LATINO            48             401
[1] 2 2
[1] FALSE

Clustering(5) Variable = MLL2 MUTATION ANALYSIS
D5V1, survival
                sevent
clus2              0   1
  MLL2 MUTATED    39  42
  MLL2 WILD-TYPE 250 178
  MLL2 MUTATED MLL2 WILD-TYPE 
            81            428 
  MLL2 MUTATED MLL2 WILD-TYPE 
            42            178 
$`MLL2 MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-6871 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
        9.30        37.28         3.55         9.07         9.24        52.08 
TCGA-CN-6997 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CR-6478 TCGA-DQ-7593 TCGA-H7-A6C5 
       32.48        48.20        32.88         6.02        40.24        21.11 
TCGA-HD-8635 TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5558 TCGA-BA-6870 
       22.85        15.19        13.64        26.50        65.59        14.83 
TCGA-BA-A6DF TCGA-BA-A6DI TCGA-BB-7870 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4737 
        7.82        11.05        66.28        32.81        57.11        20.55 
TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5370 TCGA-CN-6011 TCGA-CN-6996 TCGA-CN-A6V6 
       73.61        46.32         8.52        30.67        17.42        20.88 
TCGA-CQ-6225 TCGA-CR-5243 TCGA-CR-6473 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-7379 
       13.25        84.23        36.99        11.64         7.69        34.06 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7402 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5441 
       27.06        12.89        29.95       108.95        19.20        94.88 
TCGA-CV-6441 TCGA-CV-6950 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7248 TCGA-CV-7252 
        9.60        15.09        71.21       130.88        17.13         4.96 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7422 TCGA-CV-7430 TCGA-CV-7434 TCGA-CV-7435 
       47.97        49.71        34.09        16.27         7.17       153.86 
TCGA-CV-7437 TCGA-CV-7568 TCGA-CV-A45V TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A6JM 
       16.64        30.48         1.05        48.20        67.86         6.38 
TCGA-CV-A6K1 TCGA-CX-7086 TCGA-D6-8568 TCGA-D6-A6ES TCGA-F7-A61W TCGA-F7-A622 
       22.52        18.84        24.95        12.79         0.46        11.80 
TCGA-F7-A624 TCGA-H7-8501 TCGA-IQ-7632 TCGA-MT-A67A TCGA-MT-A67D TCGA-P3-A5QF 
       12.43        15.16        14.50        30.05         1.84        10.85 
TCGA-P3-A6T4 TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T3-A92M 
        2.04        17.82         8.32        12.72        16.96        13.71 
TCGA-T3-A92N TCGA-UF-A7JH TCGA-UF-A7JT 
        3.12        29.46        32.65 

$`MLL2 WILD-TYPE`
TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 
       20.48        68.48        28.11        30.18        25.71        51.29 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-7063 TCGA-CQ-7068 
       11.08        35.05        19.82        24.39        70.13        43.04 
TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 
       11.61        34.52         0.36        34.36        30.94        14.04 
TCGA-HD-8634 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4078 TCGA-BA-5151 
       12.66        48.03         2.96         3.35         9.07        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-6868 TCGA-BA-6869 
       42.35        57.93        17.10        23.84        15.52        21.17 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ 
       11.54         7.10         5.69        14.47         2.27        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       20.48        16.41         6.15       105.90         9.14         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ 
        4.41        18.38        71.05        20.52        10.55        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 
       12.92         8.81         6.28        12.69        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4734 
        4.67        56.68        12.89        26.86        52.14        55.56 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 
       12.99        14.33        45.83        27.58        13.05        42.02 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 
        8.58        12.39        71.31        69.70         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-5374 
       11.54        11.84        11.57        12.49        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       50.07        48.00        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 
       34.13         6.74        10.45        32.22        38.89         3.68 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 
        4.41        12.07         2.70        23.44        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 
       10.42        11.21         4.24        41.19        15.75        32.38 
TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       66.28        46.95        56.58         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       31.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       50.01        39.52        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
       11.34        12.46        22.78        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       39.16        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7380 
       24.95        29.23         0.99        31.96         9.17        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7390 TCGA-CR-7391 
       26.17        17.13        32.78        47.01        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58        24.79         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        5.95        35.41        48.39       139.43        17.16       129.21 
TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       76.24        17.95       107.51        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 
        7.07        43.23        54.74        21.07        62.43        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       140.78        19.79        12.03        42.38 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        8.42        28.34         2.50         4.14        64.83       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      111.16        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7235 
        1.84        52.31        12.92        21.80        10.75        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
        4.73        89.65        36.00        31.36        26.20        18.97 
TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       95.34        11.87         2.10        18.41        57.47        35.54 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
      210.97        89.33         9.67         0.46        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
       25.94         0.07       100.57        14.89        56.48       156.49 
TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 
        3.52        84.49        19.76         6.38        22.19        35.93 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        21.01       169.38       180.16       159.65        35.47 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 
       45.96         6.51        88.87        60.43         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO 
        7.07        15.25         5.98        35.34        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 
       28.01         3.62        21.24        23.47        19.92        10.42 
TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       10.55        51.12        13.25        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4Z9 
        2.53        16.14        11.44        18.67        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       12.36        28.77         7.63        22.59        24.95        13.94 
TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.10        23.34        58.45        37.25        33.86        18.02 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       20.45        37.58        41.59        37.18        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 
       20.25         3.02        31.13        18.94        24.95        17.85 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       20.25        13.38        15.06        20.94        33.76        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       25.74        21.93        27.48        14.66        22.03         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         3.65         6.90        15.95        38.53 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       14.37         7.96        12.62         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
       16.08        17.98        29.92        15.78        71.74        51.25 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 
       36.82        47.01        19.00        75.55        18.97        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        21.47         9.34        12.72        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J 
       19.73        12.89         5.62        14.76        12.20        15.32 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ 
        6.87        15.91         7.10        32.45        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       20.35        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ 
       44.65        74.47        17.95        24.30        55.43        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       13.94        20.75        22.36        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  MLL2 MUTATED MLL2 WILD-TYPE 
          0.46           0.07 
  MLL2 MUTATED MLL2 WILD-TYPE 
        153.86         210.97 
  MLL2 MUTATED MLL2 WILD-TYPE 
         18.84          21.07 
[1] "0.5 - 153.9 (18.8)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.3"
D5V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  MLL2 MUTATED         3        9         8        45         0         0
  MLL2 WILD-TYPE      22       66        72       208        11         1
D5V3, multiclass
           clus
vv          MLL2 MUTATED MLL2 WILD-TYPE
  STAGE I              3             22
  STAGE II             9             66
  STAGE III            8             72
  STAGE IVA           45            208
  STAGE IVB            0             11
  STAGE IVC            0              1
[1] 6 2
[1] 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       5  14  16  31
  MLL2 WILD-TYPE    42 123  83 141
D5V4, multiclass
       clus
vv      MLL2 MUTATED MLL2 WILD-TYPE
  T0+T1            5             42
  T2              14            123
  T3              16             83
  T4              31            141
[1] 4 2
[1] TRUE
[1] "dimension of 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    28   8  24   0
  MLL2 WILD-TYPE 147  59 144   7
D5V5, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  N0           28            147
  N1            8             59
  N2           24            144
  N3            0              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"
D5V6, binary
                cls
clus               0   1
  MLL2 MUTATED    29   0
  MLL2 WILD-TYPE 162   1
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     29    0
  MLL2 WILD-TYPE  162    1
   clus
vv  MLL2 MUTATED MLL2 WILD-TYPE
  0           29            162
  1            0              1
[1] 2 2
[1] FALSE
D5V7, binary
                cls
clus               0   1
  MLL2 MUTATED    22  59
  MLL2 WILD-TYPE 116 314
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     22   59
  MLL2 WILD-TYPE  116  314
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  FEMALE           22            116
  MALE             59            314
[1] 2 2
[1] FALSE
D5V8, binary
                cls
clus               0   1
  MLL2 MUTATED    24  48
  MLL2 WILD-TYPE 133 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     24   48
  MLL2 WILD-TYPE  133  245
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO            24            133
  YES           48            245
[1] 2 2
[1] FALSE
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA
  MLL2 MUTATED                                    81
  MLL2 WILD-TYPE                                 419
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  MLL2 MUTATED                                                   0
  MLL2 WILD-TYPE                                                10
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  MLL2 MUTATED                                                           0
  MLL2 WILD-TYPE                                                         1
D5V9, multiclass
                                                           clus
vv                                                          MLL2 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                 81
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT            0
                                                           clus
vv                                                          MLL2 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  419
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, continuous
D5V11, continuous
D5V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL2 MUTATED                                  0     2
  MLL2 WILD-TYPE                                2     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MLL2 MUTATED                          13    64
  MLL2 WILD-TYPE                        34   373
D5V13, multiclass
                                  clus
vv                                 MLL2 MUTATED MLL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                  13             34
  WHITE                                      64            373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
                cls
clus               0   1
  MLL2 MUTATED     2  74
  MLL2 WILD-TYPE  23 375
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      2   74
  MLL2 WILD-TYPE   23  375
                        clus
vv                       MLL2 MUTATED MLL2 WILD-TYPE
  HISPANIC OR LATINO                2             23
  NOT HISPANIC OR LATINO           74            375
[1] 2 2
[1] FALSE

Clustering(6) Variable = TGFBR2 MUTATION ANALYSIS
D6V1, survival
                  sevent
clus2                0   1
  TGFBR2 MUTATED    13  11
  TGFBR2 WILD-TYPE 276 209
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              24              485 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              11              209 
$`TGFBR2 MUTATED`
TCGA-CN-4731 TCGA-CQ-7071 TCGA-CR-7376 TCGA-CR-7402 TCGA-CV-5444 TCGA-CV-6943 
       32.81        43.10        31.96        29.95        80.12        19.79 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6961 TCGA-CV-7252 TCGA-CV-7411 TCGA-CV-A45O 
       65.82        10.98         2.50         4.96        89.33        27.98 
TCGA-CV-A45P TCGA-CV-A6K2 TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A622 TCGA-H7-8502 
       21.01        10.42        41.59        21.63        11.80        15.06 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-P3-A5QF TCGA-QK-A6II TCGA-QK-A6VB TCGA-T2-A6X2 
       37.41        33.57        10.85         9.34        21.07        32.45 

$`TGFBR2 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 
        9.14         4.80         4.41        18.38        66.28        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       12.69        55.86        38.04         4.67        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       26.86        52.14        55.56        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       46.32         8.58        12.39        71.31        69.70         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       16.21        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       32.22        38.89         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       25.41        23.57        17.29        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 
       11.21         4.24        41.19        15.75        32.38        66.28 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       64.87        53.52        41.88        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       15.75         9.27        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       35.41        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       76.24        19.20        17.95       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       91.53        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       60.49         7.07        43.23        54.74        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
        9.60        90.12         2.14         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6945 
        4.73        21.90        26.43        11.24       140.78        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6956 
       42.38        15.09        30.08         6.08        53.95         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
        8.42        28.34         4.14        64.83       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
       18.81        12.66         7.99         9.01         5.26         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
       52.31        12.92        21.80        71.21        10.75       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       77.16         4.73        89.65        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       18.97        17.13        95.34        11.87        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7413 
       49.71        18.41        57.47        35.54       210.97         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        0.46        22.85        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 
      100.57        14.89        56.48       156.49         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       84.49        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
       22.19        35.93        30.48       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
       35.47         1.05        45.96         6.51        88.87        48.20 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       60.43        67.86         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7085 
        3.62        21.24        23.47        19.92        22.52        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        51.12        13.25        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
        2.53        16.14        11.44        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 
       33.86        18.02        20.45        37.58        37.18        32.71 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A 
       17.85        20.25        12.43        13.38        15.16        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
       33.76        28.47        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         0.36        13.84         4.27         3.65         6.90 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I 
       15.95        38.53        14.50        37.71        11.84         0.07 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        6.25        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       15.78        71.74        51.25        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       12.72        27.39        19.73        12.89         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
        6.87        15.91         7.10        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.25        20.35        64.80        54.67         2.83        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.45        44.65        74.47        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       29.46        18.05        13.94        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       17.03        20.55        14.56        13.35        18.15 

  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
            2.50             0.07 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
           89.33           210.97 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
          24.805           20.550 
[1] "2.5 - 89.3 (24.8)"  "0.1 - 211.0 (20.6)"
[1] "hr=" "1.1"
D6V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  TGFBR2 MUTATED         1        4         5        11         0         0
  TGFBR2 WILD-TYPE      24       71        75       242        11         1
D6V3, multiclass
           clus
vv          TGFBR2 MUTATED TGFBR2 WILD-TYPE
  STAGE I                1               24
  STAGE II               4               71
  STAGE III              5               75
  STAGE IVA             11              242
  STAGE IVB              0               11
  STAGE IVC              0                1
[1] 6 2
[1] 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
  TGFBR2 MUTATED       1   7   3  10
  TGFBR2 WILD-TYPE    46 130  96 162
D6V4, multiclass
       clus
vv      TGFBR2 MUTATED TGFBR2 WILD-TYPE
  T0+T1              1               46
  T2                 7              130
  T3                 3               96
  T4                10              162
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  TGFBR2 MUTATED     9   3   5   0
  TGFBR2 WILD-TYPE 166  64 163   7
D6V5, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  N0              9              166
  N1              3               64
  N2              5              163
  N3              0                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
  TGFBR2 MUTATED    10   0
  TGFBR2 WILD-TYPE 181   1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     10    0
  TGFBR2 WILD-TYPE  181    1
   clus
vv  TGFBR2 MUTATED TGFBR2 WILD-TYPE
  0             10              181
  1              0                1
[1] 2 2
[1] FALSE
D6V7, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     6  18
  TGFBR2 WILD-TYPE 132 355
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      6   18
  TGFBR2 WILD-TYPE  132  355
        clus
vv       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  FEMALE              6              132
  MALE               18              355
[1] 2 2
[1] FALSE
D6V8, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     9  12
  TGFBR2 WILD-TYPE 148 281
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      9   12
  TGFBR2 WILD-TYPE  148  281
     clus
vv    TGFBR2 MUTATED TGFBR2 WILD-TYPE
  NO               9              148
  YES             12              281
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  TGFBR2 MUTATED                                    24
  TGFBR2 WILD-TYPE                                 476
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  TGFBR2 MUTATED                                                   0
  TGFBR2 WILD-TYPE                                                10
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  TGFBR2 MUTATED                                                           0
  TGFBR2 WILD-TYPE                                                         1
D6V9, multiclass
                                                           clus
vv                                                          TGFBR2 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   24
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          TGFBR2 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    476
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, continuous
D6V11, continuous
D6V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TGFBR2 MUTATED                                  0     0
  TGFBR2 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TGFBR2 MUTATED                           3    21
  TGFBR2 WILD-TYPE                        44   416
D6V13, multiclass
                                  clus
vv                                 TGFBR2 MUTATED TGFBR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     3               44
  WHITE                                        21              416
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V14, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     1  22
  TGFBR2 WILD-TYPE  24 427
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      1   22
  TGFBR2 WILD-TYPE   24  427
                        clus
vv                       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  HISPANIC OR LATINO                  1               24
  NOT HISPANIC OR LATINO             22              427
[1] 2 2
[1] FALSE

Clustering(7) Variable = HLA-B MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2               0   1
  HLA-B MUTATED    14  10
  HLA-B WILD-TYPE 275 210
  HLA-B MUTATED HLA-B WILD-TYPE 
             24             485 
  HLA-B MUTATED HLA-B WILD-TYPE 
             10             210 
$`HLA-B MUTATED`
TCGA-BA-5559 TCGA-UF-A71D TCGA-BA-A6D8 TCGA-BA-A6DJ TCGA-CN-4723 TCGA-CN-A63Y 
       68.48        48.03        27.95        13.38        55.86        16.57 
TCGA-CN-A642 TCGA-CQ-5324 TCGA-CQ-7071 TCGA-CR-6481 TCGA-CR-7395 TCGA-CV-5973 
        2.70        52.37        43.10        10.22        30.58        86.83 
TCGA-CV-7099 TCGA-CV-7255 TCGA-CV-A6JD TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-D6-6516 
        7.99         2.10         5.98        22.52        10.42        25.41 
TCGA-F7-A620 TCGA-HD-A4C1 TCGA-T2-A6X2 TCGA-UF-A71E TCGA-UF-A7JO TCGA-UF-A7JT 
       17.85         0.36        32.45        49.45        20.75        32.65 

$`HLA-B WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       22.85         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       65.59        15.52        21.17        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       41.85        29.42        20.45        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP 
       14.47         7.82         2.27        11.05        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15       105.90         9.14         4.80         4.41        18.38 
TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       66.28        71.05        20.52        10.55        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
        8.81         6.28        12.69        38.04         4.67        56.68 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.81        52.14        55.56        57.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        42.02        46.32         8.58        12.39        71.31 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       69.70         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
       12.49         8.52        52.08        56.94        50.07        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       48.00        23.90        47.44        28.04        19.07        34.13 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
        6.74        10.45        32.22        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 
       21.21         7.40        31.69        22.32        12.39         4.41 
TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5325 TCGA-CQ-5326 
       12.07        23.44        20.88        19.53        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 
        4.24        41.19        15.75        32.38        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       56.58        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       53.52        41.88        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6482 
       39.52        36.99        18.54        16.90        11.90        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       47.18        39.16        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.09        24.95        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       44.25        24.79         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        94.88        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 
       80.12        17.92        13.35        23.05        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        7.07        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       90.12         2.14         9.70         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       21.90        26.43        11.24       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       42.38        15.09        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       10.98         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 
       64.83       172.67       111.16        18.81        12.66         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        5.26         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       10.75       130.88        77.16         4.73        89.65        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       31.36        26.20        18.97        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       11.87        47.97        49.71        18.41        57.47        35.54 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
      210.97        89.33         9.67         0.46        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
       25.94         0.07        34.09       100.57        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
      156.49         3.52        16.27        84.49        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 
      153.86        16.64         6.38        22.19        35.93        30.48 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        21.01       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
        1.05        45.96         6.51        88.87        48.20        60.43 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JE 
       67.86         0.76        56.61         7.07        15.25        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       23.47        19.92        10.55        18.84        51.12        13.25 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        37.25        33.86        18.02        20.45        37.58 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A623 
       31.13        18.94        24.95         0.46        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       12.43        13.38        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         3.65         6.90        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        37.71        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        6.25        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       15.78        71.74        51.25        10.85        36.82        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       19.00        75.55        18.97         2.04        29.00        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       16.01        13.15        21.07        21.21        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       21.47         9.34        12.72        27.39        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       12.89         5.62        14.76        12.20        17.82        15.32 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
        8.32        12.72        16.96         6.87        15.91         7.10 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       13.71         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       54.67         2.83        49.51        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS 
       24.30        55.43        29.46        18.05        13.94        22.36 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       17.03        20.55        14.56        13.35        18.15 

  HLA-B MUTATED HLA-B WILD-TYPE 
           0.36            0.07 
  HLA-B MUTATED HLA-B WILD-TYPE 
          86.83          210.97 
  HLA-B MUTATED HLA-B WILD-TYPE 
         23.965          20.880 
[1] "0.4 - 86.8 (24.0)"  "0.1 - 211.0 (20.9)"
[1] "hr=" "1"  
D7V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  HLA-B MUTATED         1        3         5        11         1         0
  HLA-B WILD-TYPE      24       72        75       242        10         1
D7V3, multiclass
           clus
vv          HLA-B MUTATED HLA-B WILD-TYPE
  STAGE I               1              24
  STAGE II              3              72
  STAGE III             5              75
  STAGE IVA            11             242
  STAGE IVB             1              10
  STAGE IVC             0               1
[1] 6 2
[1] 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-B MUTATED       1   4   4  12
  HLA-B WILD-TYPE    46 133  95 160
D7V4, multiclass
       clus
vv      HLA-B MUTATED HLA-B WILD-TYPE
  T0+T1             1              46
  T2                4             133
  T3                4              95
  T4               12             160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HLA-B MUTATED    13   3   3   1
  HLA-B WILD-TYPE 162  64 165   6
D7V5, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  N0            13             162
  N1             3              64
  N2             3             165
  N3             1               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"
D7V6, binary
                 cls
clus                0   1
  HLA-B MUTATED    12   0
  HLA-B WILD-TYPE 179   1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED     12    0
  HLA-B WILD-TYPE  179    1
   clus
vv  HLA-B MUTATED HLA-B WILD-TYPE
  0            12             179
  1             0               1
[1] 2 2
[1] FALSE
D7V7, binary
                 cls
clus                0   1
  HLA-B MUTATED    10  14
  HLA-B WILD-TYPE 128 359
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED     10   14
  HLA-B WILD-TYPE  128  359
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  FEMALE            10             128
  MALE              14             359
[1] 2 2
[1] FALSE
D7V8, binary
                 cls
clus                0   1
  HLA-B MUTATED    11  11
  HLA-B WILD-TYPE 146 282
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED     11   11
  HLA-B WILD-TYPE  146  282
     clus
vv    HLA-B MUTATED HLA-B WILD-TYPE
  NO             11             146
  YES            11             282
[1] 2 2
[1] FALSE
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA
  HLA-B MUTATED                                    23
  HLA-B WILD-TYPE                                 477
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  HLA-B MUTATED                                                   1
  HLA-B WILD-TYPE                                                 9
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  HLA-B MUTATED                                                           0
  HLA-B WILD-TYPE                                                         1
D7V9, multiclass
                                                           clus
vv                                                          HLA-B MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  23
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             0
                                                           clus
vv                                                          HLA-B WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   477
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, continuous
D7V11, continuous
D7V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HLA-B MUTATED                                  0     1
  HLA-B WILD-TYPE                                2     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HLA-B MUTATED                           2    21
  HLA-B WILD-TYPE                        45   416
D7V13, multiclass
                                  clus
vv                                 HLA-B MUTATED HLA-B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              45
  WHITE                                       21             416
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V14, binary
                 cls
clus                0   1
  HLA-B MUTATED     0  18
  HLA-B WILD-TYPE  25 431
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      0   18
  HLA-B WILD-TYPE   25  431
                        clus
vv                       HLA-B MUTATED HLA-B WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO            18             431
[1] 2 2
[1] FALSE

Clustering(8) Variable = FBXW7 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED    15  18
  FBXW7 WILD-TYPE 274 202
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             33             476 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             18             202 
$`FBXW7 MUTATED`
TCGA-CN-6992 TCGA-CQ-6221 TCGA-BA-6868 TCGA-BA-A6DF TCGA-BB-4228 TCGA-BB-7870 
       35.05        32.88        15.52         7.82        18.38        66.28 
TCGA-BB-8601 TCGA-BB-A6UO TCGA-CN-4730 TCGA-CN-5366 TCGA-CN-A498 TCGA-CN-A6V7 
       20.52         8.81        26.86        11.84        25.41        19.53 
TCGA-CQ-5332 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-7379 TCGA-CR-7398 TCGA-CV-6436 
       10.42        29.49        14.14        34.06         5.13        62.43 
TCGA-CV-6948 TCGA-CV-7095 TCGA-CV-7263 TCGA-CV-7425 TCGA-CV-A45R TCGA-CV-A45V 
       42.38        18.81        18.41        56.48       180.16         1.05 
TCGA-CV-A45W TCGA-CV-A6JY TCGA-F7-A622 TCGA-MT-A67A TCGA-P3-A5QF TCGA-P3-A6T7 
       45.96        21.24        11.80        30.05        10.85        16.01 
TCGA-QK-A6II TCGA-UF-A7J9 TCGA-UF-A7JO 
        9.34        44.65        20.75 

$`FBXW7 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7063 
       11.08        32.48        19.82        24.39        48.20        70.13 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 
       43.04        11.61        34.52         6.02         0.36        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       30.94        14.04        40.24        21.11        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       48.03         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       65.59        21.17        14.83        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
       14.47         2.27        11.05        13.38        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-8596 
        6.15       105.90         9.14         4.80         4.41        71.05 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 
       10.55        27.19        12.92         6.28        12.69        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 
       38.04         4.67        56.68        12.89        32.81        52.14 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       55.56        57.11        12.99        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        73.61        13.05        42.02        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       12.39        71.31        69.70         8.32        16.21        11.54 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.57        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        48.00        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 
       34.13         6.74        10.45        32.22        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       17.42        11.74        35.01        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CQ-5324 
        4.41        12.07         2.70        23.44        20.88        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 
       11.21         4.24        41.19        15.75        32.38        66.28 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       23.24        29.36        33.60        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       11.34        11.64         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
        9.17        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       44.25        30.58        24.79         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        94.88        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6441 
       60.49         7.07        43.23        54.74        21.07         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       90.12         2.14         9.70         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       21.90        26.43        11.24       140.78        19.79        12.03 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       15.09        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
        7.13         8.42        28.34         2.50         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      172.67       111.16        12.66         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        1.84        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 
       47.97         2.10        49.71        57.47        35.54       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 
       89.33         9.67         0.46        22.85        25.08        25.94 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7429 
        0.07        34.09       100.57        14.89       156.49         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 
       16.27        84.49        19.76         7.17       153.86        16.64 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P 
        6.38        22.19        35.93        30.48        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
      169.38       159.65        35.47         6.51        88.87        48.20 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       60.43        67.86         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
        3.62        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        51.12        13.25        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
        2.53        16.14        11.44        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 
       33.86        18.02        20.45        37.58        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
       24.95         0.46        17.85        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       21.93        27.48        14.66        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65         6.90        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
       14.37         7.96         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       51.25        36.82        47.01        19.00        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        2.04        29.00        12.99        13.15        21.07        21.21 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
       23.15         7.30        21.47        12.72        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       19.73        12.89         5.62        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       15.32         8.32        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ 
        7.10        32.45        13.71         3.12        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       20.35        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       74.47        17.95        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       13.94        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           1.05            0.07 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         180.16          210.97 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          20.52           21.04 
[1] "1.1 - 180.2 (20.5)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1.3"
D8V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  FBXW7 MUTATED         1        5         8        16         1         0
  FBXW7 WILD-TYPE      24       70        72       237        10         1
D8V3, multiclass
           clus
vv          FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I               1              24
  STAGE II              5              70
  STAGE III             8              72
  STAGE IVA            16             237
  STAGE IVB             1              10
  STAGE IVC             0               1
[1] 6 2
[1] 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       1   8   9  14
  FBXW7 WILD-TYPE    46 129  90 158
D8V4, multiclass
       clus
vv      FBXW7 MUTATED FBXW7 WILD-TYPE
  T0+T1             1              46
  T2                8             129
  T3                9              90
  T4               14             158
[1] 4 2
[1] TRUE
[1] "dimension of 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    14   3   8   1
  FBXW7 WILD-TYPE 161  64 160   6
D8V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0            14             161
  N1             3              64
  N2             8             160
  N3             1               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"
D8V6, binary
                 cls
clus                0   1
  FBXW7 MUTATED    13   0
  FBXW7 WILD-TYPE 178   1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     13    0
  FBXW7 WILD-TYPE  178    1
   clus
vv  FBXW7 MUTATED FBXW7 WILD-TYPE
  0            13             178
  1             0               1
[1] 2 2
[1] FALSE
D8V7, binary
                 cls
clus                0   1
  FBXW7 MUTATED    13  20
  FBXW7 WILD-TYPE 125 353
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     13   20
  FBXW7 WILD-TYPE  125  353
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE            13             125
  MALE              20             353
[1] 2 2
[1] FALSE
D8V8, binary
                 cls
clus                0   1
  FBXW7 MUTATED    13  17
  FBXW7 WILD-TYPE 144 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     13   17
  FBXW7 WILD-TYPE  144  276
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO             13             144
  YES            17             276
[1] 2 2
[1] FALSE
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA
  FBXW7 MUTATED                                    33
  FBXW7 WILD-TYPE                                 467
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  FBXW7 MUTATED                                                   0
  FBXW7 WILD-TYPE                                                10
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  FBXW7 MUTATED                                                           0
  FBXW7 WILD-TYPE                                                         1
D8V9, multiclass
                                                           clus
vv                                                          FBXW7 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  33
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             0
                                                           clus
vv                                                          FBXW7 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   467
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, continuous
D8V11, continuous
D8V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXW7 MUTATED                                  0     0
  FBXW7 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FBXW7 MUTATED                           3    28
  FBXW7 WILD-TYPE                        44   409
D8V13, multiclass
                                  clus
vv                                 FBXW7 MUTATED FBXW7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    3              44
  WHITE                                       28             409
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
                 cls
clus                0   1
  FBXW7 MUTATED     2  27
  FBXW7 WILD-TYPE  23 422
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      2   27
  FBXW7 WILD-TYPE   23  422
                        clus
vv                       FBXW7 MUTATED FBXW7 WILD-TYPE
  HISPANIC OR LATINO                 2              23
  NOT HISPANIC OR LATINO            27             422
[1] 2 2
[1] FALSE

Clustering(9) Variable = NOTCH1 MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2                0   1
  NOTCH1 MUTATED    45  44
  NOTCH1 WILD-TYPE 244 176
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              89              420 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              44              176 
$`NOTCH1 MUTATED`
TCGA-BA-4075 TCGA-CN-6021 TCGA-HD-8635 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-6868 
        9.30         9.07        22.85        13.64        26.50        15.52 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BB-4225 
        4.01        29.42        27.95        14.47         7.82         4.80 
TCGA-BB-8596 TCGA-CN-4723 TCGA-CN-4729 TCGA-CN-4736 TCGA-CN-4742 TCGA-CN-5355 
       71.05        55.86        12.89        12.99        13.05        42.02 
TCGA-CN-5363 TCGA-CN-5369 TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6989 TCGA-CN-6994 
        8.32        12.49        30.67        47.44        32.22        38.89 
TCGA-CN-A63W TCGA-CQ-5329 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6219 TCGA-CQ-6220 
       12.39        70.45        11.21         4.24        15.75        32.38 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CR-5243 TCGA-CR-6492 TCGA-CR-7365 TCGA-CR-7376 
       43.10        44.48        84.23        15.75        39.16        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7390 TCGA-CR-7394 TCGA-CR-7395 
        9.17        34.06        19.92        49.58        44.25        30.58 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 
       19.20        17.95        94.88        17.92        23.05        86.83 
TCGA-CV-6938 TCGA-CV-6942 TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7089 
        4.73       140.78        10.98         8.42         4.14        64.83 
TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7411 TCGA-CV-7427 
        7.99         5.26         4.73        89.65        89.33       156.49 
TCGA-CV-7433 TCGA-CV-7568 TCGA-CV-A45V TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A468 
       19.76        30.48         1.05         0.76         7.07        15.25 
TCGA-CV-A6JM TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CX-7085 TCGA-D6-A6EK TCGA-D6-A6EN 
        6.38        21.24        22.52        10.55        28.77        22.59 
TCGA-DQ-5625 TCGA-DQ-5631 TCGA-F7-A50I TCGA-F7-A622 TCGA-HD-A6I0 TCGA-IQ-A61E 
       37.25        18.02         3.02        11.80         6.90        37.71 
TCGA-MT-A67A TCGA-MT-A67D TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6II TCGA-QK-A8Z7 
       30.05         1.84        13.15        21.21         9.34        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-T2-A6X2 TCGA-TN-A7HL 
        5.62        12.20         8.32        32.45        20.35 

$`NOTCH1 WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       37.28        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 
       25.71        51.29         9.24        52.08        11.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       32.48        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 
       43.04        11.61        34.52         6.02         0.36        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-UF-A71D 
       30.94        14.04        40.24        21.11        12.66        48.03 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
        2.96         3.35        15.19         9.07        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 
       57.93        17.10        23.84        65.59        21.17        14.83 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       12.62        41.85        20.45        11.54         7.10         5.69 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
        2.27        11.05        13.38        20.48        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8601 
      105.90         9.14         4.41        18.38        66.28        20.52 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       10.55        27.19        12.92         8.81         6.28        12.69 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       38.04         4.67        56.68        26.86        32.81        52.14 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       55.56        57.11        20.55        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 
       73.61        46.32         8.58        12.39        71.31        69.70 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
       16.21        11.54        11.84        11.57         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6018 
       56.94        50.07        48.00        23.90        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       34.13         6.74        10.45         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
        7.40        31.69        22.32        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 
        2.93        54.58        62.37        45.99        10.42        41.19 
TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       66.28        46.95        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 
       38.76        64.87        53.52        41.88        77.56        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6493 
       11.34        11.64         7.69        12.46        22.78         9.27 
TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       47.18        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
       24.95        29.23         0.99        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       47.01        27.06        12.89        30.02        46.85        32.65 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       24.79         5.13         5.95        35.41        29.95        48.39 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5440 
      139.43        17.16       129.21       108.95        76.24       107.51 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 
       76.50        91.53        80.12        13.35        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        7.07        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6939 
       90.12         2.14         9.70         5.46        20.52        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       26.43        11.24        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6960 
       30.08         6.08        53.95        65.82         7.13        28.34 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 
        2.50       172.67       111.16        18.81        12.66         9.01 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        1.84        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
      130.88        77.16        36.00        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       17.13        95.34         4.96        11.87        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7413 
       49.71        18.41        57.47        35.54       210.97         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        0.46        22.85        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
      100.57        14.89        56.48         3.52        16.27        84.49 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 
        7.17       153.86        16.64         6.38        22.19        35.93 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        21.01       169.38       180.16       159.65        35.47 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
       45.96         6.51        88.87        48.20        60.43        67.86 
TCGA-CV-A464 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
       56.61         5.98        35.34        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7086 TCGA-CX-A4AQ 
        3.62        23.47        19.92        10.42        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 
       58.45        33.86        20.45        37.58        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       32.71        21.63        20.25        31.13        18.94        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
        0.46        17.85        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.06        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H 
        3.65        15.95        38.53        14.50        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
        0.07        33.57         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67F 
       15.48        19.27        10.75        14.37         7.96        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        6.25        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       15.78        71.74        51.25        10.85        36.82        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       19.00        75.55        18.97         2.04        29.00        12.99 
TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ 
       16.01        21.07        23.15         7.30        21.47        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J 
       27.39        21.07        19.73        14.76        17.82        15.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T3-A92M 
       12.72        16.96         6.87        15.91         7.10        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
        3.12        13.55        13.25        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       32.65        17.03        20.55        14.56        13.35        18.15 

  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
            0.76             0.07 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
          156.49           210.97 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
           18.02            21.09 
[1] "0.8 - 156.5 (18.0)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.3"
D9V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  NOTCH1 MUTATED         2       14        16        44         2         1
  NOTCH1 WILD-TYPE      23       61        64       209         9         0
D9V3, multiclass
           clus
vv          NOTCH1 MUTATED NOTCH1 WILD-TYPE
  STAGE I                2               23
  STAGE II              14               61
  STAGE III             16               64
  STAGE IVA             44              209
  STAGE IVB              2                9
  STAGE IVC              1                0
[1] 6 2
[1] 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
  NOTCH1 MUTATED       5  21  18  37
  NOTCH1 WILD-TYPE    42 116  81 135
D9V4, multiclass
       clus
vv      NOTCH1 MUTATED NOTCH1 WILD-TYPE
  T0+T1              5               42
  T2                21              116
  T3                18               81
  T4                37              135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  NOTCH1 MUTATED    32  13  24   1
  NOTCH1 WILD-TYPE 143  54 144   6
D9V5, multiclass
    clus
vv   NOTCH1 MUTATED NOTCH1 WILD-TYPE
  N0             32              143
  N1             13               54
  N2             24              144
  N3              1                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"
D9V6, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED    32   1
  NOTCH1 WILD-TYPE 159   0
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED     32    1
  NOTCH1 WILD-TYPE  159    0
   clus
vv  NOTCH1 MUTATED NOTCH1 WILD-TYPE
  0             32              159
  1              1                0
[1] 2 2
[1] FALSE
D9V7, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED    31  59
  NOTCH1 WILD-TYPE 107 314
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED     31   59
  NOTCH1 WILD-TYPE  107  314
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  FEMALE             31              107
  MALE               59              314
[1] 2 2
[1] FALSE
D9V8, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED    37  43
  NOTCH1 WILD-TYPE 120 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED     37   43
  NOTCH1 WILD-TYPE  120  250
     clus
vv    NOTCH1 MUTATED NOTCH1 WILD-TYPE
  NO              37              120
  YES             43              250
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  NOTCH1 MUTATED                                    89
  NOTCH1 WILD-TYPE                                 411
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  NOTCH1 MUTATED                                                   1
  NOTCH1 WILD-TYPE                                                 9
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  NOTCH1 MUTATED                                                           0
  NOTCH1 WILD-TYPE                                                         1
D9V9, multiclass
                                                           clus
vv                                                          NOTCH1 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   89
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          NOTCH1 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    411
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, continuous
D9V11, continuous
D9V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOTCH1 MUTATED                                  0     1
  NOTCH1 WILD-TYPE                                2     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NOTCH1 MUTATED                           9    77
  NOTCH1 WILD-TYPE                        38   360
D9V13, multiclass
                                  clus
vv                                 NOTCH1 MUTATED NOTCH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     9               38
  WHITE                                        77              360
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED     7  79
  NOTCH1 WILD-TYPE  18 370
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      7   79
  NOTCH1 WILD-TYPE   18  370
                        clus
vv                       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  HISPANIC OR LATINO                  7               18
  NOT HISPANIC OR LATINO             79              370
[1] 2 2
[1] FALSE

Clustering(10) Variable = FAT1 MUTATION ANALYSIS
D10V1, survival
                sevent
clus2              0   1
  FAT1 MUTATED    57  55
  FAT1 WILD-TYPE 232 165
  FAT1 MUTATED FAT1 WILD-TYPE 
           112            397 
  FAT1 MUTATED FAT1 WILD-TYPE 
            55            165 
$`FAT1 MUTATED`
TCGA-BA-4075 TCGA-BA-6871 TCGA-CN-6024 TCGA-CX-7082 TCGA-DQ-5629 TCGA-UF-A71D 
        9.30         3.55        11.08         0.36        30.94        48.03 
TCGA-4P-AA8J TCGA-BA-4078 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DI TCGA-BA-A6DJ 
        3.35         9.07        41.85        29.42        11.05        13.38 
TCGA-CN-4731 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-6012 TCGA-CN-6016 
       32.81        11.84        12.49         8.52        48.00        47.44 
TCGA-CN-6018 TCGA-CN-6989 TCGA-CN-A49A TCGA-CN-A640 TCGA-CQ-5327 TCGA-CQ-6218 
       19.07        32.22        17.29         4.41        54.58        41.19 
TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-7064 TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       66.28        46.95        64.87        33.60        29.49        14.14 
TCGA-CQ-A4CI TCGA-CR-6477 TCGA-CR-6492 TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7379 
       31.23        16.90        15.75         3.45         0.99        34.06 
TCGA-CR-7382 TCGA-CR-7386 TCGA-CR-7390 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 
       26.17        47.01        49.58        44.25        30.58         5.13 
TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5966 TCGA-CV-5976 TCGA-CV-6441 TCGA-CV-6936 
      139.43       108.95        17.92        48.59         9.60         5.46 
TCGA-CV-6938 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6955 TCGA-CV-6956 
        4.73       140.78        19.79         6.08        10.98         7.13 
TCGA-CV-6959 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7103 
        8.42        64.83       111.16        18.81         7.99        52.31 
TCGA-CV-7183 TCGA-CV-7242 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7263 
      130.88        36.00        95.34         4.96        47.97        18.41 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7435 TCGA-CV-7437 
        9.67         0.46        34.09       156.49       153.86        16.64 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A463 
       27.98       169.38       180.16         1.05        45.96         0.76 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CV-A6K2 
        5.98        35.34         3.62        23.47        22.52        10.42 
TCGA-CX-7085 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN TCGA-DQ-5631 
       10.55        17.72        12.36        28.77        22.59        18.02 
TCGA-DQ-7592 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A622 TCGA-F7-A624 
       37.58        21.63         3.02        18.94        11.80        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-IQ-A61E 
       13.38        15.16         0.36        13.84         6.90        37.71 
TCGA-MT-A67A TCGA-P3-A6T0 TCGA-QK-A64Z TCGA-QK-A6II TCGA-QK-A8Z8 TCGA-UF-A7J9 
       30.05        19.00        21.07         9.34         5.62        44.65 
TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JT TCGA-WA-A7GZ 
       18.05        20.75        32.65        20.55 

$`FAT1 WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
       37.28        20.48        68.48        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 
       51.29         9.07         9.24        52.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 
       19.82        24.39        48.20        32.88        70.13        43.04 
TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-7588 TCGA-DQ-7593 
       11.61        34.52         6.02        34.36        14.04        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A7JV TCGA-BA-4074 TCGA-BA-4076 
       21.11        12.66        22.85         2.96        15.19        13.64 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       65.59        15.52        21.17        14.83        12.62         4.01 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       20.45        27.95        11.54         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
        7.82         2.27        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 
        9.14         4.80         4.41        18.38        66.28        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       12.69        55.86        38.04         4.67        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       26.86        52.14        55.56        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       46.32         8.58        12.39        71.31        69.70         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       16.21        11.54        11.57        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       30.67        23.90        28.04        34.13         6.74        10.45 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       38.89         3.68        17.42        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       23.57        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       12.39        16.57        12.07         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 
       19.53        52.37        21.50         2.93        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6219 TCGA-CQ-6220 
       45.99        10.42        11.21         4.24        15.75        32.38 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 
       56.58        13.25         4.24        14.99        38.76        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       12.46        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 
       58.42        50.01        39.52        36.99        18.54        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7380 
        3.09        24.95        29.23        31.96         9.17        19.92 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
       17.13        32.78        27.06        12.89        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       32.65        24.79         5.95        35.41        29.95        48.39 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
       17.16       129.21        76.24        19.20        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 
       94.88        76.50        91.53        80.12        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       86.83        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6939 
       62.43        90.12         2.14         9.70        20.52        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
       26.43        11.24        12.03        42.38        15.09        30.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7090 
       53.95        65.82        28.34         2.50         4.14       172.67 
TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7177 
       12.66         9.01         5.26         1.84        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 
       71.21        10.75        77.16         4.73        89.65        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 
       26.20        18.97        17.13        11.87         2.10        49.71 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7415 TCGA-CV-7416 
       57.47        35.54       210.97        89.33        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7429 
       25.94         0.07       100.57        14.89        56.48         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-7440 
       16.27        84.49        19.76         7.17         6.38        22.19 
TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45P TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45X 
       35.93        30.48        21.01       159.65        35.47         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 
       88.87        48.20        60.43        67.86        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY 
       15.25         6.38        29.79         6.48        28.01        21.24 
TCGA-CV-A6K0 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       19.92        18.84        51.12        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
       23.05         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       25.32         7.63        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7591 TCGA-DQ-7596 
       23.34        58.45        37.25        33.86        20.45        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W 
       37.18        32.71        20.25        31.13        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       17.85        20.25        15.06        20.94        33.76        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A634 
       25.74        21.93        27.48        14.66        22.03         4.27 
TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H 
        3.65        15.95        38.53        14.50        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
        0.07        33.57         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D 
       15.48        19.27        10.75        14.37         7.96         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         6.25        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        71.74        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       47.01        75.55        18.97         2.04        29.00        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       16.01        13.15        21.21        23.15         7.30        21.47 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 
       12.72        27.39        21.07        19.73        12.89        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        6.87        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.51        49.45        74.47        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       29.46        13.94        22.36        17.03        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  FAT1 MUTATED FAT1 WILD-TYPE 
          0.36           0.07 
  FAT1 MUTATED FAT1 WILD-TYPE 
        180.16         210.97 
  FAT1 MUTATED FAT1 WILD-TYPE 
        19.035         21.110 
[1] "0.4 - 180.2 (19.0)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D10V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  FAT1 MUTATED         3       20        18        53         2         1
  FAT1 WILD-TYPE      22       55        62       200         9         0
D10V3, multiclass
           clus
vv          FAT1 MUTATED FAT1 WILD-TYPE
  STAGE I              3             22
  STAGE II            20             55
  STAGE III           18             62
  STAGE IVA           53            200
  STAGE IVB            2              9
  STAGE IVC            1              0
[1] 6 2
[1] 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       3  34  19  42
  FAT1 WILD-TYPE    44 103  80 130
D10V4, multiclass
       clus
vv      FAT1 MUTATED FAT1 WILD-TYPE
  T0+T1            3             44
  T2              34            103
  T3              19             80
  T4              42            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              N0  N1  N2  N3
  FAT1 MUTATED    42  15  28   0
  FAT1 WILD-TYPE 133  52 140   7
D10V5, multiclass
    clus
vv   FAT1 MUTATED FAT1 WILD-TYPE
  N0           42            133
  N1           15             52
  N2           28            140
  N3            0              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"
D10V6, binary
                cls
clus               0   1
  FAT1 MUTATED    43   1
  FAT1 WILD-TYPE 148   0
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED     43    1
  FAT1 WILD-TYPE  148    0
   clus
vv  FAT1 MUTATED FAT1 WILD-TYPE
  0           43            148
  1            1              0
[1] 2 2
[1] FALSE
D10V7, binary
                cls
clus               0   1
  FAT1 MUTATED    43  69
  FAT1 WILD-TYPE  95 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED     43   69
  FAT1 WILD-TYPE   95  304
        clus
vv       FAT1 MUTATED FAT1 WILD-TYPE
  FEMALE           43             95
  MALE             69            304
[1] 2 2
[1] FALSE
D10V8, binary
                cls
clus               0   1
  FAT1 MUTATED    35  61
  FAT1 WILD-TYPE 122 232
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED     35   61
  FAT1 WILD-TYPE  122  232
     clus
vv    FAT1 MUTATED FAT1 WILD-TYPE
  NO            35            122
  YES           61            232
[1] 2 2
[1] FALSE
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA
  FAT1 MUTATED                                   111
  FAT1 WILD-TYPE                                 389
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  FAT1 MUTATED                                                   1
  FAT1 WILD-TYPE                                                 9
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  FAT1 MUTATED                                                           0
  FAT1 WILD-TYPE                                                         1
D10V9, multiclass
                                                           clus
vv                                                          FAT1 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                111
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT            0
                                                           clus
vv                                                          FAT1 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  389
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, continuous
D10V11, continuous
D10V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAT1 MUTATED                                  1     2
  FAT1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FAT1 MUTATED                           8    97
  FAT1 WILD-TYPE                        39   340
D10V13, multiclass
                                  clus
vv                                 FAT1 MUTATED FAT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              1
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   8             39
  WHITE                                      97            340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
                cls
clus               0   1
  FAT1 MUTATED     7  94
  FAT1 WILD-TYPE  18 355
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED      7   94
  FAT1 WILD-TYPE   18  355
                        clus
vv                       FAT1 MUTATED FAT1 WILD-TYPE
  HISPANIC OR LATINO                7             18
  NOT HISPANIC OR LATINO           94            355
[1] 2 2
[1] FALSE

Clustering(11) Variable = JUB MUTATION ANALYSIS
D11V1, survival
               sevent
clus2             0   1
  JUB MUTATED    11  23
  JUB WILD-TYPE 278 197
  JUB MUTATED JUB WILD-TYPE 
           34           475 
  JUB MUTATED JUB WILD-TYPE 
           23           197 
$`JUB MUTATED`
TCGA-CN-6997 TCGA-CX-7082 TCGA-DQ-7588 TCGA-UF-A71D TCGA-BA-5556 TCGA-BB-A5HY 
       32.48         0.36        14.04        48.03        23.84        10.55 
TCGA-BB-A6UO TCGA-CN-4738 TCGA-CN-6018 TCGA-CN-6998 TCGA-CN-A63V TCGA-CQ-5327 
        8.81        14.33        19.07        11.74        22.32        54.58 
TCGA-CR-6491 TCGA-CR-6493 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-6003 TCGA-CV-6950 
       22.78         9.27        17.16        76.24        54.74        15.09 
TCGA-CV-7099 TCGA-CV-7177 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-A45Q 
        7.99        21.80        25.94        14.89        84.49       169.38 
TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A6JM TCGA-CV-A6K2 TCGA-D6-A6EN TCGA-D6-A6EP 
       60.43         0.76         6.38        10.42        22.59        13.94 
TCGA-D6-A74Q TCGA-HD-7753 TCGA-P3-A5QF TCGA-UF-A7JF 
       23.34        28.47        10.85        55.43 

$`JUB WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       11.08        35.05        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7219 
       70.13        43.04        11.61        34.52         6.02        34.36 
TCGA-DQ-5629 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A7JV 
       30.94        40.24        21.11        12.66        22.85         2.96 
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
        3.35        15.19        13.64         9.07        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
       42.35        57.93        17.10        65.59        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH 
       14.83        12.62         4.01        41.85        29.42        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       27.95        11.54         7.10         5.69        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
        2.27        11.05        13.38        20.48        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 
      105.90         9.14         4.80         4.41        18.38        66.28 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-C9-A47Z TCGA-C9-A480 
       71.05        20.52        27.19        12.92         6.28        12.69 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       55.86        38.04         4.67        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       32.81        52.14        55.56        57.11        12.99        20.55 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       45.83        27.58        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 
        8.58        12.39        71.31        69.70         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       56.94        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
       28.04        34.13         6.74        10.45        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
        3.68        17.42        35.01        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y 
       29.72        21.21         7.40        31.69        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       52.37        21.50         2.93        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 
       10.42        11.21         4.24        41.19        15.75        32.38 
TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       66.28        46.95        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       38.76        64.87        53.52        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       44.48        23.24        29.36        33.60        29.49        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       12.46        31.23        84.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
       26.27        58.42        50.01        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       16.90        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       12.46        15.75        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58        24.79         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 
        5.95        35.41        29.95        48.39       139.43       129.21 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
      108.95        19.20        17.95       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
       48.59        60.49         7.07        43.23        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
        9.60        90.12         2.14         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       12.03        42.38        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       10.98         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 
       64.83       172.67       111.16        18.81        12.66         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7180 
        5.26         1.84        52.31        12.92        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       47.97         2.10        49.71        18.41        57.47        35.54 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
      210.97        89.33         9.67         0.46        22.85        25.08 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 
        0.07        34.09       100.57        56.48       156.49         3.52 
TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       16.27        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R 
       22.19        35.93        30.48        27.98        21.01       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       48.20        67.86        56.61         7.07        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
       35.34        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       23.47        19.92        22.52        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 
       28.77         7.63        24.95        12.10        12.79        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 
       37.25        33.86        18.02        20.45        37.58        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       37.18        32.71        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        24.95         0.46        17.85        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       12.43        13.38        15.16        15.06        20.94        33.76 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       25.74        21.93        27.48        14.66        22.03         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         3.65         6.90        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        37.71        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        6.25        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       15.78        71.74        51.25        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        27.39        21.07        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.72        16.96         6.87        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       13.71         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       17.95        24.30        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  JUB MUTATED JUB WILD-TYPE 
         0.36          0.07 
  JUB MUTATED JUB WILD-TYPE 
       169.38        210.97 
  JUB MUTATED JUB WILD-TYPE 
       20.435        20.940 
[1] "0.4 - 169.4 (20.4)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1.6"
D11V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  JUB MUTATED         1        5         3        22         0         0
  JUB WILD-TYPE      24       70        77       231        11         1
D11V3, multiclass
           clus
vv          JUB MUTATED JUB WILD-TYPE
  STAGE I             1            24
  STAGE II            5            70
  STAGE III           3            77
  STAGE IVA          22           231
  STAGE IVB           0            11
  STAGE IVC           0             1
[1] 6 2
[1] 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
  JUB MUTATED       2   7   9  13
  JUB WILD-TYPE    45 130  90 159
D11V4, multiclass
       clus
vv      JUB MUTATED JUB WILD-TYPE
  T0+T1           2            45
  T2              7           130
  T3              9            90
  T4             13           159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  JUB MUTATED    10   2  17   0
  JUB WILD-TYPE 165  65 151   7
D11V5, multiclass
    clus
vv   JUB MUTATED JUB WILD-TYPE
  N0          10           165
  N1           2            65
  N2          17           151
  N3           0             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
  JUB MUTATED    11   0
  JUB WILD-TYPE 180   1
[1] "tbl2"
               cls
clus            [,1] [,2]
  JUB MUTATED     11    0
  JUB WILD-TYPE  180    1
   clus
vv  JUB MUTATED JUB WILD-TYPE
  0          11           180
  1           0             1
[1] 2 2
[1] FALSE
D11V7, binary
               cls
clus              0   1
  JUB MUTATED    10  24
  JUB WILD-TYPE 128 349
[1] "tbl2"
               cls
clus            [,1] [,2]
  JUB MUTATED     10   24
  JUB WILD-TYPE  128  349
        clus
vv       JUB MUTATED JUB WILD-TYPE
  FEMALE          10           128
  MALE            24           349
[1] 2 2
[1] FALSE
D11V8, binary
               cls
clus              0   1
  JUB MUTATED    10  21
  JUB WILD-TYPE 147 272
[1] "tbl2"
               cls
clus            [,1] [,2]
  JUB MUTATED     10   21
  JUB WILD-TYPE  147  272
     clus
vv    JUB MUTATED JUB WILD-TYPE
  NO           10           147
  YES          21           272
[1] 2 2
[1] FALSE
               vv
clus            HEAD & NECK SQUAMOUS CELL CARCINOMA
  JUB MUTATED                                    34
  JUB WILD-TYPE                                 466
               vv
clus            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  JUB MUTATED                                                   0
  JUB WILD-TYPE                                                10
               vv
clus            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  JUB MUTATED                                                           0
  JUB WILD-TYPE                                                         1
D11V9, multiclass
                                                           clus
vv                                                          JUB MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                34
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                   0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT           0
                                                           clus
vv                                                          JUB WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                 466
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, continuous
D11V11, continuous
D11V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  JUB MUTATED                                  0     2
  JUB WILD-TYPE                                2     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  JUB MUTATED                           4    28
  JUB WILD-TYPE                        43   409
D11V13, multiclass
                                  clus
vv                                 JUB MUTATED JUB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      2             8
  BLACK OR AFRICAN AMERICAN                  4            43
  WHITE                                     28           409
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V14, binary
               cls
clus              0   1
  JUB MUTATED     2  29
  JUB WILD-TYPE  23 420
[1] "tbl2"
               cls
clus            [,1] [,2]
  JUB MUTATED      2   29
  JUB WILD-TYPE   23  420
                        clus
vv                       JUB MUTATED JUB WILD-TYPE
  HISPANIC OR LATINO               2            23
  NOT HISPANIC OR LATINO          29           420
[1] 2 2
[1] FALSE

Clustering(12) Variable = ZNF750 MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2                0   1
  ZNF750 MUTATED    12   9
  ZNF750 WILD-TYPE 277 211
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              21              488 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               9              211 
$`ZNF750 MUTATED`
TCGA-DQ-5629 TCGA-BB-7870 TCGA-CN-A63Y TCGA-CR-6481 TCGA-CR-7368 TCGA-CR-7404 
       30.94        66.28        16.57        10.22        40.93        48.39 
TCGA-CV-5434 TCGA-CV-5444 TCGA-CV-6961 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-A45Z 
      108.95        80.12         2.50         0.46        25.94        48.20 
TCGA-KU-A6H7 TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QF TCGA-QK-A8Z9 
       19.27         6.25        17.98        29.92        10.85        14.76 
TCGA-T2-A6WX TCGA-T3-A92M TCGA-TN-A7HL 
        6.87        13.71        20.35 

$`ZNF750 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
        0.36        34.36        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       23.84        65.59        15.52        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
        4.80         4.41        18.38        71.05        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 
       27.19        12.92         8.81         6.28        12.69        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       52.14        55.56        57.11        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       45.83        27.58        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 
        8.58        12.39        71.31        69.70         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       56.94        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       28.04        19.07        34.13         6.74        10.45        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       38.89         3.68        17.42        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       23.57        17.29        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       22.32        12.39         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       70.45        62.37        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       41.19        15.75        32.38        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6482 
       39.52        36.99        18.54        16.90        11.90        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       47.18        39.16        47.34        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58        24.79         5.13         5.95        35.41        29.95 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
      139.43        17.16       129.21        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 
      107.51        94.88        76.50        91.53        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       54.74        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        9.70         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       140.78        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
        8.42        28.34         4.14        64.83       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
       18.81        12.66         7.99         9.01         5.26         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
       52.31        12.92        21.80        71.21        10.75       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       77.16         4.73        89.65        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       18.97        17.13        95.34         4.96        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 
        2.10        49.71        18.41        57.47        35.54       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 
       89.33         9.67        22.85        25.08         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 
      100.57        14.89        56.48       156.49         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       84.49        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       22.19        35.93        30.48        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       88.87        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        37.25        33.86        18.02        20.45        37.58 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       31.13        18.94        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       20.25        12.43        13.38        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
       33.76        28.47        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         0.36        13.84         4.27         3.65         6.90 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
        0.07        33.57         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       15.48        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q6 TCGA-P3-A5QA 
       12.62        15.42         7.13        16.08        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       51.25        36.82        47.01        19.00        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
        2.04        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.21        23.15         7.30        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA 
       27.39        21.07        19.73        12.89         5.62        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WZ 
       17.82        15.32         8.32        12.72        16.96        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 
        7.10        32.45         3.12        13.55        13.25        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  ZNF750 MUTATED ZNF750 WILD-TYPE 
            0.46             0.07 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
          108.95           210.97 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
           19.27            21.04 
[1] "0.5 - 109.0 (19.3)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1"  
D12V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  ZNF750 MUTATED         0        3         0        14         0         0
  ZNF750 WILD-TYPE      25       72        80       239        11         1
D12V3, multiclass
           clus
vv          ZNF750 MUTATED ZNF750 WILD-TYPE
  STAGE I                0               25
  STAGE II               3               72
  STAGE III              0               80
  STAGE IVA             14              239
  STAGE IVB              0               11
  STAGE IVC              0                1
[1] 6 2
[1] 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
  ZNF750 MUTATED       2   4   2   9
  ZNF750 WILD-TYPE    45 133  97 163
D12V4, multiclass
       clus
vv      ZNF750 MUTATED ZNF750 WILD-TYPE
  T0+T1              2               45
  T2                 4              133
  T3                 2               97
  T4                 9              163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF750 MUTATED     4   2  11   0
  ZNF750 WILD-TYPE 171  65 157   7
D12V5, multiclass
    clus
vv   ZNF750 MUTATED ZNF750 WILD-TYPE
  N0              4              171
  N1              2               65
  N2             11              157
  N3              0                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"
D12V6, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     5   0
  ZNF750 WILD-TYPE 186   1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      5    0
  ZNF750 WILD-TYPE  186    1
   clus
vv  ZNF750 MUTATED ZNF750 WILD-TYPE
  0              5              186
  1              0                1
[1] 2 2
[1] FALSE
D12V7, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     3  18
  ZNF750 WILD-TYPE 135 355
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      3   18
  ZNF750 WILD-TYPE  135  355
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  FEMALE              3              135
  MALE               18              355
[1] 2 2
[1] FALSE
D12V8, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     5  15
  ZNF750 WILD-TYPE 152 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      5   15
  ZNF750 WILD-TYPE  152  278
     clus
vv    ZNF750 MUTATED ZNF750 WILD-TYPE
  NO               5              152
  YES             15              278
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  ZNF750 MUTATED                                    20
  ZNF750 WILD-TYPE                                 480
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  ZNF750 MUTATED                                                   1
  ZNF750 WILD-TYPE                                                 9
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  ZNF750 MUTATED                                                           0
  ZNF750 WILD-TYPE                                                         1
D12V9, multiclass
                                                           clus
vv                                                          ZNF750 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   20
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          ZNF750 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    480
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, continuous
D12V11, continuous
D12V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF750 MUTATED                                  0     0
  ZNF750 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF750 MUTATED                           5    16
  ZNF750 WILD-TYPE                        42   421
D12V13, multiclass
                                  clus
vv                                 ZNF750 MUTATED ZNF750 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     5               42
  WHITE                                        16              421
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     0  21
  ZNF750 WILD-TYPE  25 428
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      0   21
  ZNF750 WILD-TYPE   25  428
                        clus
vv                       ZNF750 MUTATED ZNF750 WILD-TYPE
  HISPANIC OR LATINO                  0               25
  NOT HISPANIC OR LATINO             21              428
[1] 2 2
[1] FALSE

Clustering(13) Variable = NFE2L2 MUTATION ANALYSIS
D13V1, survival
                  sevent
clus2                0   1
  NFE2L2 MUTATED    13  14
  NFE2L2 WILD-TYPE 276 206
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              27              482 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              14              206 
$`NFE2L2 MUTATED`
TCGA-UF-A71D TCGA-BA-7269 TCGA-CN-4723 TCGA-CN-6019 TCGA-CQ-5324 TCGA-CQ-A4CG 
       48.03        41.85        55.86        34.13        52.37        14.14 
TCGA-CR-7383 TCGA-CV-6935 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6951 TCGA-CV-6955 
       17.13         9.70        26.43       140.78        30.08        10.98 
TCGA-CV-7099 TCGA-CV-7177 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7437 TCGA-D6-A6EK 
        7.99        21.80        14.89         3.52        16.64        28.77 
TCGA-H7-7774 TCGA-HD-A6HZ TCGA-IQ-A61H TCGA-MT-A67A TCGA-P3-A5QF TCGA-P3-A6T4 
       13.38         3.65        37.41        30.05        10.85         2.04 
TCGA-T3-A92N TCGA-TN-A7HL TCGA-UF-A71B 
        3.12        20.35        49.51 

$`NFE2L2 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       12.66        22.85         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       23.84        65.59        15.52        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
        4.01        29.42        20.45        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       20.48        16.41         6.15       105.90         9.14         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
        4.41        18.38        66.28        71.05        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 
       27.19        12.92         8.81         6.28        12.69        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        4.67        56.68        12.89        26.86        32.81        52.14 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       55.56        57.11        12.99        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        73.61        13.05        42.02        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       12.39        71.31        69.70         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.84        11.57        12.49         8.52        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 
       19.07         6.74        10.45        32.22        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       17.42        11.74        35.01        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        31.69        22.32        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       16.57         4.41        12.07         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       19.53        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 
       45.99        10.42        11.21         4.24        41.19        15.75 
TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.38        66.28        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       14.99        38.76        64.87        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       77.56        44.48        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       12.46        31.23        84.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
       26.27        58.42        50.01        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       16.90        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       12.46        22.78        15.75         9.27        47.18        39.16 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
       47.34        40.93        35.84         3.45         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       29.23         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       26.17        32.78        47.01        27.06        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       17.16       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 
        2.14         5.46        20.52         4.73        21.90        11.24 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6953 
       19.79        12.03        42.38        15.09         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       65.82         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 
       64.83       172.67       111.16        18.81        12.66         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7180 
        5.26         1.84        52.31        12.92        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       47.97         2.10        49.71        18.41        57.47        35.54 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
      210.97        89.33         9.67         0.46        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 
       25.94         0.07        34.09       100.57        56.48       156.49 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7438 
       16.27        84.49        19.76         7.17       153.86         6.38 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       22.19        35.93        30.48        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
        7.07        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM 
       18.67        24.95        25.32        17.72        12.36         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        37.25        33.86        18.02        20.45        37.58 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       31.13        18.94        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       20.25        12.43        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
        0.36        13.84         4.27         6.90        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       14.50        37.71        11.84         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
       14.37         7.96         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       51.25        36.82        47.01        19.00        75.55        18.97 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       29.00        12.99        16.01        13.15        21.07        21.21 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       23.15         7.30        21.47         9.34        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        19.73        12.89         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       17.82        15.32         8.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HJ 
       15.91         7.10        32.45        13.71        13.55        13.25 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       64.80        54.67         2.83        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            2.04             0.07 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
          140.78           210.97 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
          20.350           20.975 
[1] "2.0 - 140.8 (20.4)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1.3"
D13V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  NFE2L2 MUTATED         2        6         6        13         0         0
  NFE2L2 WILD-TYPE      23       69        74       240        11         1
D13V3, multiclass
           clus
vv          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE I                2               23
  STAGE II               6               69
  STAGE III              6               74
  STAGE IVA             13              240
  STAGE IVB              0               11
  STAGE IVC              0                1
[1] 6 2
[1] 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       2  11   5   9
  NFE2L2 WILD-TYPE    45 126  94 163
D13V4, multiclass
       clus
vv      NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T0+T1              2               45
  T2                11              126
  T3                 5               94
  T4                 9              163
[1] 4 2
[1] TRUE
[1] "dimension of 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    10   5   7   0
  NFE2L2 WILD-TYPE 165  62 161   7
D13V5, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0             10              165
  N1              5               62
  N2              7              161
  N3              0                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"
D13V6, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     6   0
  NFE2L2 WILD-TYPE 185   1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      6    0
  NFE2L2 WILD-TYPE  185    1
   clus
vv  NFE2L2 MUTATED NFE2L2 WILD-TYPE
  0              6              185
  1              0                1
[1] 2 2
[1] FALSE
D13V7, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED    11  16
  NFE2L2 WILD-TYPE 127 357
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     11   16
  NFE2L2 WILD-TYPE  127  357
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE             11              127
  MALE               16              357
[1] 2 2
[1] FALSE
D13V8, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED    11   9
  NFE2L2 WILD-TYPE 146 284
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     11    9
  NFE2L2 WILD-TYPE  146  284
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  NO              11              146
  YES              9              284
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  NFE2L2 MUTATED                                    27
  NFE2L2 WILD-TYPE                                 473
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  NFE2L2 MUTATED                                                   0
  NFE2L2 WILD-TYPE                                                10
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  NFE2L2 MUTATED                                                           0
  NFE2L2 WILD-TYPE                                                         1
D13V9, multiclass
                                                           clus
vv                                                          NFE2L2 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   27
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          NFE2L2 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    473
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, continuous
D13V11, continuous
D13V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFE2L2 MUTATED                                  0     1
  NFE2L2 WILD-TYPE                                2     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NFE2L2 MUTATED                           1    24
  NFE2L2 WILD-TYPE                        46   413
D13V13, multiclass
                                  clus
vv                                 NFE2L2 MUTATED NFE2L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         1                9
  BLACK OR AFRICAN AMERICAN                     1               46
  WHITE                                        24              413
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V14, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     2  21
  NFE2L2 WILD-TYPE  23 428
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      2   21
  NFE2L2 WILD-TYPE   23  428
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  2               23
  NOT HISPANIC OR LATINO             21              428
[1] 2 2
[1] FALSE

Clustering(14) Variable = HLA-A MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2               0   1
  HLA-A MUTATED    14   8
  HLA-A WILD-TYPE 275 212
  HLA-A MUTATED HLA-A WILD-TYPE 
             22             487 
  HLA-A MUTATED HLA-A WILD-TYPE 
              8             212 
$`HLA-A MUTATED`
TCGA-CN-A6V1 TCGA-BA-5152 TCGA-BA-6868 TCGA-CQ-7071 TCGA-CR-6467 TCGA-CR-7373 
       19.82        42.35        15.52        43.10        58.42        29.23 
TCGA-CR-7395 TCGA-CV-5976 TCGA-CV-6937 TCGA-CV-6943 TCGA-CV-7099 TCGA-CV-A461 
       30.58        48.59        20.52        19.79         7.99        67.86 
TCGA-CV-A6K2 TCGA-D6-A6EK TCGA-F7-A624 TCGA-H7-8501 TCGA-HD-A4C1 TCGA-QK-A6IF 
       10.42        28.77        12.43        15.16         0.36        23.15 
TCGA-RS-A6TO TCGA-T3-A92M TCGA-UF-A7JJ TCGA-UF-A7JT 
       12.72        13.71        18.05        32.65 

$`HLA-A WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       11.08        35.05        32.48        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
        9.07        26.50        23.74        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       65.59        21.17        14.83        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.80         4.41 
TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ 
       18.38        66.28        71.05        20.52        10.55        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 
       12.92         8.81         6.28        12.69        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        4.67        56.68        12.89        26.86        32.81        52.14 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       55.56        57.11        12.99        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        73.61        13.05        42.02        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       12.39        71.31        69.70         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.84        11.57        12.49         8.52        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
       19.07        34.13         6.74        10.45        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       17.29        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       70.45        62.37        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       41.19        15.75        32.38        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       41.88        77.56        44.48        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.49        14.14        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       54.67        37.87        26.27        50.01        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        22.78        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       39.16        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       24.95         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       26.17        17.13        32.78        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 
       49.58        30.02        46.85        32.65        44.25        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       17.16       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       13.35        23.05        86.83        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       54.74        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        9.70         5.46         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
      140.78        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        2.50         4.14        64.83       172.67       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
       12.66         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       89.65        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       95.34         4.96        11.87        47.97         2.10        49.71 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       18.41        57.47        35.54       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        0.46        22.85        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 
      100.57        14.89        56.48       156.49         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       84.49        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       22.19        35.93        30.48        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       88.87        48.20        60.43         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        51.12        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
       23.05         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       25.32        17.72        12.36         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 
       33.86        18.02        20.45        37.58        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-7774 
       24.95         0.46        17.85        11.80        20.25        13.38 
TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.06        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       27.48        14.66        22.03        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        6.90        15.95        38.53        14.50        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       37.41         0.07        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       19.04        15.48        19.27        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       30.05         1.84        12.62         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
       16.08        17.98        29.92        15.78        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       10.85        36.82        47.01        19.00        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
        2.04        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.21         7.30        21.47         9.34        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        19.73        12.89         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       17.82        15.32         8.32        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
        7.10        32.45         3.12        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
       64.80        54.67         2.83        49.51        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK 
       74.47        17.95        24.30        55.43        29.46        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       20.75        22.36        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  HLA-A MUTATED HLA-A WILD-TYPE 
           0.36            0.07 
  HLA-A MUTATED HLA-A WILD-TYPE 
          67.86          210.97 
  HLA-A MUTATED HLA-A WILD-TYPE 
          20.17           21.01 
[1] "0.4 - 67.9 (20.2)"  "0.1 - 211.0 (21.0)"
[1] "hr=" "1.1"
D14V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  HLA-A MUTATED         0        4         4        11         0         0
  HLA-A WILD-TYPE      25       71        76       242        11         1
D14V3, multiclass
           clus
vv          HLA-A MUTATED HLA-A WILD-TYPE
  STAGE I               0              25
  STAGE II              4              71
  STAGE III             4              76
  STAGE IVA            11             242
  STAGE IVB             0              11
  STAGE IVC             0               1
[1] 6 2
[1] 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   8   1  10
  HLA-A WILD-TYPE    47 129  98 162
D14V4, multiclass
       clus
vv      HLA-A MUTATED HLA-A WILD-TYPE
  T0+T1             0              47
  T2                8             129
  T3                1              98
  T4               10             162
[1] 4 2
[1] TRUE
[1] "dimension of 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     6   5   5   0
  HLA-A WILD-TYPE 169  62 163   7
D14V5, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  N0             6             169
  N1             5              62
  N2             5             163
  N3             0               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"
D14V6, binary
                 cls
clus                0   1
  HLA-A MUTATED    12   0
  HLA-A WILD-TYPE 179   1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     12    0
  HLA-A WILD-TYPE  179    1
   clus
vv  HLA-A MUTATED HLA-A WILD-TYPE
  0            12             179
  1             0               1
[1] 2 2
[1] FALSE
D14V7, binary
                 cls
clus                0   1
  HLA-A MUTATED     6  16
  HLA-A WILD-TYPE 132 357
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      6   16
  HLA-A WILD-TYPE  132  357
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  FEMALE             6             132
  MALE              16             357
[1] 2 2
[1] FALSE
D14V8, binary
                 cls
clus                0   1
  HLA-A MUTATED     3  15
  HLA-A WILD-TYPE 154 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      3   15
  HLA-A WILD-TYPE  154  278
     clus
vv    HLA-A MUTATED HLA-A WILD-TYPE
  NO              3             154
  YES            15             278
[1] 2 2
[1] FALSE
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA
  HLA-A MUTATED                                    22
  HLA-A WILD-TYPE                                 478
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  HLA-A MUTATED                                                   0
  HLA-A WILD-TYPE                                                10
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  HLA-A MUTATED                                                           0
  HLA-A WILD-TYPE                                                         1
D14V9, multiclass
                                                           clus
vv                                                          HLA-A MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  22
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             0
                                                           clus
vv                                                          HLA-A WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   478
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, continuous
D14V11, continuous
D14V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HLA-A MUTATED                                  0     0
  HLA-A WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HLA-A MUTATED                           3    18
  HLA-A WILD-TYPE                        44   419
D14V13, multiclass
                                  clus
vv                                 HLA-A MUTATED HLA-A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    3              44
  WHITE                                       18             419
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V14, binary
                 cls
clus                0   1
  HLA-A MUTATED     0  18
  HLA-A WILD-TYPE  25 431
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      0   18
  HLA-A WILD-TYPE   25  431
                        clus
vv                       HLA-A MUTATED HLA-A WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO            18             431
[1] 2 2
[1] FALSE

Clustering(15) Variable = EPHA2 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  EPHA2 MUTATED    12  12
  EPHA2 WILD-TYPE 277 208
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             24             485 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             12             208 
$`EPHA2 MUTATED`
TCGA-BA-4077 TCGA-BA-5152 TCGA-BA-6873 TCGA-CN-4726 TCGA-CN-4734 TCGA-CN-5355 
       37.28        42.35         4.01         4.67        55.56        42.02 
TCGA-CN-A63T TCGA-CQ-5327 TCGA-CQ-5334 TCGA-CQ-7069 TCGA-CV-7104 TCGA-CV-7252 
        7.40        54.58         4.24        41.88        12.92         4.96 
TCGA-CV-7425 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45W TCGA-CV-A6K2 TCGA-D6-A6EN 
       56.48         6.38        22.19        45.96        10.42        22.59 
TCGA-F7-A624 TCGA-IQ-A61E TCGA-P3-A5QF TCGA-RS-A6TP TCGA-T2-A6X2 TCGA-UF-A7JD 
       12.43        37.71        10.85        16.96        32.45        24.30 

$`EPHA2 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
        9.07        26.50        23.74        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 
       65.59        15.52        21.17        14.83        12.62        41.85 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.80         4.41 
TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ 
       18.38        66.28        71.05        20.52        10.55        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 
       12.92         8.81         6.28        12.69        55.86        38.04 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       56.68        12.89        26.86        32.81        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 
       13.05        46.32         8.58        12.39        71.31        69.70 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
        8.32        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        8.52        52.08        56.94        50.07        30.67        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       23.90        47.44        28.04        19.07        34.13         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       10.45        32.22        38.89         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        2.93        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       41.19        15.75        32.38        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        77.56        44.48        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.49        14.14        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       47.18        39.16        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.09        24.95        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       29.95        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       76.24        19.20        17.95       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        2.50         4.14        64.83       172.67       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 
       12.66         7.99         9.01         5.26         1.84        52.31 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       89.65        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 
       95.34        11.87        47.97         2.10        49.71        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       57.47        35.54       210.97        89.33         9.67         0.46 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
       22.85        25.08        25.94         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       14.89       156.49         3.52        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O 
        7.17       153.86        16.64        35.93        30.48        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       21.01       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       56.61         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       19.92        22.52        10.55        18.84        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        37.25        33.86        18.02        20.45        37.58 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       31.13        18.94        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       20.25        13.38        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 
        0.36        13.84         4.27         3.65         6.90        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       38.53        14.50        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        6.25        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       15.78        71.74        51.25        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        27.39        21.07        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T3-A92M TCGA-T3-A92N 
       12.72         6.87        15.91         7.10        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF 
       49.51        49.45        44.65        74.47        17.95        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       29.46        18.05        13.94        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       17.03        20.55        14.56        13.35        18.15 

  EPHA2 MUTATED EPHA2 WILD-TYPE 
           4.01            0.07 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
          56.48          210.97 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
          22.39           20.88 
[1] "4.0 - 56.5 (22.4)"  "0.1 - 211.0 (20.9)"
[1] "hr=" "1.4"
D15V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  EPHA2 MUTATED         1        6         4        13         0         0
  EPHA2 WILD-TYPE      24       69        76       240        11         1
D15V3, multiclass
           clus
vv          EPHA2 MUTATED EPHA2 WILD-TYPE
  STAGE I               1              24
  STAGE II              6              69
  STAGE III             4              76
  STAGE IVA            13             240
  STAGE IVB             0              11
  STAGE IVC             0               1
[1] 6 2
[1] 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       1   8   7   8
  EPHA2 WILD-TYPE    46 129  92 164
D15V4, multiclass
       clus
vv      EPHA2 MUTATED EPHA2 WILD-TYPE
  T0+T1             1              46
  T2                8             129
  T3                7              92
  T4                8             164
[1] 4 2
[1] TRUE
[1] "dimension of 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    11   1   8   0
  EPHA2 WILD-TYPE 164  66 160   7
D15V5, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  N0            11             164
  N1             1              66
  N2             8             160
  N3             0               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"
D15V6, binary
                 cls
clus                0   1
  EPHA2 MUTATED     9   0
  EPHA2 WILD-TYPE 182   1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      9    0
  EPHA2 WILD-TYPE  182    1
   clus
vv  EPHA2 MUTATED EPHA2 WILD-TYPE
  0             9             182
  1             0               1
[1] 2 2
[1] FALSE
D15V7, binary
                 cls
clus                0   1
  EPHA2 MUTATED     8  16
  EPHA2 WILD-TYPE 130 357
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      8   16
  EPHA2 WILD-TYPE  130  357
        clus
vv       EPHA2 MUTATED EPHA2 WILD-TYPE
  FEMALE             8             130
  MALE              16             357
[1] 2 2
[1] FALSE
D15V8, binary
                 cls
clus                0   1
  EPHA2 MUTATED    11  11
  EPHA2 WILD-TYPE 146 282
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED     11   11
  EPHA2 WILD-TYPE  146  282
     clus
vv    EPHA2 MUTATED EPHA2 WILD-TYPE
  NO             11             146
  YES            11             282
[1] 2 2
[1] FALSE
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA
  EPHA2 MUTATED                                    24
  EPHA2 WILD-TYPE                                 476
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  EPHA2 MUTATED                                                   0
  EPHA2 WILD-TYPE                                                10
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  EPHA2 MUTATED                                                           0
  EPHA2 WILD-TYPE                                                         1
D15V9, multiclass
                                                           clus
vv                                                          EPHA2 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  24
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             0
                                                           clus
vv                                                          EPHA2 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   476
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, continuous
D15V11, continuous
D15V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPHA2 MUTATED                                  0     1
  EPHA2 WILD-TYPE                                2     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EPHA2 MUTATED                           2    20
  EPHA2 WILD-TYPE                        45   417
D15V13, multiclass
                                  clus
vv                                 EPHA2 MUTATED EPHA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    2              45
  WHITE                                       20             417
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                 cls
clus                0   1
  EPHA2 MUTATED     1  22
  EPHA2 WILD-TYPE  24 427
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      1   22
  EPHA2 WILD-TYPE   24  427
                        clus
vv                       EPHA2 MUTATED EPHA2 WILD-TYPE
  HISPANIC OR LATINO                 1              24
  NOT HISPANIC OR LATINO            22             427
[1] 2 2
[1] FALSE

Clustering(16) Variable = RAC1 MUTATION ANALYSIS
D16V1, survival
                sevent
clus2              0   1
  RAC1 MUTATED     7   8
  RAC1 WILD-TYPE 282 212
  RAC1 MUTATED RAC1 WILD-TYPE 
            15            494 
  RAC1 MUTATED RAC1 WILD-TYPE 
             8            212 
$`RAC1 MUTATED`
TCGA-BA-4078 TCGA-BA-A6DJ TCGA-CN-5369 TCGA-CN-A640 TCGA-CQ-6223 TCGA-CR-5250 
        9.07        13.38        12.49         4.41        46.95        26.27 
TCGA-CR-7367 TCGA-CR-7388 TCGA-CV-7427 TCGA-CV-A45P TCGA-CV-A6JD TCGA-CV-A6K1 
       47.34        27.06       156.49        21.01         5.98        22.52 
TCGA-CX-7085 TCGA-H7-7774 TCGA-UF-A7JT 
       10.55        13.38        32.65 

$`RAC1 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
       13.64        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       23.84        65.59        15.52        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       20.48        16.41         6.15       105.90         9.14         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
        4.41        18.38        66.28        71.05        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 
       27.19        12.92         8.81         6.28        12.69        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       52.14        55.56        57.11        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       45.83        27.58        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 
        8.58        12.39        71.31        69.70         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.54        11.84        11.57         8.52        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
       19.07        34.13         6.74        10.45        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       17.29        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       12.39        16.57        12.07         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       19.53        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       15.75        32.38        66.28        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       14.99        38.76        64.87        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       77.56        44.48        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       14.14        12.46        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
       37.87        58.42        50.01        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       16.90        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       12.46        22.78        15.75         9.27        47.18        39.16 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       40.93        35.84         3.45         3.09        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
        0.99        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       17.13        32.78        47.01        12.89        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58        24.79         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        5.95        35.41        29.95        48.39       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
      129.21       108.95        76.24        19.20        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       54.74        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        9.70         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       140.78        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        8.42        28.34         2.50         4.14        64.83       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      111.16        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        1.84        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       47.97         2.10        49.71        18.41        57.47        35.54 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
      210.97        89.33         9.67         0.46        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
       25.94         0.07        34.09       100.57        14.89        56.48 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        3.52        16.27        84.49        19.76         7.17       153.86 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O 
       16.64         6.38        22.19        35.93        30.48        27.98 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
      169.38       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
       56.61         7.07        15.25        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K2 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.42        18.84        51.12        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
       23.05         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN 
       25.32        17.72        12.36        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        13.94        12.10        12.79        23.34        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 
       37.25        33.86        18.02        20.45        37.58        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       37.18        32.71        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        24.95         0.46        17.85        11.80        20.25 
TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       12.43        15.16        15.06        20.94        33.76        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       25.74        21.93        27.48        14.66        22.03         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         3.65         6.90        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        37.71        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        6.25        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       15.78        71.74        51.25        10.85        36.82        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       19.00        75.55        18.97         2.04        29.00        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       16.01        13.15        21.07        21.21        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       21.47         9.34        12.72        27.39        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       12.89         5.62        14.76        12.20        17.82        15.32 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
        8.32        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       32.45        13.71         3.12        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
       64.80        54.67         2.83        49.51        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       74.47        17.95        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       13.94        20.75        22.36        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  RAC1 MUTATED RAC1 WILD-TYPE 
          4.41           0.07 
  RAC1 MUTATED RAC1 WILD-TYPE 
        156.49         210.97 
  RAC1 MUTATED RAC1 WILD-TYPE 
         21.01          20.91 
[1] "4.4 - 156.5 (21.0)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1.3"
D16V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  RAC1 MUTATED         2        2         0         7         0         0
  RAC1 WILD-TYPE      23       73        80       246        11         1
D16V3, multiclass
           clus
vv          RAC1 MUTATED RAC1 WILD-TYPE
  STAGE I              2             23
  STAGE II             2             73
  STAGE III            0             80
  STAGE IVA            7            246
  STAGE IVB            0             11
  STAGE IVC            0              1
[1] 6 2
[1] 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
  RAC1 MUTATED       2   3   0   6
  RAC1 WILD-TYPE    45 134  99 166
D16V4, multiclass
       clus
vv      RAC1 MUTATED RAC1 WILD-TYPE
  T0+T1            2             45
  T2               3            134
  T3               0             99
  T4               6            166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RAC1 MUTATED     7   1   2   0
  RAC1 WILD-TYPE 168  66 166   7
D16V5, multiclass
    clus
vv   RAC1 MUTATED RAC1 WILD-TYPE
  N0            7            168
  N1            1             66
  N2            2            166
  N3            0              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"
D16V6, binary
                cls
clus               0   1
  RAC1 MUTATED     6   0
  RAC1 WILD-TYPE 185   1
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      6    0
  RAC1 WILD-TYPE  185    1
   clus
vv  RAC1 MUTATED RAC1 WILD-TYPE
  0            6            185
  1            0              1
[1] 2 2
[1] FALSE
D16V7, binary
                cls
clus               0   1
  RAC1 MUTATED     9   6
  RAC1 WILD-TYPE 129 367
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      9    6
  RAC1 WILD-TYPE  129  367
        clus
vv       RAC1 MUTATED RAC1 WILD-TYPE
  FEMALE            9            129
  MALE              6            367
[1] 2 2
[1] FALSE
D16V8, binary
                cls
clus               0   1
  RAC1 MUTATED     5  10
  RAC1 WILD-TYPE 152 283
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      5   10
  RAC1 WILD-TYPE  152  283
     clus
vv    RAC1 MUTATED RAC1 WILD-TYPE
  NO             5            152
  YES           10            283
[1] 2 2
[1] FALSE
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA
  RAC1 MUTATED                                    15
  RAC1 WILD-TYPE                                 485
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  RAC1 MUTATED                                                   0
  RAC1 WILD-TYPE                                                10
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  RAC1 MUTATED                                                           0
  RAC1 WILD-TYPE                                                         1
D16V9, multiclass
                                                           clus
vv                                                          RAC1 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                 15
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT            0
                                                           clus
vv                                                          RAC1 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  485
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, continuous
D16V11, continuous
D16V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAC1 MUTATED                                  0     1
  RAC1 WILD-TYPE                                2     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RAC1 MUTATED                           0    14
  RAC1 WILD-TYPE                        47   423
D16V13, multiclass
                                  clus
vv                                 RAC1 MUTATED RAC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   0             47
  WHITE                                      14            423
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                cls
clus               0   1
  RAC1 MUTATED     0  14
  RAC1 WILD-TYPE  25 435
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      0   14
  RAC1 WILD-TYPE   25  435
                        clus
vv                       RAC1 MUTATED RAC1 WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO           14            435
[1] 2 2
[1] FALSE

Clustering(17) Variable = HRAS MUTATION ANALYSIS
D17V1, survival
                sevent
clus2              0   1
  HRAS MUTATED    21  10
  HRAS WILD-TYPE 268 210
  HRAS MUTATED HRAS WILD-TYPE 
            31            478 
  HRAS MUTATED HRAS WILD-TYPE 
            10            210 
$`HRAS MUTATED`
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-BA-5556 TCGA-BA-A6DJ TCGA-CN-A63V TCGA-CN-A642 
       70.13        43.04        23.84        13.38        22.32         2.70 
TCGA-CQ-5324 TCGA-CQ-5333 TCGA-CQ-7071 TCGA-CQ-A4CG TCGA-CR-7382 TCGA-CR-7394 
       52.37        11.21        43.10        14.14        26.17        44.25 
TCGA-CR-7395 TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-7183 TCGA-CV-7250 TCGA-CV-7568 
       30.58        62.43         4.73       130.88        95.34        30.48 
TCGA-CV-A45P TCGA-CV-A6JD TCGA-CV-A6JO TCGA-D6-8569 TCGA-D6-A6EN TCGA-H7-8501 
       21.01         5.98         6.48        25.32        22.59        15.16 
TCGA-HD-A4C1 TCGA-HD-A6I0 TCGA-IQ-7631 TCGA-IQ-A61E TCGA-P3-A5Q5 TCGA-P3-A6T2 
        0.36         6.90        38.53        37.71        29.92        75.55 
TCGA-T2-A6WX 
        6.87 

$`HRAS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 
       32.88        11.61        34.52         6.02         0.36        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       30.94        14.04        40.24        21.11        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       48.03         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 
       26.50        23.74        42.35        57.93        17.10        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       15.52        21.17        14.83        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP 
       14.47         7.82         2.27        11.05        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15       105.90         9.14         4.80         4.41        18.38 
TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       66.28        71.05        20.52        10.55        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        8.81         6.28        12.69        55.86        38.04         4.67 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       56.68        12.89        26.86        32.81        52.14        55.56 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       57.11        12.99        20.55        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       73.61        13.05        42.02        46.32         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       71.31        69.70         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.57        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        48.00        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 
       34.13         6.74        10.45        32.22        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       17.42        11.74        35.01        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y 
       29.72        21.21         7.40        31.69        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5325 
        4.41        12.07        23.44        20.88        19.53        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 
        4.24        41.19        15.75        32.38        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       56.58        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       53.52        41.88        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       33.60        29.49        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       47.18        39.16        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.09        24.95        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       34.06        19.92        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7397 
       12.89        49.58        30.02        46.85        32.65        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       17.16       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       43.23        54.74        21.07         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        9.70         5.46        20.52        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      140.78        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
        6.08        53.95        65.82        10.98         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
       28.34         2.50         4.14        64.83       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
       18.81        12.66         7.99         9.01         5.26         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7235 
       52.31        12.92        21.80        71.21        10.75        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
        4.73        89.65        36.00        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       17.13         4.96        11.87        47.97         2.10        49.71 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       18.41        57.47        35.54       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        0.46        22.85        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 
      100.57        14.89        56.48       156.49         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       84.49        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
       22.19        35.93        27.98       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
       35.47         1.05        45.96         6.51        88.87        48.20 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       60.43        67.86         0.76        56.61         7.07        15.25 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
       35.34         6.38        29.79        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       23.47        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       16.14        11.44        18.67        24.95        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       28.77         7.63        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 
       23.34        58.45        37.25        33.86        18.02        20.45 
TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       37.58        41.59        37.18        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8502 TCGA-H7-A76A 
       11.80        20.25        12.43        13.38        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
       33.76        28.47        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-7632 
       22.03        13.84         4.27         3.65        15.95        14.50 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        37.41         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       13.84        19.04        15.48        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
        7.13        16.08        17.98        15.78        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 
       10.85        36.82        47.01        19.00        18.97         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       29.00        12.99        16.01        13.15        21.07        21.21 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       23.15         7.30        21.47         9.34        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        19.73        12.89         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WZ 
       17.82        15.32         8.32        12.72        16.96        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ 
        7.10        32.45        13.71         3.12        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       20.35        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       18.05        13.94        20.75        22.36        32.65        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.55        14.56        13.35        18.15 

  HRAS MUTATED HRAS WILD-TYPE 
          0.36           0.07 
  HRAS MUTATED HRAS WILD-TYPE 
        130.88         210.97 
  HRAS MUTATED HRAS WILD-TYPE 
        25.320         20.535 
[1] "0.4 - 130.9 (25.3)" "0.1 - 211.0 (20.5)"
[1] "hr=" "1.5"
D17V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  HRAS MUTATED         2        8         5        13         1         0
  HRAS WILD-TYPE      23       67        75       240        10         1
D17V3, multiclass
           clus
vv          HRAS MUTATED HRAS WILD-TYPE
  STAGE I              2             23
  STAGE II             8             67
  STAGE III            5             75
  STAGE IVA           13            240
  STAGE IVB            1             10
  STAGE IVC            0              1
[1] 6 2
[1] 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       2  12   5  10
  HRAS WILD-TYPE    45 125  94 162
D17V4, multiclass
       clus
vv      HRAS MUTATED HRAS WILD-TYPE
  T0+T1            2             45
  T2              12            125
  T3               5             94
  T4              10            162
[1] 4 2
[1] TRUE
[1] "dimension of 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    15   4   6   1
  HRAS WILD-TYPE 160  63 162   6
D17V5, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  N0           15            160
  N1            4             63
  N2            6            162
  N3            1              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"
D17V6, binary
                cls
clus               0   1
  HRAS MUTATED    13   0
  HRAS WILD-TYPE 178   1
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED     13    0
  HRAS WILD-TYPE  178    1
   clus
vv  HRAS MUTATED HRAS WILD-TYPE
  0           13            178
  1            0              1
[1] 2 2
[1] FALSE
D17V7, binary
                cls
clus               0   1
  HRAS MUTATED    13  18
  HRAS WILD-TYPE 125 355
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED     13   18
  HRAS WILD-TYPE  125  355
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  FEMALE           13            125
  MALE             18            355
[1] 2 2
[1] FALSE
D17V8, binary
                cls
clus               0   1
  HRAS MUTATED    13  15
  HRAS WILD-TYPE 144 278
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED     13   15
  HRAS WILD-TYPE  144  278
     clus
vv    HRAS MUTATED HRAS WILD-TYPE
  NO            13            144
  YES           15            278
[1] 2 2
[1] FALSE
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA
  HRAS MUTATED                                    30
  HRAS WILD-TYPE                                 470
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  HRAS MUTATED                                                   1
  HRAS WILD-TYPE                                                 9
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  HRAS MUTATED                                                           0
  HRAS WILD-TYPE                                                         1
D17V9, multiclass
                                                           clus
vv                                                          HRAS MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                 30
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT            0
                                                           clus
vv                                                          HRAS WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  470
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, continuous
D17V11, continuous
D17V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HRAS MUTATED                                  0     1
  HRAS WILD-TYPE                                2     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HRAS MUTATED                           1    29
  HRAS WILD-TYPE                        46   408
D17V13, multiclass
                                  clus
vv                                 HRAS MUTATED HRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             46
  WHITE                                      29            408
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V14, binary
                cls
clus               0   1
  HRAS MUTATED     0  31
  HRAS WILD-TYPE  25 418
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0   31
  HRAS WILD-TYPE   25  418
                        clus
vv                       HRAS MUTATED HRAS WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO           31            418
[1] 2 2
[1] FALSE

Clustering(18) Variable = EP300 MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2               0   1
  EP300 MUTATED    18  20
  EP300 WILD-TYPE 271 200
  EP300 MUTATED EP300 WILD-TYPE 
             38             471 
  EP300 MUTATED EP300 WILD-TYPE 
             20             200 
$`EP300 MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-CX-7219 TCGA-DQ-7593 TCGA-BA-4076 TCGA-BA-A6DA 
        9.30        68.48        34.36        40.24        13.64        11.54 
TCGA-BB-7870 TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-A63W TCGA-CN-A642 TCGA-CN-A6V6 
       66.28        12.92         8.81        12.39         2.70        20.88 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6487 
        2.93        54.58        45.99        50.01        39.52         7.69 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CV-5434 TCGA-CV-6938 TCGA-CV-6943 TCGA-CV-7095 
       44.25        30.58       108.95         4.73        19.79        18.81 
TCGA-CV-7100 TCGA-CV-7178 TCGA-CV-7427 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6K2 
        9.01        71.21       156.49        15.25         5.98        10.42 
TCGA-D6-6516 TCGA-F7-A623 TCGA-H7-7774 TCGA-HD-A6HZ TCGA-MZ-A7D7 TCGA-P3-A5Q5 
       25.41        20.25        13.38         3.65        17.98        29.92 
TCGA-P3-A6T4 TCGA-QK-A6IG 
        2.04         7.30 

$`EP300 WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
       37.28        20.48         3.55        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 
       51.29         9.07         9.24        52.08        11.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       32.48        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-5629 
       43.04        11.61        34.52         6.02         0.36        30.94 
TCGA-DQ-7588 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV 
       14.04        21.11        12.66        22.85        48.03         2.96 
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
        3.35        15.19         9.07        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
       57.93        17.10        23.84        65.59        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH 
       14.83        12.62         4.01        41.85        29.42        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       27.95         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-8596 TCGA-BB-8601 
        9.14         4.80         4.41        18.38        71.05        20.52 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 
       10.55        27.19         6.28        12.69        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        4.67        56.68        12.89        26.86        32.81        52.14 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       55.56        57.11        12.99        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        73.61        13.05        42.02        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       12.39        71.31        69.70         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.84        11.57        12.49         8.52        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
       19.07        34.13         6.74        10.45        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       17.29        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 
       16.57         4.41        12.07        23.44        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       21.50        70.45        62.37        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       41.19        15.75        32.38        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6473 
       11.77        54.67        37.87        26.27        58.42        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       12.46        22.78        15.75         9.27        47.18        39.16 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
       47.34        40.93        35.84         3.45         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       29.23         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       26.17        17.13        32.78        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7397 TCGA-CR-7398 
       49.58        30.02        46.85        32.65        24.79         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        5.95        35.41        29.95        48.39       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      129.21        76.24        19.20        17.95       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
        5.46        20.52        21.90        26.43        11.24       140.78 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       65.82        10.98         7.13         8.42        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 
        4.14        64.83       172.67       111.16        12.66         7.99 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 
        5.26         1.84        52.31        12.92        21.80        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       47.97         2.10        49.71        18.41        57.47        35.54 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
      210.97        89.33         9.67         0.46        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
       25.94         0.07        34.09       100.57        14.89        56.48 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        3.52        16.27        84.49        19.76         7.17       153.86 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O 
       16.64         6.38        22.19        35.93        30.48        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       21.01       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
       45.96         6.51        88.87        48.20        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
        0.76        56.61         7.07        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 
       22.52        10.55        18.84        51.12        13.25         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
       23.05         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN 
       25.32        17.72        12.36        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        13.94        12.10        12.79        23.34        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 
       37.25        33.86        18.02        20.45        37.58        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       37.18        32.71        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 
       18.94        24.95         0.46        17.85        11.80        12.43 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       21.93        27.48        14.66        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        4.27         6.90        15.95        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        37.41         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       13.84        19.04        15.48        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
        7.13        16.08        15.78        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 
       36.82        47.01        19.00        75.55        18.97        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       21.47         9.34        12.72        27.39        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       12.89         5.62        14.76        12.20        17.82        15.32 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
        8.32        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       32.45        13.71         3.12        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
       64.80        54.67         2.83        49.51        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       74.47        17.95        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       13.94        20.75        22.36        32.65        17.03        20.55 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  EP300 MUTATED EP300 WILD-TYPE 
           2.04            0.07 
  EP300 MUTATED EP300 WILD-TYPE 
         156.49          210.97 
  EP300 MUTATED EP300 WILD-TYPE 
         18.395          21.070 
[1] "2.0 - 156.5 (18.4)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.3"
D18V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  EP300 MUTATED         2        5         6        19         1         0
  EP300 WILD-TYPE      23       70        74       234        10         1
D18V3, multiclass
           clus
vv          EP300 MUTATED EP300 WILD-TYPE
  STAGE I               2              23
  STAGE II              5              70
  STAGE III             6              74
  STAGE IVA            19             234
  STAGE IVB             1              10
  STAGE IVC             0               1
[1] 6 2
[1] 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       4  11   4  15
  EP300 WILD-TYPE    43 126  95 157
D18V4, multiclass
       clus
vv      EP300 MUTATED EP300 WILD-TYPE
  T0+T1             4              43
  T2               11             126
  T3                4              95
  T4               15             157
[1] 4 2
[1] TRUE
[1] "dimension of 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     9   5  14   1
  EP300 WILD-TYPE 166  62 154   6
D18V5, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  N0             9             166
  N1             5              62
  N2            14             154
  N3             1               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"
D18V6, binary
                 cls
clus                0   1
  EP300 MUTATED    12   0
  EP300 WILD-TYPE 179   1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     12    0
  EP300 WILD-TYPE  179    1
   clus
vv  EP300 MUTATED EP300 WILD-TYPE
  0            12             179
  1             0               1
[1] 2 2
[1] FALSE
D18V7, binary
                 cls
clus                0   1
  EP300 MUTATED    12  26
  EP300 WILD-TYPE 126 347
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     12   26
  EP300 WILD-TYPE  126  347
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  FEMALE            12             126
  MALE              26             347
[1] 2 2
[1] FALSE
D18V8, binary
                 cls
clus                0   1
  EP300 MUTATED    10  23
  EP300 WILD-TYPE 147 270
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     10   23
  EP300 WILD-TYPE  147  270
     clus
vv    EP300 MUTATED EP300 WILD-TYPE
  NO             10             147
  YES            23             270
[1] 2 2
[1] FALSE
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA
  EP300 MUTATED                                    37
  EP300 WILD-TYPE                                 463
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  EP300 MUTATED                                                   1
  EP300 WILD-TYPE                                                 9
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  EP300 MUTATED                                                           0
  EP300 WILD-TYPE                                                         1
D18V9, multiclass
                                                           clus
vv                                                          EP300 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  37
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             0
                                                           clus
vv                                                          EP300 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   463
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, continuous
D18V11, continuous
D18V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EP300 MUTATED                                  0     1
  EP300 WILD-TYPE                                2     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EP300 MUTATED                           3    32
  EP300 WILD-TYPE                        44   405
D18V13, multiclass
                                  clus
vv                                 EP300 MUTATED EP300 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    3              44
  WHITE                                       32             405
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
                 cls
clus                0   1
  EP300 MUTATED     2  34
  EP300 WILD-TYPE  23 415
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      2   34
  EP300 WILD-TYPE   23  415
                        clus
vv                       EP300 MUTATED EP300 WILD-TYPE
  HISPANIC OR LATINO                 2              23
  NOT HISPANIC OR LATINO            34             415
[1] 2 2
[1] FALSE

Clustering(19) Variable = OR6C65 MUTATION ANALYSIS
D19V1, survival
                  sevent
clus2                0   1
  OR6C65 MUTATED    11   5
  OR6C65 WILD-TYPE 278 215
  OR6C65 MUTATED OR6C65 WILD-TYPE 
              16              493 
  OR6C65 MUTATED OR6C65 WILD-TYPE 
               5              215 
$`OR6C65 MUTATED`
TCGA-BA-5559 TCGA-BA-4074 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-CN-4728 
       68.48        15.19       105.90         4.80        18.38        56.68 
TCGA-CN-4729 TCGA-CN-6013 TCGA-CN-A498 TCGA-CQ-5325 TCGA-CR-7390 TCGA-CV-5976 
       12.89        23.90        25.41        21.50        49.58        48.59 
TCGA-F7-7848 TCGA-F7-A624 TCGA-H7-7774 TCGA-P3-A5QA 
       37.18        12.43        13.38        71.74 

$`OR6C65 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4078 
       22.85        48.03         2.96         3.35        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       65.59        15.52        21.17        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       41.85        29.42        20.45        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7870 
       20.48        16.41         6.15         9.14         4.41        66.28 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       71.05        20.52        10.55        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4730 
        6.28        12.69        55.86        38.04         4.67        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       32.81        52.14        55.56        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       46.32         8.58        12.39        71.31        69.70         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       16.21        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 
       52.08        56.94        50.07        30.67        48.00        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       28.04        19.07        34.13         6.74        10.45        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 
       38.89         3.68        17.42        11.74        35.01        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       17.29        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       20.88        19.53        52.37         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       15.75        32.38        66.28        46.95        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
        4.24        14.99        38.76        64.87        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        77.56        44.48        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.49        14.14        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       47.18        39.16        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.09        24.95        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       27.06        12.89        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58        24.79         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        94.88        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 
       80.12        17.92        13.35        23.05        86.83        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        7.07        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       90.12         2.14         9.70         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       21.90        26.43        11.24       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       42.38        15.09        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       10.98         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       172.67       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        9.01         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        89.65 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 
       36.00        31.36        26.20        18.97        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 
        4.96        11.87        47.97         2.10        49.71        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       57.47        35.54       210.97        89.33         9.67         0.46 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
       22.85        25.08        25.94         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       14.89        56.48       156.49         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       19.76         7.17       153.86        16.64         6.38        22.19 
TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       35.93        30.48        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       48.20        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        37.25        33.86        18.02        20.45        37.58 
TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       41.59        32.71        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        24.95         0.46        17.85        11.80        20.25 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       21.93        27.48        14.66        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65         6.90        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       18.97         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        27.39        21.07        19.73        12.89         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       16.96         6.87        15.91         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        3.12        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        2.83        49.51        49.45        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  OR6C65 MUTATED OR6C65 WILD-TYPE 
            4.80             0.07 
  OR6C65 MUTATED OR6C65 WILD-TYPE 
          105.90           210.97 
  OR6C65 MUTATED OR6C65 WILD-TYPE 
          24.655           20.750 
[1] "4.8 - 105.9 (24.7)" "0.1 - 211.0 (20.8)"
[1] "hr=" "1.7"
D19V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  OR6C65 MUTATED         2        1         3         8         0         0
  OR6C65 WILD-TYPE      23       74        77       245        11         1
D19V3, multiclass
           clus
vv          OR6C65 MUTATED OR6C65 WILD-TYPE
  STAGE I                2               23
  STAGE II               1               74
  STAGE III              3               77
  STAGE IVA              8              245
  STAGE IVB              0               11
  STAGE IVC              0                1
[1] 6 2
[1] 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
  OR6C65 MUTATED       2   4   3   5
  OR6C65 WILD-TYPE    45 133  96 167
D19V4, multiclass
       clus
vv      OR6C65 MUTATED OR6C65 WILD-TYPE
  T0+T1              2               45
  T2                 4              133
  T3                 3               96
  T4                 5              167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  OR6C65 MUTATED     4   2   5   0
  OR6C65 WILD-TYPE 171  65 163   7
D19V5, multiclass
    clus
vv   OR6C65 MUTATED OR6C65 WILD-TYPE
  N0              4              171
  N1              2               65
  N2              5              163
  N3              0                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"
D19V6, binary
                  cls
clus                 0   1
  OR6C65 MUTATED     5   0
  OR6C65 WILD-TYPE 186   1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C65 MUTATED      5    0
  OR6C65 WILD-TYPE  186    1
   clus
vv  OR6C65 MUTATED OR6C65 WILD-TYPE
  0              5              186
  1              0                1
[1] 2 2
[1] FALSE
D19V7, binary
                  cls
clus                 0   1
  OR6C65 MUTATED     2  14
  OR6C65 WILD-TYPE 136 359
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C65 MUTATED      2   14
  OR6C65 WILD-TYPE  136  359
        clus
vv       OR6C65 MUTATED OR6C65 WILD-TYPE
  FEMALE              2              136
  MALE               14              359
[1] 2 2
[1] FALSE
D19V8, binary
                  cls
clus                 0   1
  OR6C65 MUTATED     3  12
  OR6C65 WILD-TYPE 154 281
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C65 MUTATED      3   12
  OR6C65 WILD-TYPE  154  281
     clus
vv    OR6C65 MUTATED OR6C65 WILD-TYPE
  NO               3              154
  YES             12              281
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  OR6C65 MUTATED                                    16
  OR6C65 WILD-TYPE                                 484
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  OR6C65 MUTATED                                                   0
  OR6C65 WILD-TYPE                                                10
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  OR6C65 MUTATED                                                           0
  OR6C65 WILD-TYPE                                                         1
D19V9, multiclass
                                                           clus
vv                                                          OR6C65 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   16
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          OR6C65 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    484
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, continuous
D19V11, continuous
D19V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR6C65 MUTATED                                  0     0
  OR6C65 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR6C65 MUTATED                           0    15
  OR6C65 WILD-TYPE                        47   422
D19V13, multiclass
                                  clus
vv                                 OR6C65 MUTATED OR6C65 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               47
  WHITE                                        15              422
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V14, binary
                  cls
clus                 0   1
  OR6C65 MUTATED     0  15
  OR6C65 WILD-TYPE  25 434
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C65 MUTATED      0   15
  OR6C65 WILD-TYPE   25  434
                        clus
vv                       OR6C65 MUTATED OR6C65 WILD-TYPE
  HISPANIC OR LATINO                  0               25
  NOT HISPANIC OR LATINO             15              434
[1] 2 2
[1] FALSE

Clustering(20) Variable = PIK3CA MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    49  45
  PIK3CA WILD-TYPE 240 175
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              94              415 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              45              175 
$`PIK3CA MUTATED`
TCGA-BA-4077 TCGA-BA-5557 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-A6V1 TCGA-CR-6472 
       37.28        20.48         9.07        11.08        19.82        34.52 
TCGA-CX-7082 TCGA-HD-8634 TCGA-UF-A7JV TCGA-BA-5149 TCGA-BA-A4IF TCGA-BA-A6DF 
        0.36        12.66         2.96        26.50        29.42         7.82 
TCGA-BA-A8YP TCGA-BB-4223 TCGA-CN-4723 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5360 
       16.41       105.90        55.86        45.83        73.61        71.31 
TCGA-CN-5365 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6994 TCGA-CN-6998 
       11.54        52.08        50.07        23.90        38.89        11.74 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CQ-5331 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6222 
       25.41        17.29        45.99        41.19        15.75        66.28 
TCGA-CQ-A4C6 TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-6471 TCGA-CR-6487 
       44.48        14.14        84.23        37.87        39.52         7.69 
TCGA-CR-7367 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7399 
       47.34         3.09         0.99        44.25        30.58         5.95 
TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5435 TCGA-CV-5442 TCGA-CV-6436 TCGA-CV-6935 
       35.41        48.39        76.24        76.50        62.43         9.70 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6952 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 
       12.03        42.38         6.08        10.98         7.13        28.34 
TCGA-CV-7177 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 
       21.80        95.34        49.71        57.47       210.97        89.33 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7438 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45R 
       34.09        14.89         6.38        30.48        27.98       180.16 
TCGA-CV-A45V TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A6JM TCGA-CV-A6JO TCGA-D6-6515 
        1.05        60.43        67.86         6.38         6.48        13.25 
TCGA-D6-6517 TCGA-D6-6824 TCGA-DQ-5630 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S 
        9.60         2.53        33.86        21.63        31.13        18.94 
TCGA-H7-7774 TCGA-HD-7754 TCGA-HD-7832 TCGA-IQ-A61E TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       13.38        25.74        27.48        37.71        16.08        29.92 
TCGA-P3-A5QF TCGA-P3-A6T0 TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-TN-A7HI TCGA-TN-A7HL 
       10.85        19.00         8.32        15.91        13.55        20.35 
TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JF TCGA-UF-A7JO 
       49.51        44.65        55.43        20.75 

$`PIK3CA WILD-TYPE`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
        9.30        68.48         3.55        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V3 
       51.29         9.24        52.08        35.05        32.48        24.39 
TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6478 
       48.20        32.88        70.13        43.04        11.61         6.02 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8635 
       34.36        30.94        14.04        40.24        21.11        22.85 
TCGA-UF-A71D TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 
       48.03         3.35        15.19        13.64         9.07        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 
       42.35        57.93        17.10        23.84        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH 
       21.17        14.83        12.62         4.01        41.85        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DG 
       27.95        11.54         7.10         5.69        14.47         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4225 
       11.05        13.38        20.48         6.15         9.14         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
        4.41        18.38        66.28        71.05        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 
       27.19        12.92         8.81         6.28        12.69        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        4.67        56.68        12.89        26.86        32.81        52.14 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 
       55.56        57.11        12.99        20.55        14.33        27.58 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5361 
       13.05        42.02        46.32         8.58        12.39        69.70 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
        8.32        16.21        11.84        11.57        12.49         8.52 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       56.94        30.67        48.00        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 
       34.13         6.74        10.45        32.22         3.68        17.42 
TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       35.01        23.57        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       23.44        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        70.45        62.37        10.42        11.21         4.24 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       32.38        46.95        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       38.76        64.87        53.52        41.88        43.10        77.56 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI 
       23.24        29.36        33.60        29.49        12.46        31.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6473 
       11.77        54.67        26.27        58.42        50.01        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       12.46        22.78        15.75         9.27        47.18        39.16 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 
       40.93        35.84         3.45        24.95        29.23        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 
       32.65        24.79         5.13        29.95       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      129.21       108.95        19.20        17.95       107.51        94.88 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
        9.60        90.12         2.14         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6950 
       21.90        26.43        11.24       140.78        19.79        15.09 
TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-6962 
       30.08        53.95        65.82         8.42         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       172.67       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7178 
        9.01         5.26         1.84        52.31        12.92        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       10.75       130.88        77.16         4.73        89.65        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 
       31.36        26.20        18.97        17.13         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7413 TCGA-CV-7414 
       47.97         2.10        18.41        35.54         9.67         0.46 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7425 
       22.85        25.08        25.94         0.07       100.57        56.48 
TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
      156.49         3.52        16.27        84.49        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A45P TCGA-CV-A45Q 
      153.86        16.64        22.19        35.93        21.01       169.38 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
      159.65        35.47        45.96         6.51        88.87        48.20 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        0.76        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
       29.79        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6516 
       22.52        10.42        10.55        18.84        51.12        25.41 
TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
       23.05        16.14        11.44        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        23.34        58.45        37.25 
TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       18.02        20.45        37.58        41.59        37.18        32.71 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       20.25         3.02        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       20.25        12.43        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       28.47        21.93        14.66        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65         6.90        15.95        38.53        14.50 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        37.41         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       13.84        19.04        15.48        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
        7.13        17.98        15.78        71.74        51.25        36.82 
TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       47.01        75.55        18.97         2.04        29.00        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       16.01        13.15        21.07        21.21        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       21.47         9.34        12.72        27.39        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       12.89         5.62        14.76        12.20        17.82        15.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       12.72        16.96         6.87         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71E 
        3.12        13.25        64.80        54.67         2.83        49.45 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       74.47        17.95        24.30        29.46        18.05        13.94 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.36             0.07 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          210.97           172.67 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           26.99            20.48 
[1] "0.4 - 211.0 (27.0)" "0.1 - 172.7 (20.5)"
[1] "hr=" "1"  
D20V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  PIK3CA MUTATED         5        9        12        51         4         0
  PIK3CA WILD-TYPE      20       66        68       202         7         1
D20V3, multiclass
           clus
vv          PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                5               20
  STAGE II               9               66
  STAGE III             12               68
  STAGE IVA             51              202
  STAGE IVB              4                7
  STAGE IVC              0                1
[1] 6 2
[1] 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       7  19  21  36
  PIK3CA WILD-TYPE    40 118  78 136
D20V4, multiclass
       clus
vv      PIK3CA MUTATED PIK3CA WILD-TYPE
  T0+T1              7               40
  T2                19              118
  T3                21               78
  T4                36              136
[1] 4 2
[1] TRUE
[1] "dimension of 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    38   8  29   3
  PIK3CA WILD-TYPE 137  59 139   4
D20V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             38              137
  N1              8               59
  N2             29              139
  N3              3                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"
D20V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    33   0
  PIK3CA WILD-TYPE 158   1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     33    0
  PIK3CA WILD-TYPE  158    1
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             33              158
  1              0                1
[1] 2 2
[1] FALSE
D20V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    33  61
  PIK3CA WILD-TYPE 105 312
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     33   61
  PIK3CA WILD-TYPE  105  312
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             33              105
  MALE               61              312
[1] 2 2
[1] FALSE
D20V8, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    28  54
  PIK3CA WILD-TYPE 129 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     28   54
  PIK3CA WILD-TYPE  129  239
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              28              129
  YES             54              239
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  PIK3CA MUTATED                                    93
  PIK3CA WILD-TYPE                                 407
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  PIK3CA MUTATED                                                   1
  PIK3CA WILD-TYPE                                                 9
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  PIK3CA MUTATED                                                           0
  PIK3CA WILD-TYPE                                                         1
D20V9, multiclass
                                                           clus
vv                                                          PIK3CA MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   93
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          PIK3CA WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    407
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, continuous
D20V11, continuous
D20V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3CA MUTATED                                  0     2
  PIK3CA WILD-TYPE                                2     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED                           3    88
  PIK3CA WILD-TYPE                        44   349
D20V13, multiclass
                                  clus
vv                                 PIK3CA MUTATED PIK3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     3               44
  WHITE                                        88              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V14, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     3  84
  PIK3CA WILD-TYPE  22 365
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      3   84
  PIK3CA WILD-TYPE   22  365
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  3               22
  NOT HISPANIC OR LATINO             84              365
[1] 2 2
[1] FALSE

Clustering(21) Variable = PTEN MUTATION ANALYSIS
D21V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    11   3
  PTEN WILD-TYPE 278 217
  PTEN MUTATED PTEN WILD-TYPE 
            14            495 
  PTEN MUTATED PTEN WILD-TYPE 
             3            217 
$`PTEN MUTATED`
TCGA-BA-5559 TCGA-BA-4074 TCGA-BB-A6UM TCGA-CN-4723 TCGA-CN-A499 TCGA-CR-7369 
       68.48        15.19        12.92        55.86        23.57        35.84 
TCGA-CR-7374 TCGA-CV-7238 TCGA-D6-A6ES TCGA-MT-A67F TCGA-MT-A7BN TCGA-QK-A6VB 
        0.99        89.65        12.79        12.62        15.42        21.07 
TCGA-T2-A6X0 TCGA-UF-A7JF 
        7.10        55.43 

$`PTEN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4078 
       22.85        48.03         2.96         3.35        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       65.59        15.52        21.17        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       41.85        29.42        20.45        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       20.48        16.41         6.15       105.90         9.14         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
        4.41        18.38        66.28        71.05        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 
       27.19         8.81         6.28        12.69        38.04         4.67 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       56.68        12.89        26.86        32.81        52.14        55.56 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       57.11        12.99        20.55        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       73.61        13.05        42.02        46.32         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       71.31        69.70         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.57        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        48.00        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 
       34.13         6.74        10.45        32.22        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B 
       17.42        11.74        35.01        25.41        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 
       45.99        10.42        11.21         4.24        41.19        15.75 
TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.38        66.28        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       14.99        38.76        64.87        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       77.56        44.48        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       14.14        12.46        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       37.87        26.27        58.42        50.01        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        22.78        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
       39.16        47.34        40.93         3.45         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
       29.23        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       17.13        32.78        47.01        27.06        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       17.16       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       140.78        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       15.09        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
        7.13         8.42        28.34         2.50         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      172.67       111.16        18.81        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        5.26         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7242 TCGA-CV-7243 
       10.75       130.88        77.16         4.73        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       47.97         2.10        49.71        18.41        57.47        35.54 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
      210.97        89.33         9.67         0.46        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
       25.94         0.07        34.09       100.57        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
      156.49         3.52        16.27        84.49        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 
      153.86        16.64         6.38        22.19        35.93        30.48 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        21.01       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
        1.05        45.96         6.51        88.87        48.20        60.43 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       67.86         0.76        56.61         7.07        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       35.34         6.38        29.79         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        51.12        13.25        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
        2.53        16.14        11.44        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       13.94        12.10        23.34        58.45        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       18.02        20.45        37.58        41.59        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       21.63        20.25         3.02        31.13        18.94        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
        0.46        17.85        11.80        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       21.93        27.48        14.66        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65         6.90        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A5BI 
       14.37         7.96        30.05         1.84         6.25         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
       16.08        17.98        29.92        15.78        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       10.85        36.82        47.01        19.00        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
        2.04        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.21        23.15         7.30        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       27.39        19.73        12.89         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       17.82        15.32         8.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ 
       15.91        32.45        13.71         3.12        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       20.35        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ 
       44.65        74.47        17.95        24.30        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       13.94        20.75        22.36        32.65        17.03        20.55 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  PTEN MUTATED PTEN WILD-TYPE 
          0.99           0.07 
  PTEN MUTATED PTEN WILD-TYPE 
         89.65         210.97 
  PTEN MUTATED PTEN WILD-TYPE 
        18.245         20.940 
[1] "1.0 - 89.7 (18.2)"  "0.1 - 211.0 (20.9)"
[1] "hr=" "2.1"
D21V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  PTEN MUTATED         0        2         1         8         0         0
  PTEN WILD-TYPE      25       73        79       245        11         1
D21V3, multiclass
           clus
vv          PTEN MUTATED PTEN WILD-TYPE
  STAGE I              0             25
  STAGE II             2             73
  STAGE III            1             79
  STAGE IVA            8            245
  STAGE IVB            0             11
  STAGE IVC            0              1
[1] 6 2
[1] 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       1   3   0   6
  PTEN WILD-TYPE    46 134  99 166
D21V4, multiclass
       clus
vv      PTEN MUTATED PTEN WILD-TYPE
  T0+T1            1             46
  T2               3            134
  T3               0             99
  T4               6            166
[1] 4 2
[1] TRUE
[1] "dimension of 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     6   0   4   0
  PTEN WILD-TYPE 169  67 164   7
D21V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0            6            169
  N1            0             67
  N2            4            164
  N3            0              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"
D21V6, binary
                cls
clus               0   1
  PTEN MUTATED     5   0
  PTEN WILD-TYPE 186   1
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      5    0
  PTEN WILD-TYPE  186    1
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            5            186
  1            0              1
[1] 2 2
[1] FALSE
D21V7, binary
                cls
clus               0   1
  PTEN MUTATED     4  10
  PTEN WILD-TYPE 134 363
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4   10
  PTEN WILD-TYPE  134  363
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            4            134
  MALE             10            363
[1] 2 2
[1] FALSE
D21V8, binary
                cls
clus               0   1
  PTEN MUTATED     4  10
  PTEN WILD-TYPE 153 283
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4   10
  PTEN WILD-TYPE  153  283
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             4            153
  YES           10            283
[1] 2 2
[1] FALSE
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA
  PTEN MUTATED                                    14
  PTEN WILD-TYPE                                 486
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  PTEN MUTATED                                                   0
  PTEN WILD-TYPE                                                10
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  PTEN MUTATED                                                           0
  PTEN WILD-TYPE                                                         1
D21V9, multiclass
                                                           clus
vv                                                          PTEN MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                 14
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT            0
                                                           clus
vv                                                          PTEN WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  486
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V10, continuous
D21V11, continuous
D21V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTEN MUTATED                                  0     0
  PTEN WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED                           0    14
  PTEN WILD-TYPE                        47   423
D21V13, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             47
  WHITE                                      14            423
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V14, binary
                cls
clus               0   1
  PTEN MUTATED     0  12
  PTEN WILD-TYPE  25 437
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0   12
  PTEN WILD-TYPE   25  437
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO           12            437
[1] 2 2
[1] FALSE

Clustering(22) Variable = RASA1 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2               0   1
  RASA1 MUTATED    10   8
  RASA1 WILD-TYPE 279 212
  RASA1 MUTATED RASA1 WILD-TYPE 
             18             491 
  RASA1 MUTATED RASA1 WILD-TYPE 
              8             212 
$`RASA1 MUTATED`
TCGA-CN-6023 TCGA-DQ-5629 TCGA-BB-8601 TCGA-CN-4723 TCGA-CN-5366 TCGA-CQ-6219 
       52.08        30.94        20.52        55.86        11.84        15.75 
TCGA-CQ-6224 TCGA-CR-6492 TCGA-CR-7365 TCGA-CV-6959 TCGA-CV-7243 TCGA-CV-7413 
       56.58        15.75        39.16         8.42        31.36         9.67 
TCGA-CV-7414 TCGA-CV-A6K1 TCGA-HD-7831 TCGA-IQ-7630 TCGA-QK-A8Z8 TCGA-T3-A92N 
        0.46        22.52        21.93        15.95         5.62         3.12 

$`RASA1 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 
       30.18        25.71        51.29         9.07         9.24        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       34.36        14.04        40.24        21.11        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       48.03         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       65.59        15.52        21.17        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       41.85        29.42        20.45        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       20.48        16.41         6.15       105.90         9.14         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-A5HY TCGA-BB-A5HZ 
        4.41        18.38        66.28        71.05        10.55        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 
       12.92         8.81         6.28        12.69        38.04         4.67 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       56.68        12.89        26.86        32.81        52.14        55.56 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       57.11        12.99        20.55        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       73.61        13.05        42.02        46.32         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 
       71.31        69.70         8.32        16.21        11.54        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
       12.49         8.52        52.08        56.94        50.07        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       48.00        23.90        47.44        28.04        19.07        34.13 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
        6.74        10.45        32.22        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       45.99        10.42        11.21         4.24        41.19        32.38 
TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       66.28        46.95        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       58.42        50.01        39.52        36.99        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       22.78         9.27        47.18        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      108.95        76.24        19.20        17.95       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      140.78        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 
        6.08        53.95        65.82        10.98         7.13        28.34 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        2.50         4.14        64.83       172.67       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 
       12.66         7.99         9.01         5.26         1.84        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
       12.92        21.80        71.21        10.75       130.88        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
        4.73        89.65        36.00        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       95.34         4.96        11.87        47.97         2.10        49.71 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7415 
       18.41        57.47        35.54       210.97        89.33        22.85 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 
       25.08        25.94         0.07        34.09       100.57        14.89 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       56.48       156.49         3.52        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 
        7.17       153.86        16.64         6.38        22.19        35.93 
TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
       30.48        27.98        21.01       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
       35.47         1.05        45.96         6.51        88.87        48.20 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       60.43        67.86         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 
        3.62        21.24        23.47        19.92        10.42        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        51.12        13.25        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
        2.53        16.14        11.44        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 
       33.86        18.02        20.45        37.58        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       24.95         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       13.38        15.16        15.06        20.94        33.76        28.47 
TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       25.74        27.48        14.66        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        4.27         3.65         6.90        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        37.41         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       13.84        19.04        15.48        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       18.97         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 
       12.72        27.39        21.07        19.73        12.89        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HI 
        6.87        15.91         7.10        32.45        13.71        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.25        20.35        64.80        54.67         2.83        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.45        44.65        74.47        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       29.46        18.05        13.94        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       17.03        20.55        14.56        13.35        18.15 

  RASA1 MUTATED RASA1 WILD-TYPE 
           0.46            0.07 
  RASA1 MUTATED RASA1 WILD-TYPE 
          56.58          210.97 
  RASA1 MUTATED RASA1 WILD-TYPE 
         18.235          21.010 
[1] "0.5 - 56.6 (18.2)"  "0.1 - 211.0 (21.0)"
[1] "hr=" "1.3"
D22V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  RASA1 MUTATED         0        2         4        10         0         1
  RASA1 WILD-TYPE      25       73        76       243        11         0
D22V3, multiclass
           clus
vv          RASA1 MUTATED RASA1 WILD-TYPE
  STAGE I               0              25
  STAGE II              2              73
  STAGE III             4              76
  STAGE IVA            10             243
  STAGE IVB             0              11
  STAGE IVC             1               0
[1] 6 2
[1] 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
  RASA1 MUTATED       0   7   5   5
  RASA1 WILD-TYPE    47 130  94 167
D22V4, multiclass
       clus
vv      RASA1 MUTATED RASA1 WILD-TYPE
  T0+T1             0              47
  T2                7             130
  T3                5              94
  T4                5             167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RASA1 MUTATED     6   4   7   0
  RASA1 WILD-TYPE 169  63 161   7
D22V5, multiclass
    clus
vv   RASA1 MUTATED RASA1 WILD-TYPE
  N0             6             169
  N1             4              63
  N2             7             161
  N3             0               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"
D22V6, binary
                 cls
clus                0   1
  RASA1 MUTATED     6   1
  RASA1 WILD-TYPE 185   0
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      6    1
  RASA1 WILD-TYPE  185    0
   clus
vv  RASA1 MUTATED RASA1 WILD-TYPE
  0             6             185
  1             1               0
[1] 2 2
[1] FALSE
D22V7, binary
                 cls
clus                0   1
  RASA1 MUTATED     3  15
  RASA1 WILD-TYPE 135 358
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      3   15
  RASA1 WILD-TYPE  135  358
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  FEMALE             3             135
  MALE              15             358
[1] 2 2
[1] FALSE
D22V8, binary
                 cls
clus                0   1
  RASA1 MUTATED     8   9
  RASA1 WILD-TYPE 149 284
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      8    9
  RASA1 WILD-TYPE  149  284
     clus
vv    RASA1 MUTATED RASA1 WILD-TYPE
  NO              8             149
  YES             9             284
[1] 2 2
[1] FALSE
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA
  RASA1 MUTATED                                    18
  RASA1 WILD-TYPE                                 482
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  RASA1 MUTATED                                                   0
  RASA1 WILD-TYPE                                                10
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  RASA1 MUTATED                                                           0
  RASA1 WILD-TYPE                                                         1
D22V9, multiclass
                                                           clus
vv                                                          RASA1 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  18
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             0
                                                           clus
vv                                                          RASA1 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   482
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, continuous
D22V11, continuous
D22V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RASA1 MUTATED                                  0     0
  RASA1 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RASA1 MUTATED                           3    15
  RASA1 WILD-TYPE                        44   422
D22V13, multiclass
                                  clus
vv                                 RASA1 MUTATED RASA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    3              44
  WHITE                                       15             422
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                 cls
clus                0   1
  RASA1 MUTATED     1  17
  RASA1 WILD-TYPE  24 432
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      1   17
  RASA1 WILD-TYPE   24  432
                        clus
vv                       RASA1 MUTATED RASA1 WILD-TYPE
  HISPANIC OR LATINO                 1              24
  NOT HISPANIC OR LATINO            17             432
[1] 2 2
[1] FALSE

Clustering(23) Variable = MAPK1 MUTATION ANALYSIS
D23V1, survival
                 sevent
clus2               0   1
  MAPK1 MUTATED     8   1
  MAPK1 WILD-TYPE 281 219
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             500 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              1             219 
$`MAPK1 MUTATED`
TCGA-C9-A480 TCGA-CN-A63Y TCGA-CQ-5334 TCGA-CV-5442 TCGA-CV-5971 TCGA-CV-7261 
       12.69        16.57         4.24        76.50        23.05        49.71 
TCGA-D6-A74Q TCGA-MT-A67F TCGA-TN-A7HL 
       23.34        12.62        20.35 

$`MAPK1 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 
        9.14         4.80         4.41        18.38        66.28        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        10.55        27.19        12.92         8.81         6.28 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       55.86        38.04         4.67        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       32.81        52.14        55.56        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       46.32         8.58        12.39        71.31        69.70         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       16.21        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       32.22        38.89         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       25.41        23.57        17.29        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       31.69        22.32        12.39         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       23.44        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       41.19        15.75        32.38        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       11.34        11.64         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      108.95        76.24        19.20        17.95       107.51        94.88 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 
       91.53        80.12        17.92        13.35        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       60.49         7.07        43.23        54.74        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
        9.60        90.12         2.14         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       65.82        10.98         7.13         8.42        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        4.14        64.83       172.67       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       89.65        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 
       95.34         4.96        11.87        47.97         2.10        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       57.47        35.54       210.97        89.33         9.67         0.46 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
       22.85        25.08        25.94         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       14.89        56.48       156.49         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       19.76         7.17       153.86        16.64         6.38        22.19 
TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       35.93        30.48        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       48.20        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 
       22.59        24.95        13.94        12.10        12.79        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 
       37.25        33.86        18.02        20.45        37.58        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       37.18        32.71        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        24.95         0.46        17.85        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       12.43        13.38        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 
        0.36        13.84         4.27         3.65         6.90        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
       33.57         5.29        13.68        13.84        19.04        15.48 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.27        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        6.25        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       15.78        71.74        51.25        10.85        36.82        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       19.00        75.55        18.97         2.04        29.00        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       16.01        13.15        21.07        21.21        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       21.47         9.34        12.72        27.39        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       12.89         5.62        14.76        12.20        17.82        15.32 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
        8.32        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 
       32.45        13.71         3.12        13.55        13.25        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  MAPK1 MUTATED MAPK1 WILD-TYPE 
           4.24            0.07 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
          76.50          210.97 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
         20.350          20.975 
[1] "4.2 - 76.5 (20.4)"  "0.1 - 211.0 (21.0)"
[1] "hr=" "3.7"
D23V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  MAPK1 MUTATED         0        1         1         7         0         0
  MAPK1 WILD-TYPE      25       74        79       246        11         1
D23V3, multiclass
           clus
vv          MAPK1 MUTATED MAPK1 WILD-TYPE
  STAGE I               0              25
  STAGE II              1              74
  STAGE III             1              79
  STAGE IVA             7             246
  STAGE IVB             0              11
  STAGE IVC             0               1
[1] 6 2
[1] 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
  MAPK1 MUTATED       0   1   3   5
  MAPK1 WILD-TYPE    47 136  96 167
D23V4, multiclass
       clus
vv      MAPK1 MUTATED MAPK1 WILD-TYPE
  T0+T1             0              47
  T2                1             136
  T3                3              96
  T4                5             167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MAPK1 MUTATED     5   0   4   0
  MAPK1 WILD-TYPE 170  67 164   7
D23V5, multiclass
    clus
vv   MAPK1 MUTATED MAPK1 WILD-TYPE
  N0             5             170
  N1             0              67
  N2             4             164
  N3             0               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"
D23V6, binary
                 cls
clus                0   1
  MAPK1 MUTATED     3   0
  MAPK1 WILD-TYPE 188   1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      3    0
  MAPK1 WILD-TYPE  188    1
   clus
vv  MAPK1 MUTATED MAPK1 WILD-TYPE
  0             3             188
  1             0               1
[1] 2 2
[1] FALSE
D23V7, binary
                 cls
clus                0   1
  MAPK1 MUTATED     3   6
  MAPK1 WILD-TYPE 135 367
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      3    6
  MAPK1 WILD-TYPE  135  367
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  FEMALE             3             135
  MALE               6             367
[1] 2 2
[1] FALSE
D23V8, binary
                 cls
clus                0   1
  MAPK1 MUTATED     4   5
  MAPK1 WILD-TYPE 153 288
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      4    5
  MAPK1 WILD-TYPE  153  288
     clus
vv    MAPK1 MUTATED MAPK1 WILD-TYPE
  NO              4             153
  YES             5             288
[1] 2 2
[1] FALSE
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA
  MAPK1 MUTATED                                     9
  MAPK1 WILD-TYPE                                 491
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  MAPK1 MUTATED                                                   0
  MAPK1 WILD-TYPE                                                10
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  MAPK1 MUTATED                                                           0
  MAPK1 WILD-TYPE                                                         1
D23V9, multiclass
                                                           clus
vv                                                          MAPK1 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   9
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             0
                                                           clus
vv                                                          MAPK1 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   491
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, continuous
[1] "Remove cluster labels:" "MAPK1 MUTATED"         
clus
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              2             288 
     TCGA-BA-4075      TCGA-BA-4077      TCGA-BA-6871      TCGA-BA-A4II 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-4727      TCGA-CN-6021      TCGA-CN-6023      TCGA-CN-6024 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-6992      TCGA-CN-6997      TCGA-CN-A6V3      TCGA-CQ-5323 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CQ-6221      TCGA-CQ-7063      TCGA-CQ-A4C7      TCGA-CX-7082 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CX-7219      TCGA-DQ-5629      TCGA-DQ-7588      TCGA-DQ-7593 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-H7-A6C4      TCGA-H7-A6C5      TCGA-HD-8634      TCGA-HD-8635 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-UF-A71D      TCGA-BA-4074      TCGA-BA-4076      TCGA-BA-4078 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-BA-5149      TCGA-BA-5151      TCGA-BA-5555      TCGA-BA-5556 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-BA-6868      TCGA-BA-6869      TCGA-BA-6870      TCGA-BA-6872 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-BA-6873      TCGA-BA-7269      TCGA-BA-A4IF      TCGA-BA-A4IH 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-BA-A6D8      TCGA-BA-A6DA      TCGA-BA-A6DD      TCGA-BA-A6DE 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-BA-A6DG      TCGA-BA-A6DI      TCGA-BA-A6DJ      TCGA-BA-A6DL 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-BA-A8YP      TCGA-BB-4217      TCGA-BB-4225      TCGA-BB-4227 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-BB-4228      TCGA-BB-7870      TCGA-BB-8596      TCGA-BB-A5HY 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-BB-A6UM      TCGA-BB-A6UO      TCGA-CN-4726      TCGA-CN-4728 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-4729      TCGA-CN-4730      TCGA-CN-4731      TCGA-CN-4735 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-4736      TCGA-CN-4738      TCGA-CN-4739      TCGA-CN-4740 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-4741      TCGA-CN-4742      TCGA-CN-5355      TCGA-CN-5358 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-5359      TCGA-CN-5360      TCGA-CN-5361      TCGA-CN-5363 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-5365      TCGA-CN-5366      TCGA-CN-5367      TCGA-CN-5373 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-5374      TCGA-CN-6010      TCGA-CN-6011      TCGA-CN-6012 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-6016      TCGA-CN-6017      TCGA-CN-6019      TCGA-CN-6988 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-6989      TCGA-CN-6994      TCGA-CN-6998      TCGA-CN-A498 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-A49B      TCGA-CN-A49C      TCGA-CN-A63T      TCGA-CN-A63U 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-A63V      TCGA-CN-A641      TCGA-CN-A642      TCGA-CN-A6UY 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-A6V6      TCGA-CQ-5324      TCGA-CQ-5325      TCGA-CQ-5326 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CQ-5330      TCGA-CQ-5331      TCGA-CQ-5332      TCGA-CQ-5333 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CQ-6218      TCGA-CQ-6219      TCGA-CQ-6222      TCGA-CQ-6223 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CQ-6224      TCGA-CQ-6227      TCGA-CQ-6228      TCGA-CQ-7072 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CQ-A4C6      TCGA-CQ-A4C9      TCGA-CQ-A4CA      TCGA-CQ-A4CB 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CQ-A4CG      TCGA-CQ-A4CI      TCGA-CR-5247      TCGA-CR-5248 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-5250      TCGA-CR-6467      TCGA-CR-6471      TCGA-CR-6473 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-6474      TCGA-CR-6482      TCGA-CR-6487      TCGA-CR-6491 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-6492      TCGA-CR-6493      TCGA-CR-7364      TCGA-CR-7367 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-7368      TCGA-CR-7369      TCGA-CR-7370      TCGA-CR-7371 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-7373      TCGA-CR-7374      TCGA-CR-7376      TCGA-CR-7377 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-7379      TCGA-CR-7383      TCGA-CR-7385      TCGA-CR-7386 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-7388      TCGA-CR-7389      TCGA-CR-7390      TCGA-CR-7392 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-7394      TCGA-CR-7395      TCGA-CR-7398      TCGA-CR-7399 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-7401      TCGA-CR-7402      TCGA-CV-6436      TCGA-CV-6441 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-6933      TCGA-CV-6934      TCGA-CV-6940      TCGA-CV-6941 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-6945      TCGA-CV-6952      TCGA-CV-6961      TCGA-CV-7095 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-7097      TCGA-CV-7235      TCGA-CV-7242      TCGA-CV-7245 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-7248      TCGA-CV-7250      TCGA-CV-7254      TCGA-CV-7263 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-7406      TCGA-CV-7410      TCGA-CV-7418      TCGA-CV-7422 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-7424      TCGA-CV-7427      TCGA-CV-7430      TCGA-CV-7432 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-7433      TCGA-CV-7434      TCGA-CV-7440      TCGA-CV-7446 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-7568      TCGA-CV-A45Y      TCGA-CV-A45Z      TCGA-CV-A460 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-A464      TCGA-CV-A468      TCGA-CV-A6JD      TCGA-CV-A6JN 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-A6JO      TCGA-CV-A6JU      TCGA-CV-A6JZ      TCGA-CV-A6K1 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-A6K2      TCGA-CX-7085      TCGA-CX-7086      TCGA-CX-A4AQ 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-D6-6516      TCGA-D6-6517      TCGA-D6-6823      TCGA-D6-6824 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-D6-6825      TCGA-D6-6827      TCGA-D6-8568      TCGA-D6-8569 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-D6-A4Z9      TCGA-D6-A4ZB      TCGA-D6-A6EK      TCGA-D6-A6EP 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-DQ-5625      TCGA-DQ-5630      TCGA-DQ-5631      TCGA-DQ-7591 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-DQ-7592      TCGA-F7-7848      TCGA-F7-8298      TCGA-F7-8489 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-F7-A50G      TCGA-F7-A50I      TCGA-F7-A50J      TCGA-F7-A61S 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-F7-A61V      TCGA-F7-A61W      TCGA-F7-A620      TCGA-F7-A623 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-H7-7774      TCGA-H7-8502      TCGA-HD-7753      TCGA-HD-7754 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-HD-7832      TCGA-HD-A634      TCGA-HD-A6I0      TCGA-IQ-7631 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-IQ-7632      TCGA-IQ-A61E      TCGA-IQ-A61G      TCGA-IQ-A61H 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-IQ-A61K      TCGA-IQ-A6SH      TCGA-KU-A6H7      TCGA-KU-A6H8 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-MT-A51W      TCGA-MT-A51X      TCGA-MT-A67D      TCGA-MZ-A6I9 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-MZ-A7D7      TCGA-P3-A5Q5      TCGA-P3-A5Q6      TCGA-P3-A6SW 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-P3-A6SX      TCGA-P3-A6T0      TCGA-P3-A6T4      TCGA-P3-A6T5 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-P3-A6T7      TCGA-P3-A6T8      TCGA-QK-A6IG      TCGA-QK-A6II 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-QK-A6IJ      TCGA-QK-A8Z7      TCGA-QK-A8Z8      TCGA-QK-A8Z9 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-QK-A8ZA      TCGA-RS-A6TP      TCGA-T2-A6WZ      TCGA-T2-A6X0 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-T2-A6X2      TCGA-T3-A92M      TCGA-T3-A92N      TCGA-TN-A7HI 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-UF-A718      TCGA-UF-A71B      TCGA-UF-A7J9      TCGA-UF-A7JC 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-UF-A7JD      TCGA-UF-A7JF      TCGA-UF-A7JH      TCGA-UF-A7JJ 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-UF-A7JS      TCGA-WA-A7GZ      TCGA-WA-A7H4      TCGA-KU-A66S 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
D23V11, continuous
D23V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAPK1 MUTATED                                  0     1
  MAPK1 WILD-TYPE                                2     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MAPK1 MUTATED                           0     8
  MAPK1 WILD-TYPE                        47   429
D23V13, multiclass
                                  clus
vv                                 MAPK1 MUTATED MAPK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              47
  WHITE                                        8             429
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V14, binary
                 cls
clus                0   1
  MAPK1 MUTATED     0   9
  MAPK1 WILD-TYPE  25 440
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      0    9
  MAPK1 WILD-TYPE   25  440
                        clus
vv                       MAPK1 MUTATED MAPK1 WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO             9             440
[1] 2 2
[1] FALSE

Clustering(24) Variable = NUDT11 MUTATION ANALYSIS
D24V1, survival
                  sevent
clus2                0   1
  NUDT11 MUTATED     7   2
  NUDT11 WILD-TYPE 282 218
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               9              500 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               2              218 
$`NUDT11 MUTATED`
TCGA-CN-4727 TCGA-BA-5151 TCGA-CN-A63U TCGA-CV-7103 TCGA-CV-7245 TCGA-CV-7247 
       51.29        23.74        31.69        52.31        26.20        18.97 
TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7754 
       15.06        33.76        25.74 

$`NUDT11 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       30.18        25.71         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
        9.07        26.50        42.35        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       65.59        15.52        21.17        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       41.85        29.42        20.45        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       20.48        16.41         6.15       105.90         9.14         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
        4.41        18.38        66.28        71.05        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 
       27.19        12.92         8.81         6.28        12.69        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       52.14        55.56        57.11        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       45.83        27.58        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 
        8.58        12.39        71.31        69.70         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       56.94        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       28.04        19.07        34.13         6.74        10.45        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       38.89         3.68        17.42        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V 
       23.57        17.29        29.72        21.21         7.40        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       70.45        62.37        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       41.19        15.75        32.38        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       11.34        11.64         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      108.95        76.24        19.20        17.95       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      140.78        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
        6.08        53.95        65.82        10.98         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
       28.34         2.50         4.14        64.83       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
       18.81        12.66         7.99         9.01         5.26         1.84 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
       12.92        21.80        71.21        10.75       130.88        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 
        4.73        89.65        36.00        31.36        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 
        4.96        11.87        47.97         2.10        49.71        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       57.47        35.54       210.97        89.33         9.67         0.46 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
       22.85        25.08        25.94         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       14.89        56.48       156.49         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       19.76         7.17       153.86        16.64         6.38        22.19 
TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       35.93        30.48        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       48.20        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        37.25        33.86        18.02        20.45        37.58 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       31.13        18.94        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7753 
       20.25        12.43        13.38        15.16        20.94        28.47 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       21.93        27.48        14.66        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65         6.90        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        27.39        21.07        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.72        16.96         6.87        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       13.71         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  NUDT11 MUTATED NUDT11 WILD-TYPE 
           15.06             0.07 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           52.31           210.97 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           26.20            20.65 
[1] "15.1 - 52.3 (26.2)" "0.1 - 211.0 (20.6)"
[1] "hr=" "2.2"
D24V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  NUDT11 MUTATED         0        0         1         8         0         0
  NUDT11 WILD-TYPE      25       75        79       245        11         1
D24V3, multiclass
           clus
vv          NUDT11 MUTATED NUDT11 WILD-TYPE
  STAGE I                0               25
  STAGE II               0               75
  STAGE III              1               79
  STAGE IVA              8              245
  STAGE IVB              0               11
  STAGE IVC              0                1
[1] 6 2
[1] 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       0   2   2   5
  NUDT11 WILD-TYPE    47 135  97 167
D24V4, multiclass
       clus
vv      NUDT11 MUTATED NUDT11 WILD-TYPE
  T0+T1              0               47
  T2                 2              135
  T3                 2               97
  T4                 5              167
[1] 4 2
[1] TRUE
[1] "dimension of 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     5   0   4   0
  NUDT11 WILD-TYPE 170  67 164   7
D24V5, multiclass
    clus
vv   NUDT11 MUTATED NUDT11 WILD-TYPE
  N0              5              170
  N1              0               67
  N2              4              164
  N3              0                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"
D24V6, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     1   0
  NUDT11 WILD-TYPE 190   1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      1    0
  NUDT11 WILD-TYPE  190    1
   clus
vv  NUDT11 MUTATED NUDT11 WILD-TYPE
  0              1              190
  1              0                1
[1] 2 2
[1] FALSE
D24V7, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     0   9
  NUDT11 WILD-TYPE 138 364
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      0    9
  NUDT11 WILD-TYPE  138  364
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  FEMALE              0              138
  MALE                9              364
[1] 2 2
[1] FALSE
D24V8, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     0   6
  NUDT11 WILD-TYPE 157 287
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      0    6
  NUDT11 WILD-TYPE  157  287
     clus
vv    NUDT11 MUTATED NUDT11 WILD-TYPE
  NO               0              157
  YES              6              287
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  NUDT11 MUTATED                                     9
  NUDT11 WILD-TYPE                                 491
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  NUDT11 MUTATED                                                   0
  NUDT11 WILD-TYPE                                                10
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  NUDT11 MUTATED                                                           0
  NUDT11 WILD-TYPE                                                         1
D24V9, multiclass
                                                           clus
vv                                                          NUDT11 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    9
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          NUDT11 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    491
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, continuous
D24V11, continuous
D24V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUDT11 MUTATED                                  0     0
  NUDT11 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUDT11 MUTATED                           0     9
  NUDT11 WILD-TYPE                        47   428
D24V13, multiclass
                                  clus
vv                                 NUDT11 MUTATED NUDT11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               47
  WHITE                                         9              428
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V14, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     1   8
  NUDT11 WILD-TYPE  24 441
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      1    8
  NUDT11 WILD-TYPE   24  441
                        clus
vv                       NUDT11 MUTATED NUDT11 WILD-TYPE
  HISPANIC OR LATINO                  1               24
  NOT HISPANIC OR LATINO              8              441
[1] 2 2
[1] FALSE

Clustering(25) Variable = KDM6A MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED    11   6
  KDM6A WILD-TYPE 278 214
  KDM6A MUTATED KDM6A WILD-TYPE 
             17             492 
  KDM6A MUTATED KDM6A WILD-TYPE 
              6             214 
$`KDM6A MUTATED`
TCGA-BA-A6DE TCGA-CN-5355 TCGA-CR-7368 TCGA-CV-5441 TCGA-CV-6935 TCGA-CV-7177 
       14.47        42.02        40.93        94.88         9.70        21.80 
TCGA-CV-7253 TCGA-CV-A45Q TCGA-CV-A45W TCGA-CV-A6JE TCGA-D6-8568 TCGA-F7-A623 
       11.87       169.38        45.96        35.34        24.95        20.25 
TCGA-F7-A624 TCGA-HD-7229 TCGA-HD-7753 TCGA-MT-A67G TCGA-P3-A6SX 
       12.43        33.76        28.47         6.25        47.01 

$`KDM6A WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
       11.54         7.10         5.69         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 
        4.80         4.41        18.38        66.28        71.05        20.52 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       10.55        27.19        12.92         8.81         6.28        12.69 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       55.86        38.04         4.67        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       32.81        52.14        55.56        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 
       14.33        45.83        27.58        73.61        13.05        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 
        8.58        12.39        71.31        69.70         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       56.94        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       28.04        19.07        34.13         6.74        10.45        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       38.89         3.68        17.42        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       23.57        17.29        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       23.44        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 
        4.24        41.19        15.75        32.38        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       56.58        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       53.52        41.88        43.10        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 
       15.75         9.27        47.18        39.16        47.34        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 
      108.95        76.24        19.20        17.95       107.51        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 
       62.43         9.60        90.12         2.14         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       65.82        10.98         7.13         8.42        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        4.14        64.83       172.67       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        89.65 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 
       36.00        31.36        26.20        18.97        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
        4.96        47.97         2.10        49.71        18.41        57.47 
TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       35.54       210.97        89.33         9.67         0.46        22.85 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 
       25.08        25.94         0.07        34.09       100.57        14.89 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       56.48       156.49         3.52        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 
        7.17       153.86        16.64         6.38        22.19        35.93 
TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       30.48        27.98        21.01       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
        1.05         6.51        88.87        48.20        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM 
        0.76        56.61         7.07        15.25         5.98         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       11.44        18.67        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        7.63        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 
       23.34        58.45        37.25        33.86        18.02        20.45 
TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       37.58        41.59        37.18        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7754 
       11.80        13.38        15.16        15.06        20.94        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       21.93        27.48        14.66        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65         6.90        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN 
       14.37         7.96        30.05         1.84        12.62        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       51.25        10.85        36.82        19.00        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
        2.04        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.21        23.15         7.30        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       27.39        21.07        19.73        12.89         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        6.87        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       32.65        17.03        20.55        14.56        13.35        18.15 

  KDM6A MUTATED KDM6A WILD-TYPE 
           6.25            0.07 
  KDM6A MUTATED KDM6A WILD-TYPE 
         169.38          210.97 
  KDM6A MUTATED KDM6A WILD-TYPE 
          28.47           20.65 
[1] "6.2 - 169.4 (28.5)" "0.1 - 211.0 (20.6)"
[1] "hr=" "1.6"
D25V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  KDM6A MUTATED         1        5         1         8         0         0
  KDM6A WILD-TYPE      24       70        79       245        11         1
D25V3, multiclass
           clus
vv          KDM6A MUTATED KDM6A WILD-TYPE
  STAGE I               1              24
  STAGE II              5              70
  STAGE III             1              79
  STAGE IVA             8             245
  STAGE IVB             0              11
  STAGE IVC             0               1
[1] 6 2
[1] 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       3   6   1   5
  KDM6A WILD-TYPE    44 131  98 167
D25V4, multiclass
       clus
vv      KDM6A MUTATED KDM6A WILD-TYPE
  T0+T1             3              44
  T2                6             131
  T3                1              98
  T4                5             167
[1] 4 2
[1] TRUE
[1] "dimension of 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     7   2   4   0
  KDM6A WILD-TYPE 168  65 164   7
D25V5, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  N0             7             168
  N1             2              65
  N2             4             164
  N3             0               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
  KDM6A MUTATED     6   0
  KDM6A WILD-TYPE 185   1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      6    0
  KDM6A WILD-TYPE  185    1
   clus
vv  KDM6A MUTATED KDM6A WILD-TYPE
  0             6             185
  1             0               1
[1] 2 2
[1] FALSE
D25V7, binary
                 cls
clus                0   1
  KDM6A MUTATED     4  13
  KDM6A WILD-TYPE 134 360
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      4   13
  KDM6A WILD-TYPE  134  360
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE             4             134
  MALE              13             360
[1] 2 2
[1] FALSE
D25V8, binary
                 cls
clus                0   1
  KDM6A MUTATED     6   9
  KDM6A WILD-TYPE 151 284
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      6    9
  KDM6A WILD-TYPE  151  284
     clus
vv    KDM6A MUTATED KDM6A WILD-TYPE
  NO              6             151
  YES             9             284
[1] 2 2
[1] FALSE
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA
  KDM6A MUTATED                                    17
  KDM6A WILD-TYPE                                 483
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  KDM6A MUTATED                                                   0
  KDM6A WILD-TYPE                                                10
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  KDM6A MUTATED                                                           0
  KDM6A WILD-TYPE                                                         1
D25V9, multiclass
                                                           clus
vv                                                          KDM6A MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  17
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             0
                                                           clus
vv                                                          KDM6A WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   483
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, continuous
D25V11, continuous
D25V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM6A MUTATED                                  0     0
  KDM6A WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED                           3    14
  KDM6A WILD-TYPE                        44   423
D25V13, multiclass
                                  clus
vv                                 KDM6A MUTATED KDM6A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    3              44
  WHITE                                       14             423
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V14, binary
                 cls
clus                0   1
  KDM6A MUTATED     0  17
  KDM6A WILD-TYPE  25 432
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      0   17
  KDM6A WILD-TYPE   25  432
                        clus
vv                       KDM6A MUTATED KDM6A WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO            17             432
[1] 2 2
[1] FALSE

Clustering(26) Variable = RB1 MUTATION ANALYSIS
D26V1, survival
               sevent
clus2             0   1
  RB1 MUTATED    15   2
  RB1 WILD-TYPE 274 218
  RB1 MUTATED RB1 WILD-TYPE 
           17           492 
  RB1 MUTATED RB1 WILD-TYPE 
            2           218 
$`RB1 MUTATED`
TCGA-CN-5360 TCGA-CN-A499 TCGA-CQ-5327 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CR-6487 
       71.31        23.57        54.58        41.88        43.10         7.69 
TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-6939 TCGA-CX-7085 
        3.45         0.99         5.13        29.95        21.90        10.55 
TCGA-F7-A50J TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-QK-A6V9 TCGA-T2-A6WZ 
       31.13        19.04        19.27        27.39        15.91 

$`RB1 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 
        9.14         4.80         4.41        18.38        66.28        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       12.69        55.86        38.04         4.67        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
       26.86        32.81        52.14        55.56        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        45.83        27.58        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5361 TCGA-CN-5363 
       42.02        46.32         8.58        12.39        69.70         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       16.21        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       32.22        38.89         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       25.41        17.29        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       23.44        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       70.45        62.37        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       41.19        15.75        32.38        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       77.56        44.48        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       14.14        12.46        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       37.87        26.27        58.42        50.01        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       12.46        22.78        15.75         9.27        47.18        39.16 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       47.34        40.93        35.84         3.09        24.95        29.23 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 
       46.85        32.65        44.25        30.58        24.79         5.95 
TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       35.41        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       76.24        19.20        17.95       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
       20.52         4.73        26.43        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       65.82        10.98         7.13         8.42        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        4.14        64.83       172.67       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       89.65        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       95.34         4.96        11.87        47.97         2.10        49.71 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       18.41        57.47        35.54       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        0.46        22.85        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 
      100.57        14.89        56.48       156.49         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       84.49        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       22.19        35.93        30.48        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
        7.07        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       22.52        10.42        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        37.25        33.86        18.02        20.45        37.58 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        24.95         0.46        17.85        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       12.43        13.38        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 
        0.36        13.84         4.27         3.65         6.90        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-KU-A6H8 
       33.57         5.29        13.68        13.84        15.48        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
        9.34        12.72        21.07        19.73        12.89         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
       16.96         6.87         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       32.65        17.03        20.55        14.56        13.35        18.15 

  RB1 MUTATED RB1 WILD-TYPE 
         0.99          0.07 
  RB1 MUTATED RB1 WILD-TYPE 
        71.31        210.97 
  RB1 MUTATED RB1 WILD-TYPE 
        21.90         20.91 
[1] "1.0 - 71.3 (21.9)"  "0.1 - 211.0 (20.9)"
[1] "hr=" "3.3"
D26V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  RB1 MUTATED         2        4         3         4         0         0
  RB1 WILD-TYPE      23       71        77       249        11         1
D26V3, multiclass
           clus
vv          RB1 MUTATED RB1 WILD-TYPE
  STAGE I             2            23
  STAGE II            4            71
  STAGE III           3            77
  STAGE IVA           4           249
  STAGE IVB           0            11
  STAGE IVC           0             1
[1] 6 2
[1] 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       2   6   4   2
  RB1 WILD-TYPE    45 131  95 170
D26V4, multiclass
       clus
vv      RB1 MUTATED RB1 WILD-TYPE
  T0+T1           2            45
  T2              6           131
  T3              4            95
  T4              2           170
[1] 4 2
[1] TRUE
[1] "dimension of 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     8   1   4   0
  RB1 WILD-TYPE 167  66 164   7
D26V5, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  N0           8           167
  N1           1            66
  N2           4           164
  N3           0             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"
D26V6, binary
               cls
clus              0   1
  RB1 MUTATED     8   0
  RB1 WILD-TYPE 183   1
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      8    0
  RB1 WILD-TYPE  183    1
   clus
vv  RB1 MUTATED RB1 WILD-TYPE
  0           8           183
  1           0             1
[1] 2 2
[1] FALSE
D26V7, binary
               cls
clus              0   1
  RB1 MUTATED    11   6
  RB1 WILD-TYPE 127 367
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     11    6
  RB1 WILD-TYPE  127  367
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE          11           127
  MALE             6           367
[1] 2 2
[1] FALSE
D26V8, binary
               cls
clus              0   1
  RB1 MUTATED     6  10
  RB1 WILD-TYPE 151 283
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      6   10
  RB1 WILD-TYPE  151  283
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO            6           151
  YES          10           283
[1] 2 2
[1] FALSE
               vv
clus            HEAD & NECK SQUAMOUS CELL CARCINOMA
  RB1 MUTATED                                    17
  RB1 WILD-TYPE                                 483
               vv
clus            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  RB1 MUTATED                                                   0
  RB1 WILD-TYPE                                                10
               vv
clus            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  RB1 MUTATED                                                           0
  RB1 WILD-TYPE                                                         1
D26V9, multiclass
                                                           clus
vv                                                          RB1 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                17
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                   0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT           0
                                                           clus
vv                                                          RB1 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                 483
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, continuous
D26V11, continuous
D26V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RB1 MUTATED                                  0     1
  RB1 WILD-TYPE                                2     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED                           0    16
  RB1 WILD-TYPE                        47   421
D26V13, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  0            47
  WHITE                                     16           421
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V14, binary
               cls
clus              0   1
  RB1 MUTATED     1  15
  RB1 WILD-TYPE  24 434
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      1   15
  RB1 WILD-TYPE   24  434
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               1            24
  NOT HISPANIC OR LATINO          15           434
[1] 2 2
[1] FALSE

Clustering(27) Variable = KEAP1 MUTATION ANALYSIS
D27V1, survival
                 sevent
clus2               0   1
  KEAP1 MUTATED    12  10
  KEAP1 WILD-TYPE 277 210
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             487 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             10             210 
$`KEAP1 MUTATED`
TCGA-CN-4727 TCGA-DQ-7588 TCGA-BA-7269 TCGA-BB-7870 TCGA-CN-4723 TCGA-CN-5359 
       51.29        14.04        41.85        66.28        55.86        12.39 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CR-6492 TCGA-CV-5434 TCGA-CV-5978 TCGA-CV-7238 
       50.07        48.00        15.75       108.95         7.07        89.65 
TCGA-CV-7248 TCGA-CV-A6JU TCGA-HD-A633 TCGA-P3-A6T0 TCGA-T2-A6WX TCGA-UF-A71E 
       17.13         3.62        13.84        19.00         6.87        49.45 
TCGA-UF-A7JF TCGA-UF-A7JO TCGA-UF-A7JT TCGA-KU-A66S 
       55.43        20.75        32.65        13.35 

$`KEAP1 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       30.18        25.71         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       34.36        30.94        40.24        21.11        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       48.03         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       65.59        15.52        21.17        14.83        12.62         4.01 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.80         4.41 
TCGA-BB-4228 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       18.38        71.05        20.52        10.55        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
        8.81         6.28        12.69        38.04         4.67        56.68 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.81        52.14        55.56        57.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5361 
       13.05        42.02        46.32         8.58        71.31        69.70 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
        8.32        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
        8.52        52.08        56.94        30.67        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       28.04        19.07        34.13         6.74        10.45        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       38.89         3.68        17.42        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       23.57        17.29        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       23.44        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 
        4.24        41.19        15.75        32.38        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       56.58        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       53.52        41.88        43.10        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       76.24        19.20        17.95       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       48.59        60.49        43.23        54.74        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
        9.60        90.12         2.14         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       65.82        10.98         7.13         8.42        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        4.14        64.83       172.67       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 
       36.00        31.36        26.20        18.97        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
       11.87        47.97         2.10        49.71        18.41        57.47 
TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       35.54       210.97        89.33         9.67         0.46        22.85 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 
       25.08        25.94         0.07        34.09       100.57        14.89 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       56.48       156.49         3.52        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 
        7.17       153.86        16.64         6.38        22.19        35.93 
TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
       30.48        27.98        21.01       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
       35.47         1.05        45.96         6.51        88.87        48.20 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       60.43        67.86         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        28.01 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        51.12        13.25        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
        2.53        16.14        11.44        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 
       33.86        18.02        20.45        37.58        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       24.95         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       13.38        15.16        15.06        20.94        33.76        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       25.74        21.93        27.48        14.66        22.03         0.36 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65         6.90        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
       71.74        51.25        10.85        36.82        47.01        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       18.97         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        27.39        21.07        19.73        12.89         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
       16.96        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
       49.51        44.65        74.47        17.95        24.30        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       18.05        13.94        22.36        17.03        20.55        14.56 
TCGA-KU-A66T 
       18.15 

  KEAP1 MUTATED KEAP1 WILD-TYPE 
           3.62            0.07 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
         108.95          210.97 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
          26.70           20.94 
[1] "3.6 - 109.0 (26.7)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1.1"
D27V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  KEAP1 MUTATED         0        1         3        14         2         0
  KEAP1 WILD-TYPE      25       74        77       239         9         1
D27V3, multiclass
           clus
vv          KEAP1 MUTATED KEAP1 WILD-TYPE
  STAGE I               0              25
  STAGE II              1              74
  STAGE III             3              77
  STAGE IVA            14             239
  STAGE IVB             2               9
  STAGE IVC             0               1
[1] 6 2
[1] 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
  KEAP1 MUTATED       1   3   1  15
  KEAP1 WILD-TYPE    46 134  98 157
D27V4, multiclass
       clus
vv      KEAP1 MUTATED KEAP1 WILD-TYPE
  T0+T1             1              46
  T2                3             134
  T3                1              98
  T4               15             157
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KEAP1 MUTATED    10   3   6   1
  KEAP1 WILD-TYPE 165  64 162   6
D27V5, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  N0            10             165
  N1             3              64
  N2             6             162
  N3             1               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"
D27V6, binary
                 cls
clus                0   1
  KEAP1 MUTATED     7   0
  KEAP1 WILD-TYPE 184   1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      7    0
  KEAP1 WILD-TYPE  184    1
   clus
vv  KEAP1 MUTATED KEAP1 WILD-TYPE
  0             7             184
  1             0               1
[1] 2 2
[1] FALSE
D27V7, binary
                 cls
clus                0   1
  KEAP1 MUTATED     9  13
  KEAP1 WILD-TYPE 129 360
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      9   13
  KEAP1 WILD-TYPE  129  360
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  FEMALE             9             129
  MALE              13             360
[1] 2 2
[1] FALSE
D27V8, binary
                 cls
clus                0   1
  KEAP1 MUTATED     2  18
  KEAP1 WILD-TYPE 155 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      2   18
  KEAP1 WILD-TYPE  155  275
     clus
vv    KEAP1 MUTATED KEAP1 WILD-TYPE
  NO              2             155
  YES            18             275
[1] 2 2
[1] FALSE
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA
  KEAP1 MUTATED                                    20
  KEAP1 WILD-TYPE                                 480
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  KEAP1 MUTATED                                                   2
  KEAP1 WILD-TYPE                                                 8
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  KEAP1 MUTATED                                                           0
  KEAP1 WILD-TYPE                                                         1
D27V9, multiclass
                                                           clus
vv                                                          KEAP1 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  20
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             0
                                                           clus
vv                                                          KEAP1 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   480
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, continuous
D27V11, continuous
D27V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KEAP1 MUTATED                                  0     0
  KEAP1 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KEAP1 MUTATED                           3    19
  KEAP1 WILD-TYPE                        44   418
D27V13, multiclass
                                  clus
vv                                 KEAP1 MUTATED KEAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    3              44
  WHITE                                       19             418
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                 cls
clus                0   1
  KEAP1 MUTATED     0  18
  KEAP1 WILD-TYPE  25 431
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      0   18
  KEAP1 WILD-TYPE   25  431
                        clus
vv                       KEAP1 MUTATED KEAP1 WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO            18             431
[1] 2 2
[1] FALSE

Clustering(28) Variable = KRT17 MUTATION ANALYSIS
D28V1, survival
                 sevent
clus2               0   1
  KRT17 MUTATED     2   4
  KRT17 WILD-TYPE 287 216
  KRT17 MUTATED KRT17 WILD-TYPE 
              6             503 
  KRT17 MUTATED KRT17 WILD-TYPE 
              4             216 
$`KRT17 MUTATED`
TCGA-CN-6021 TCGA-CN-6013 TCGA-CQ-5324 TCGA-CQ-5330 TCGA-CQ-5334 TCGA-CV-5978 
        9.07        23.90        52.37        62.37         4.24         7.07 

$`KRT17 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       30.18        25.71        51.29         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       23.84        65.59        15.52        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 
        4.80         4.41        18.38        66.28        71.05        20.52 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       10.55        27.19        12.92         8.81         6.28        12.69 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       55.86        38.04         4.67        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       32.81        52.14        55.56        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       46.32         8.58        12.39        71.31        69.70         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       16.21        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 
       52.08        56.94        50.07        30.67        48.00        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       28.04        19.07        34.13         6.74        10.45        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       38.89         3.68        17.42        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       23.57        17.29        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       23.44        20.88        19.53        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6219 
       70.45        45.99        10.42        11.21        41.19        15.75 
TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.38        66.28        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       14.99        38.76        64.87        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       77.56        44.48        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       14.14        12.46        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       37.87        26.27        58.42        50.01        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        22.78        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       39.16        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58        24.79         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        94.88        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
       60.49        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       90.12         2.14         9.70         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       21.90        26.43        11.24       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       42.38        15.09        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       10.98         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       172.67       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        9.01         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        89.65 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 
       36.00        31.36        26.20        18.97        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 
        4.96        11.87        47.97         2.10        49.71        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       57.47        35.54       210.97        89.33         9.67         0.46 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
       22.85        25.08        25.94         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       14.89        56.48       156.49         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       19.76         7.17       153.86        16.64         6.38        22.19 
TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       35.93        30.48        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       48.20        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        37.25        33.86        18.02        20.45        37.58 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       31.13        18.94        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       20.25        12.43        13.38        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
       33.76        28.47        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         0.36        13.84         4.27         3.65         6.90 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
        0.07        33.57         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       15.48        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
        1.84        12.62         6.25        15.42         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       17.98        29.92        15.78        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       36.82        47.01        19.00        75.55        18.97         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       29.00        12.99        16.01        13.15        21.07        21.21 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       23.15         7.30        21.47         9.34        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        19.73        12.89         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       17.82        15.32         8.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
       15.91         7.10        32.45        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.25        20.35        64.80        54.67         2.83        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.45        44.65        74.47        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       29.46        18.05        13.94        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       17.03        20.55        14.56        13.35        18.15 

  KRT17 MUTATED KRT17 WILD-TYPE 
           4.24            0.07 
  KRT17 MUTATED KRT17 WILD-TYPE 
          62.37          210.97 
  KRT17 MUTATED KRT17 WILD-TYPE 
         16.485          20.940 
[1] "4.2 - 62.4 (16.5)"  "0.1 - 211.0 (20.9)"
[1] "hr=" "1.9"
D28V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  KRT17 MUTATED         0        0         1         3         1         0
  KRT17 WILD-TYPE      25       75        79       250        10         1
D28V3, multiclass
           clus
vv          KRT17 MUTATED KRT17 WILD-TYPE
  STAGE I               0              25
  STAGE II              0              75
  STAGE III             1              79
  STAGE IVA             3             250
  STAGE IVB             1              10
  STAGE IVC             0               1
[1] 6 2
[1] 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
  KRT17 MUTATED       0   0   3   2
  KRT17 WILD-TYPE    47 137  96 170
D28V4, multiclass
       clus
vv      KRT17 MUTATED KRT17 WILD-TYPE
  T0+T1             0              47
  T2                0             137
  T3                3              96
  T4                2             170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KRT17 MUTATED     1   0   3   1
  KRT17 WILD-TYPE 174  67 165   6
D28V5, multiclass
    clus
vv   KRT17 MUTATED KRT17 WILD-TYPE
  N0             1             174
  N1             0              67
  N2             3             165
  N3             1               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"
D28V6, binary
                 cls
clus                0   1
  KRT17 MUTATED     0   0
  KRT17 WILD-TYPE 191   1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT17 MUTATED      0    0
  KRT17 WILD-TYPE  191    1
D28V7, binary
                 cls
clus                0   1
  KRT17 MUTATED     3   3
  KRT17 WILD-TYPE 135 370
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT17 MUTATED      3    3
  KRT17 WILD-TYPE  135  370
        clus
vv       KRT17 MUTATED KRT17 WILD-TYPE
  FEMALE             3             135
  MALE               3             370
[1] 2 2
[1] FALSE
D28V8, binary
                 cls
clus                0   1
  KRT17 MUTATED     2   2
  KRT17 WILD-TYPE 155 291
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT17 MUTATED      2    2
  KRT17 WILD-TYPE  155  291
     clus
vv    KRT17 MUTATED KRT17 WILD-TYPE
  NO              2             155
  YES             2             291
[1] 2 2
[1] FALSE
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA
  KRT17 MUTATED                                     6
  KRT17 WILD-TYPE                                 494
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  KRT17 MUTATED                                                   0
  KRT17 WILD-TYPE                                                10
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  KRT17 MUTATED                                                           0
  KRT17 WILD-TYPE                                                         1
D28V9, multiclass
                                                           clus
vv                                                          KRT17 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   6
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             0
                                                           clus
vv                                                          KRT17 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   494
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, continuous
D28V11, continuous
D28V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT17 MUTATED                                  0     0
  KRT17 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KRT17 MUTATED                           1     5
  KRT17 WILD-TYPE                        46   432
D28V13, multiclass
                                  clus
vv                                 KRT17 MUTATED KRT17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              46
  WHITE                                        5             432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                 cls
clus                0   1
  KRT17 MUTATED     0   6
  KRT17 WILD-TYPE  25 443
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT17 MUTATED      0    6
  KRT17 WILD-TYPE   25  443
                        clus
vv                       KRT17 MUTATED KRT17 WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO             6             443
[1] 2 2
[1] FALSE

Clustering(29) Variable = RHOA MUTATION ANALYSIS
D29V1, survival
                sevent
clus2              0   1
  RHOA MUTATED     5   5
  RHOA WILD-TYPE 284 215
  RHOA MUTATED RHOA WILD-TYPE 
            10            499 
  RHOA MUTATED RHOA WILD-TYPE 
             5            215 
$`RHOA MUTATED`
TCGA-CN-A6V3 TCGA-BB-8596 TCGA-BB-A5HZ TCGA-CN-6998 TCGA-CV-7102 TCGA-CV-7410 
       24.39        71.05        27.19        11.74         1.84       210.97 
TCGA-DQ-5625 TCGA-F7-A624 TCGA-TN-A7HL TCGA-KU-A66S 
       37.25        12.43        20.35        13.35 

$`RHOA WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-6221 
       11.08        35.05        32.48        19.82        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       23.84        65.59        15.52        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8601 TCGA-BB-A5HY 
        4.80         4.41        18.38        66.28        20.52        10.55 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 
       12.92         8.81         6.28        12.69        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        4.67        56.68        12.89        26.86        32.81        52.14 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       55.56        57.11        12.99        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        73.61        13.05        42.02        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       12.39        71.31        69.70         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.84        11.57        12.49         8.52        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
       19.07        34.13         6.74        10.45        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
        3.68        17.42        35.01        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        31.69        22.32        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       16.57         4.41        12.07         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       19.53        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       15.75        32.38        66.28        46.95        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
        4.24        14.99        38.76        64.87        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        77.56        44.48        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.49        14.14        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       47.18        39.16        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.09        24.95        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       29.95        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       76.24        19.20        17.95       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        2.50         4.14        64.83       172.67       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 
       12.66         7.99         9.01         5.26        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       89.65        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       95.34         4.96        11.87        47.97         2.10        49.71 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       18.41        57.47        35.54        89.33         9.67         0.46 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
       22.85        25.08        25.94         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       14.89        56.48       156.49         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       19.76         7.17       153.86        16.64         6.38        22.19 
TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       35.93        30.48        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       48.20        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 
       58.45        33.86        18.02        20.45        37.58        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       37.18        32.71        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        24.95         0.46        17.85        11.80        20.25 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       13.38        15.16        15.06        20.94        33.76        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       25.74        21.93        27.48        14.66        22.03         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         3.65         6.90        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        37.71        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        6.25        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       15.78        71.74        51.25        10.85        36.82        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       19.00        75.55        18.97         2.04        29.00        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       16.01        13.15        21.07        21.21        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       21.47         9.34        12.72        27.39        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       12.89         5.62        14.76        12.20        17.82        15.32 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
        8.32        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 
       32.45        13.71         3.12        13.55        13.25        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66T 
       18.15 

  RHOA MUTATED RHOA WILD-TYPE 
          1.84           0.07 
  RHOA MUTATED RHOA WILD-TYPE 
        210.97         180.16 
  RHOA MUTATED RHOA WILD-TYPE 
         22.37          20.94 
[1] "1.8 - 211.0 (22.4)" "0.1 - 180.2 (20.9)"
[1] "hr=" "1.4"
D29V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  RHOA MUTATED         0        1         2         6         0         0
  RHOA WILD-TYPE      25       74        78       247        11         1
D29V3, multiclass
           clus
vv          RHOA MUTATED RHOA WILD-TYPE
  STAGE I              0             25
  STAGE II             1             74
  STAGE III            2             78
  STAGE IVA            6            247
  STAGE IVB            0             11
  STAGE IVC            0              1
[1] 6 2
[1] 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       1   2   4   2
  RHOA WILD-TYPE    46 135  95 170
D29V4, multiclass
       clus
vv      RHOA MUTATED RHOA WILD-TYPE
  T0+T1            1             46
  T2               2            135
  T3               4             95
  T4               2            170
[1] 4 2
[1] TRUE
[1] "dimension of 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     0   3   4   0
  RHOA WILD-TYPE 175  64 164   7
D29V5, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  N0            0            175
  N1            3             64
  N2            4            164
  N3            0              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
  RHOA MUTATED     4   0
  RHOA WILD-TYPE 187   1
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      4    0
  RHOA WILD-TYPE  187    1
   clus
vv  RHOA MUTATED RHOA WILD-TYPE
  0            4            187
  1            0              1
[1] 2 2
[1] FALSE
D29V7, binary
                cls
clus               0   1
  RHOA MUTATED     4   6
  RHOA WILD-TYPE 134 367
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      4    6
  RHOA WILD-TYPE  134  367
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  FEMALE            4            134
  MALE              6            367
[1] 2 2
[1] FALSE
D29V8, binary
                cls
clus               0   1
  RHOA MUTATED     2   7
  RHOA WILD-TYPE 155 286
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      2    7
  RHOA WILD-TYPE  155  286
     clus
vv    RHOA MUTATED RHOA WILD-TYPE
  NO             2            155
  YES            7            286
[1] 2 2
[1] FALSE
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA
  RHOA MUTATED                                     9
  RHOA WILD-TYPE                                 491
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  RHOA MUTATED                                                   1
  RHOA WILD-TYPE                                                 9
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  RHOA MUTATED                                                           0
  RHOA WILD-TYPE                                                         1
D29V9, multiclass
                                                           clus
vv                                                          RHOA MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  9
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT            0
                                                           clus
vv                                                          RHOA WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  491
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, continuous
D29V11, continuous
D29V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RHOA MUTATED                                  0     0
  RHOA WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RHOA MUTATED                           0    10
  RHOA WILD-TYPE                        47   427
D29V13, multiclass
                                  clus
vv                                 RHOA MUTATED RHOA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             47
  WHITE                                      10            427
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V14, binary
                cls
clus               0   1
  RHOA MUTATED     0  10
  RHOA WILD-TYPE  25 439
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      0   10
  RHOA WILD-TYPE   25  439
                        clus
vv                       RHOA MUTATED RHOA WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO           10            439
[1] 2 2
[1] FALSE

Clustering(30) Variable = PTPN14 MUTATION ANALYSIS
D30V1, survival
                  sevent
clus2                0   1
  PTPN14 MUTATED    12   4
  PTPN14 WILD-TYPE 277 216
  PTPN14 MUTATED PTPN14 WILD-TYPE 
              16              493 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
               4              216 
$`PTPN14 MUTATED`
TCGA-CN-4727 TCGA-DQ-7588 TCGA-CN-5363 TCGA-CN-A63U TCGA-CQ-5327 TCGA-CQ-7071 
       51.29        14.04         8.32        31.69        54.58        43.10 
TCGA-CQ-A4C6 TCGA-CR-7365 TCGA-CV-5430 TCGA-CV-5441 TCGA-CV-A6JD TCGA-D6-6516 
       44.48        39.16       139.43        94.88         5.98        25.41 
TCGA-D6-A6EN TCGA-D6-A6ES TCGA-MT-A67F TCGA-QK-A8Z8 
       22.59        12.79        12.62         5.62 

$`PTPN14 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       30.18        25.71         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       34.36        30.94        40.24        21.11        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       48.03         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       65.59        15.52        21.17        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       41.85        29.42        20.45        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       20.48        16.41         6.15       105.90         9.14         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
        4.41        18.38        66.28        71.05        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 
       27.19        12.92         8.81         6.28        12.69        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       52.14        55.56        57.11        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       45.83        27.58        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5364 TCGA-CN-5365 
        8.58        12.39        71.31        69.70        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.84        11.57        12.49         8.52        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
       19.07        34.13         6.74        10.45        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W 
       17.29        29.72        21.21         7.40        22.32        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       16.57         4.41        12.07         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 
       19.53        52.37        21.50         2.93        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 
       45.99        10.42        11.21         4.24        41.19        15.75 
TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.38        66.28        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 
       14.99        38.76        64.87        53.52        41.88        77.56 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       58.42        50.01        39.52        36.99        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
       22.78        15.75         9.27        47.18        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58        24.79         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 
        5.95        35.41        29.95        48.39        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 
      108.95        76.24        19.20        17.95       107.51        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        2.50         4.14        64.83       172.67       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 
       12.66         7.99         9.01         5.26         1.84        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
       12.92        21.80        71.21        10.75       130.88        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
        4.73        89.65        36.00        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       17.13        95.34         4.96        11.87        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 
       49.71        18.41        57.47        35.54       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
        9.67         0.46        22.85        25.08        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 
       34.09       100.57        14.89        56.48       156.49         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 
       16.27        84.49        19.76         7.17       153.86        16.64 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P 
        6.38        22.19        35.93        30.48        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
      169.38       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
       56.61         7.07        15.25        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        13.25 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       24.95        13.94        12.10        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 
       33.86        18.02        20.45        37.58        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       24.95         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       13.38        15.16        15.06        20.94        33.76        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       25.74        21.93        27.48        14.66        22.03         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         3.65         6.90        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        37.71        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G 
       10.75        14.37         7.96        30.05         1.84         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        27.39        21.07        19.73        12.89 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       16.96         6.87        15.91         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        3.12        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        2.83        49.51        49.45        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  PTPN14 MUTATED PTPN14 WILD-TYPE 
            5.62             0.07 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
          139.43           210.97 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
           28.55            20.75 
[1] "5.6 - 139.4 (28.6)" "0.1 - 211.0 (20.8)"
[1] "hr=" "2"  
D30V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  PTPN14 MUTATED         1        1         2         8         1         1
  PTPN14 WILD-TYPE      24       74        78       245        10         0
D30V3, multiclass
           clus
vv          PTPN14 MUTATED PTPN14 WILD-TYPE
  STAGE I                1               24
  STAGE II               1               74
  STAGE III              2               78
  STAGE IVA              8              245
  STAGE IVB              1               10
  STAGE IVC              1                0
[1] 6 2
[1] 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
  PTPN14 MUTATED       1   3   3   7
  PTPN14 WILD-TYPE    46 134  96 165
D30V4, multiclass
       clus
vv      PTPN14 MUTATED PTPN14 WILD-TYPE
  T0+T1              1               46
  T2                 3              134
  T3                 3               96
  T4                 7              165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PTPN14 MUTATED     6   3   4   1
  PTPN14 WILD-TYPE 169  64 164   6
D30V5, multiclass
    clus
vv   PTPN14 MUTATED PTPN14 WILD-TYPE
  N0              6              169
  N1              3               64
  N2              4              164
  N3              1                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
  PTPN14 MUTATED     6   1
  PTPN14 WILD-TYPE 185   0
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED      6    1
  PTPN14 WILD-TYPE  185    0
   clus
vv  PTPN14 MUTATED PTPN14 WILD-TYPE
  0              6              185
  1              1                0
[1] 2 2
[1] FALSE
D30V7, binary
                  cls
clus                 0   1
  PTPN14 MUTATED     5  11
  PTPN14 WILD-TYPE 133 362
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED      5   11
  PTPN14 WILD-TYPE  133  362
        clus
vv       PTPN14 MUTATED PTPN14 WILD-TYPE
  FEMALE              5              133
  MALE               11              362
[1] 2 2
[1] FALSE
D30V8, binary
                  cls
clus                 0   1
  PTPN14 MUTATED     4  11
  PTPN14 WILD-TYPE 153 282
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED      4   11
  PTPN14 WILD-TYPE  153  282
     clus
vv    PTPN14 MUTATED PTPN14 WILD-TYPE
  NO               4              153
  YES             11              282
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  PTPN14 MUTATED                                    16
  PTPN14 WILD-TYPE                                 484
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  PTPN14 MUTATED                                                   0
  PTPN14 WILD-TYPE                                                10
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  PTPN14 MUTATED                                                           0
  PTPN14 WILD-TYPE                                                         1
D30V9, multiclass
                                                           clus
vv                                                          PTPN14 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   16
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          PTPN14 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    484
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, continuous
D30V11, continuous
D30V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPN14 MUTATED                                  0     2
  PTPN14 WILD-TYPE                                2     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PTPN14 MUTATED                           2    12
  PTPN14 WILD-TYPE                        45   425
D30V13, multiclass
                                  clus
vv                                 PTPN14 MUTATED PTPN14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     2               45
  WHITE                                        12              425
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                  cls
clus                 0   1
  PTPN14 MUTATED     1  15
  PTPN14 WILD-TYPE  24 434
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED      1   15
  PTPN14 WILD-TYPE   24  434
                        clus
vv                       PTPN14 MUTATED PTPN14 WILD-TYPE
  HISPANIC OR LATINO                  1               24
  NOT HISPANIC OR LATINO             15              434
[1] 2 2
[1] FALSE

Clustering(31) Variable = KRTAP5-5 MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  KRTAP5-5 MUTATED     2   2
  KRTAP5-5 WILD-TYPE 287 218
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 4                505 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 2                218 
$`KRTAP5-5 MUTATED`
TCGA-CQ-5325 TCGA-CQ-5330 TCGA-CV-5439 TCGA-CV-A6JU 
       21.50        62.37        17.95         3.62 

$`KRTAP5-5 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 
        9.14         4.80         4.41        18.38        66.28        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       12.69        55.86        38.04         4.67        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
       26.86        32.81        52.14        55.56        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        45.83        27.58        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 
       42.02        46.32         8.58        12.39        71.31        69.70 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
        8.32        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        8.52        52.08        56.94        50.07        30.67        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       23.90        47.44        28.04        19.07        34.13         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       10.45        32.22        38.89         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        31.69        22.32        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
       12.07         2.70        23.44        20.88        19.53        52.37 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        2.93        54.58        70.45        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 
        4.24        41.19        15.75        32.38        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       56.58        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       53.52        41.88        43.10        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       15.75         9.27        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58        24.79         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        5.95        35.41        29.95        48.39       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 
      129.21       108.95        76.24        19.20       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      140.78        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
        6.08        53.95        65.82        10.98         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
       28.34         2.50         4.14        64.83       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
       18.81        12.66         7.99         9.01         5.26         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
       52.31        12.92        21.80        71.21        10.75       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       77.16         4.73        89.65        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       18.97        17.13        95.34         4.96        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 
        2.10        49.71        18.41        57.47        35.54       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 
       89.33         9.67         0.46        22.85        25.08        25.94 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
        0.07        34.09       100.57        14.89        56.48       156.49 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        3.52        16.27        84.49        19.76         7.17       153.86 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O 
       16.64         6.38        22.19        35.93        30.48        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       21.01       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
       45.96         6.51        88.87        48.20        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        0.76        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ 
        6.38        29.79         6.48        28.01        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       28.77         7.63        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        23.34        58.45        37.25        33.86        18.02 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       20.45        37.58        41.59        37.18        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       17.85        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.06        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        3.65         6.90        15.95        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        37.41         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       13.84        19.04        15.48        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       18.97         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        27.39        21.07        19.73        12.89         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       16.96         6.87        15.91         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        3.12        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        2.83        49.51        49.45        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
              3.62               0.07 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
             62.37             210.97 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
            19.725             20.940 
[1] "3.6 - 62.4 (19.7)"  "0.1 - 211.0 (20.9)"
[1] "hr=" "1.3"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  KRTAP5-5 MUTATED         1        0         0         2         1         0
  KRTAP5-5 WILD-TYPE      24       75        80       251        10         1
D31V3, multiclass
           clus
vv          KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  STAGE I                  1                 24
  STAGE II                 0                 75
  STAGE III                0                 80
  STAGE IVA                2                251
  STAGE IVB                1                 10
  STAGE IVC                0                  1
[1] 6 2
[1] 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
  KRTAP5-5 MUTATED       1   0   2   1
  KRTAP5-5 WILD-TYPE    46 137  97 171
D31V4, multiclass
       clus
vv      KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  T0+T1                1                 46
  T2                   0                137
  T3                   2                 97
  T4                   1                171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KRTAP5-5 MUTATED     2   0   2   0
  KRTAP5-5 WILD-TYPE 173  67 166   7
D31V5, multiclass
    clus
vv   KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  N0                2                173
  N1                0                 67
  N2                2                166
  N3                0                  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"
D31V6, binary
                    cls
clus                   0   1
  KRTAP5-5 MUTATED     1   0
  KRTAP5-5 WILD-TYPE 190   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      1    0
  KRTAP5-5 WILD-TYPE  190    1
   clus
vv  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  0                1                190
  1                0                  1
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  KRTAP5-5 MUTATED     2   2
  KRTAP5-5 WILD-TYPE 136 371
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      2    2
  KRTAP5-5 WILD-TYPE  136  371
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  FEMALE                2                136
  MALE                  2                371
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  KRTAP5-5 MUTATED     1   3
  KRTAP5-5 WILD-TYPE 156 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      1    3
  KRTAP5-5 WILD-TYPE  156  290
     clus
vv    KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  NO                 1                156
  YES                3                290
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  KRTAP5-5 MUTATED                                     4
  KRTAP5-5 WILD-TYPE                                 496
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  KRTAP5-5 MUTATED                                                   0
  KRTAP5-5 WILD-TYPE                                                10
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  KRTAP5-5 MUTATED                                                           0
  KRTAP5-5 WILD-TYPE                                                         1
D31V9, multiclass
                                                           clus
vv                                                          KRTAP5-5 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      4
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          KRTAP5-5 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      496
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, continuous
D31V11, continuous
D31V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRTAP5-5 MUTATED                                  0     0
  KRTAP5-5 WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KRTAP5-5 MUTATED                           0     4
  KRTAP5-5 WILD-TYPE                        47   433
D31V13, multiclass
                                  clus
vv                                 KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 47
  WHITE                                           4                433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V14, binary
                    cls
clus                   0   1
  KRTAP5-5 MUTATED     0   4
  KRTAP5-5 WILD-TYPE  25 445
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      0    4
  KRTAP5-5 WILD-TYPE   25  445
                        clus
vv                       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  HISPANIC OR LATINO                    0                 25
  NOT HISPANIC OR LATINO                4                445
[1] 2 2
[1] FALSE

Clustering(32) Variable = ZNF623 MUTATION ANALYSIS
D32V1, survival
                  sevent
clus2                0   1
  ZNF623 MUTATED     8   4
  ZNF623 WILD-TYPE 281 216
  ZNF623 MUTATED ZNF623 WILD-TYPE 
              12              497 
  ZNF623 MUTATED ZNF623 WILD-TYPE 
               4              216 
$`ZNF623 MUTATED`
TCGA-CN-4727 TCGA-BA-5152 TCGA-BA-A6DA TCGA-BB-4223 TCGA-BB-4225 TCGA-CN-4736 
       51.29        42.35        11.54       105.90         4.80        12.99 
TCGA-CN-5356 TCGA-CN-5361 TCGA-CN-6020 TCGA-CQ-7069 TCGA-CV-7432 TCGA-QK-A6VC 
       46.32        69.70         6.74        41.88        84.49        19.73 

$`ZNF623 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       30.18        25.71         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
        9.07        26.50        23.74        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       65.59        15.52        21.17        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD 
       41.85        29.42        20.45        27.95         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 
       16.41         6.15         9.14         4.41        18.38        66.28 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       71.05        20.52        10.55        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
        6.28        12.69        55.86        38.04         4.67        56.68 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.81        52.14        55.56        57.11 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        45.83        27.58        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 
       42.02         8.58        12.39        71.31         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       56.94        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
       28.04        19.07        34.13        10.45        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       17.29        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       70.45        62.37        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       41.19        15.75        32.38        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        77.56        44.48        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.49        14.14        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       47.18        39.16        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.09        24.95        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       29.95        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       76.24        19.20        17.95       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        2.50         4.14        64.83       172.67       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 
       12.66         7.99         9.01         5.26         1.84        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
       12.92        21.80        71.21        10.75       130.88        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
        4.73        89.65        36.00        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       17.13        95.34         4.96        11.87        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 
       49.71        18.41        57.47        35.54       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
        9.67         0.46        22.85        25.08        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 
       34.09       100.57        14.89        56.48       156.49         3.52 
TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       16.27        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       22.19        35.93        30.48        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
        7.07        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        7.63        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 
       23.34        58.45        37.25        33.86        18.02        20.45 
TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       37.58        41.59        37.18        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       20.94        33.76        28.47        25.74        21.93        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       14.66        22.03         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        6.90        15.95        38.53        14.50        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       37.41         0.07        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       19.04        15.48        19.27        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       30.05         1.84        12.62         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
       16.08        17.98        29.92        15.78        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       10.85        36.82        47.01        19.00        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
        2.04        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.21        23.15         7.30        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       27.39        21.07        12.89         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       17.82        15.32         8.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
       15.91         7.10        32.45        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.25        20.35        64.80        54.67         2.83        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.45        44.65        74.47        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       29.46        18.05        13.94        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       17.03        20.55        14.56        13.35        18.15 

  ZNF623 MUTATED ZNF623 WILD-TYPE 
            4.80             0.07 
  ZNF623 MUTATED ZNF623 WILD-TYPE 
          105.90           210.97 
  ZNF623 MUTATED ZNF623 WILD-TYPE 
          42.115           20.880 
[1] "4.8 - 105.9 (42.1)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1.7"
D32V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  ZNF623 MUTATED         0        2         2         6         0         0
  ZNF623 WILD-TYPE      25       73        78       247        11         1
D32V3, multiclass
           clus
vv          ZNF623 MUTATED ZNF623 WILD-TYPE
  STAGE I                0               25
  STAGE II               2               73
  STAGE III              2               78
  STAGE IVA              6              247
  STAGE IVB              0               11
  STAGE IVC              0                1
[1] 6 2
[1] 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
  ZNF623 MUTATED       1   4   1   5
  ZNF623 WILD-TYPE    46 133  98 167
D32V4, multiclass
       clus
vv      ZNF623 MUTATED ZNF623 WILD-TYPE
  T0+T1              1               46
  T2                 4              133
  T3                 1               98
  T4                 5              167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF623 MUTATED     5   2   3   0
  ZNF623 WILD-TYPE 170  65 165   7
D32V5, multiclass
    clus
vv   ZNF623 MUTATED ZNF623 WILD-TYPE
  N0              5              170
  N1              2               65
  N2              3              165
  N3              0                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"
D32V6, binary
                  cls
clus                 0   1
  ZNF623 MUTATED     6   0
  ZNF623 WILD-TYPE 185   1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF623 MUTATED      6    0
  ZNF623 WILD-TYPE  185    1
   clus
vv  ZNF623 MUTATED ZNF623 WILD-TYPE
  0              6              185
  1              0                1
[1] 2 2
[1] FALSE
D32V7, binary
                  cls
clus                 0   1
  ZNF623 MUTATED     4   8
  ZNF623 WILD-TYPE 134 365
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF623 MUTATED      4    8
  ZNF623 WILD-TYPE  134  365
        clus
vv       ZNF623 MUTATED ZNF623 WILD-TYPE
  FEMALE              4              134
  MALE                8              365
[1] 2 2
[1] FALSE
D32V8, binary
                  cls
clus                 0   1
  ZNF623 MUTATED     3   8
  ZNF623 WILD-TYPE 154 285
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF623 MUTATED      3    8
  ZNF623 WILD-TYPE  154  285
     clus
vv    ZNF623 MUTATED ZNF623 WILD-TYPE
  NO               3              154
  YES              8              285
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  ZNF623 MUTATED                                    12
  ZNF623 WILD-TYPE                                 488
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  ZNF623 MUTATED                                                   0
  ZNF623 WILD-TYPE                                                10
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  ZNF623 MUTATED                                                           0
  ZNF623 WILD-TYPE                                                         1
D32V9, multiclass
                                                           clus
vv                                                          ZNF623 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   12
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          ZNF623 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    488
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, continuous
D32V11, continuous
D32V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF623 MUTATED                                  0     0
  ZNF623 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF623 MUTATED                           2    10
  ZNF623 WILD-TYPE                        45   427
D32V13, multiclass
                                  clus
vv                                 ZNF623 MUTATED ZNF623 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               45
  WHITE                                        10              427
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V14, binary
                  cls
clus                 0   1
  ZNF623 MUTATED     0  12
  ZNF623 WILD-TYPE  25 437
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF623 MUTATED      0   12
  ZNF623 WILD-TYPE   25  437
                        clus
vv                       ZNF623 MUTATED ZNF623 WILD-TYPE
  HISPANIC OR LATINO                  0               25
  NOT HISPANIC OR LATINO             12              437
[1] 2 2
[1] FALSE

Clustering(33) Variable = TIGD4 MUTATION ANALYSIS
D33V1, survival
                 sevent
clus2               0   1
  TIGD4 MUTATED     4   3
  TIGD4 WILD-TYPE 285 217
  TIGD4 MUTATED TIGD4 WILD-TYPE 
              7             502 
  TIGD4 MUTATED TIGD4 WILD-TYPE 
              3             217 
$`TIGD4 MUTATED`
TCGA-CN-A49B TCGA-CV-6961 TCGA-CV-7101 TCGA-CV-7430 TCGA-CX-7086 TCGA-F7-A624 
       29.72         2.50         5.26        16.27        18.84        12.43 
TCGA-H7-7774 
       13.38 

$`TIGD4 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 
        9.14         4.80         4.41        18.38        66.28        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       12.69        55.86        38.04         4.67        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
       26.86        32.81        52.14        55.56        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        45.83        27.58        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 
       42.02        46.32         8.58        12.39        71.31        69.70 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
        8.32        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        8.52        52.08        56.94        50.07        30.67        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       23.90        47.44        28.04        19.07        34.13         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       10.45        32.22        38.89         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T 
       35.01        25.41        23.57        17.29        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 
       11.21         4.24        41.19        15.75        32.38        66.28 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       58.42        50.01        39.52        36.99        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       22.78        15.75         9.27        47.18        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       40.93        35.84         3.45         3.09        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
        0.99        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       17.13        32.78        47.01        27.06        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       17.16       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       140.78        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       15.09        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        7.13         8.42        28.34         4.14        64.83       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
      111.16        18.81        12.66         7.99         9.01         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
       52.31        12.92        21.80        71.21        10.75       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       77.16         4.73        89.65        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       18.97        17.13        95.34         4.96        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 
        2.10        49.71        18.41        57.47        35.54       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 
       89.33         9.67         0.46        22.85        25.08        25.94 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
        0.07        34.09       100.57        14.89        56.48       156.49 
TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 
        3.52        84.49        19.76         7.17       153.86        16.64 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P 
        6.38        22.19        35.93        30.48        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
      169.38       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       56.61         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 
       19.92        22.52        10.42        10.55        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        7.63        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 
       23.34        58.45        37.25        33.86        18.02        20.45 
TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       37.58        41.59        37.18        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       11.80        20.25        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 
        0.36        13.84         4.27         3.65         6.90        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
       33.57         5.29        13.68        13.84        19.04        15.48 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.27        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         6.25        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        71.74        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        21.47         9.34        12.72        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       19.73        12.89         5.62        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       15.32         8.32        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ 
        7.10        32.45        13.71         3.12        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       20.35        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       18.05        13.94        20.75        22.36        32.65        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.55        14.56        13.35        18.15 

  TIGD4 MUTATED TIGD4 WILD-TYPE 
           2.50            0.07 
  TIGD4 MUTATED TIGD4 WILD-TYPE 
          29.72          210.97 
  TIGD4 MUTATED TIGD4 WILD-TYPE 
          13.38           21.07 
[1] "2.5 - 29.7 (13.4)"  "0.1 - 211.0 (21.1)"
[1] "hr=" "1.8"
D33V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  TIGD4 MUTATED         0        3         2         2         0         0
  TIGD4 WILD-TYPE      25       72        78       251        11         1
D33V3, multiclass
           clus
vv          TIGD4 MUTATED TIGD4 WILD-TYPE
  STAGE I               0              25
  STAGE II              3              72
  STAGE III             2              78
  STAGE IVA             2             251
  STAGE IVB             0              11
  STAGE IVC             0               1
[1] 6 2
[1] 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
  TIGD4 MUTATED       0   3   2   2
  TIGD4 WILD-TYPE    47 134  97 170
D33V4, multiclass
       clus
vv      TIGD4 MUTATED TIGD4 WILD-TYPE
  T0+T1             0              47
  T2                3             134
  T3                2              97
  T4                2             170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TIGD4 MUTATED     3   2   0   0
  TIGD4 WILD-TYPE 172  65 168   7
D33V5, multiclass
    clus
vv   TIGD4 MUTATED TIGD4 WILD-TYPE
  N0             3             172
  N1             2              65
  N2             0             168
  N3             0               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
  TIGD4 MUTATED     1   0
  TIGD4 WILD-TYPE 190   1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD4 MUTATED      1    0
  TIGD4 WILD-TYPE  190    1
   clus
vv  TIGD4 MUTATED TIGD4 WILD-TYPE
  0             1             190
  1             0               1
[1] 2 2
[1] FALSE
D33V7, binary
                 cls
clus                0   1
  TIGD4 MUTATED     1   6
  TIGD4 WILD-TYPE 137 367
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD4 MUTATED      1    6
  TIGD4 WILD-TYPE  137  367
        clus
vv       TIGD4 MUTATED TIGD4 WILD-TYPE
  FEMALE             1             137
  MALE               6             367
[1] 2 2
[1] FALSE
D33V8, binary
                 cls
clus                0   1
  TIGD4 MUTATED     1   4
  TIGD4 WILD-TYPE 156 289
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD4 MUTATED      1    4
  TIGD4 WILD-TYPE  156  289
     clus
vv    TIGD4 MUTATED TIGD4 WILD-TYPE
  NO              1             156
  YES             4             289
[1] 2 2
[1] FALSE
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA
  TIGD4 MUTATED                                     7
  TIGD4 WILD-TYPE                                 493
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  TIGD4 MUTATED                                                   0
  TIGD4 WILD-TYPE                                                10
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  TIGD4 MUTATED                                                           0
  TIGD4 WILD-TYPE                                                         1
D33V9, multiclass
                                                           clus
vv                                                          TIGD4 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   7
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             0
                                                           clus
vv                                                          TIGD4 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   493
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, continuous
D33V11, continuous
D33V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TIGD4 MUTATED                                  0     0
  TIGD4 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TIGD4 MUTATED                           1     6
  TIGD4 WILD-TYPE                        46   431
D33V13, multiclass
                                  clus
vv                                 TIGD4 MUTATED TIGD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              46
  WHITE                                        6             431
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V14, binary
                 cls
clus                0   1
  TIGD4 MUTATED     0   7
  TIGD4 WILD-TYPE  25 442
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD4 MUTATED      0    7
  TIGD4 WILD-TYPE   25  442
                        clus
vv                       TIGD4 MUTATED TIGD4 WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO             7             442
[1] 2 2
[1] FALSE

Clustering(34) Variable = NAP1L2 MUTATION ANALYSIS
D34V1, survival
                  sevent
clus2                0   1
  NAP1L2 MUTATED     4   3
  NAP1L2 WILD-TYPE 285 217
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               7              502 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               3              217 
$`NAP1L2 MUTATED`
TCGA-CQ-5331 TCGA-CQ-6218 TCGA-CV-5436 TCGA-CV-A6K2 TCGA-IQ-A61G TCGA-IQ-A61L 
       45.99        41.19        19.20        10.42        11.84        13.68 
TCGA-UF-A71E 
       49.45 

$`NAP1L2 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 
        9.14         4.80         4.41        18.38        66.28        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       12.69        55.86        38.04         4.67        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
       26.86        32.81        52.14        55.56        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        45.83        27.58        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 
       42.02        46.32         8.58        12.39        71.31        69.70 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
        8.32        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        8.52        52.08        56.94        50.07        30.67        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       23.90        47.44        28.04        19.07        34.13         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       10.45        32.22        38.89         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        31.69        22.32        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
       12.07         2.70        23.44        20.88        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 
       21.50         2.93        54.58        70.45        62.37        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 
       11.21         4.24        15.75        32.38        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       56.58        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       53.52        41.88        43.10        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       15.75         9.27        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58        24.79         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        5.95        35.41        29.95        48.39       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      129.21       108.95        76.24        17.95       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      140.78        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
        6.08        53.95        65.82        10.98         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
       28.34         2.50         4.14        64.83       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
       18.81        12.66         7.99         9.01         5.26         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
       52.31        12.92        21.80        71.21        10.75       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       77.16         4.73        89.65        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       18.97        17.13        95.34         4.96        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 
        2.10        49.71        18.41        57.47        35.54       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 
       89.33         9.67         0.46        22.85        25.08        25.94 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
        0.07        34.09       100.57        14.89        56.48       156.49 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        3.52        16.27        84.49        19.76         7.17       153.86 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O 
       16.64         6.38        22.19        35.93        30.48        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       21.01       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
       45.96         6.51        88.87        48.20        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        0.76        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       23.47        19.92        22.52        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       28.77         7.63        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        23.34        58.45        37.25        33.86        18.02 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       20.45        37.58        41.59        37.18        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       17.85        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.06        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        3.65         6.90        15.95        38.53        14.50        37.71 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG 
       37.41         0.07        33.57         5.29        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       15.48        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
        1.84        12.62         6.25        15.42         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       17.98        29.92        15.78        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       36.82        47.01        19.00        75.55        18.97         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       29.00        12.99        16.01        13.15        21.07        21.21 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       23.15         7.30        21.47         9.34        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        19.73        12.89         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       17.82        15.32         8.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
       15.91         7.10        32.45        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.25        20.35        64.80        54.67         2.83        49.51 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       18.05        13.94        20.75        22.36        32.65        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.55        14.56        13.35        18.15 

  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
           10.42             0.07 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
           49.45           210.97 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
          19.200           20.975 
[1] "10.4 - 49.5 (19.2)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1.1"
D34V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  NAP1L2 MUTATED         0        1         0         5         0         0
  NAP1L2 WILD-TYPE      25       74        80       248        11         1
D34V3, multiclass
           clus
vv          NAP1L2 MUTATED NAP1L2 WILD-TYPE
  STAGE I                0               25
  STAGE II               1               74
  STAGE III              0               80
  STAGE IVA              5              248
  STAGE IVB              0               11
  STAGE IVC              0                1
[1] 6 2
[1] 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
  NAP1L2 MUTATED       0   2   2   3
  NAP1L2 WILD-TYPE    47 135  97 169
D34V4, multiclass
       clus
vv      NAP1L2 MUTATED NAP1L2 WILD-TYPE
  T0+T1              0               47
  T2                 2              135
  T3                 2               97
  T4                 3              169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  NAP1L2 MUTATED     3   0   3   0
  NAP1L2 WILD-TYPE 172  67 165   7
D34V5, multiclass
    clus
vv   NAP1L2 MUTATED NAP1L2 WILD-TYPE
  N0              3              172
  N1              0               67
  N2              3              165
  N3              0                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"
D34V6, binary
                  cls
clus                 0   1
  NAP1L2 MUTATED     3   0
  NAP1L2 WILD-TYPE 188   1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      3    0
  NAP1L2 WILD-TYPE  188    1
   clus
vv  NAP1L2 MUTATED NAP1L2 WILD-TYPE
  0              3              188
  1              0                1
[1] 2 2
[1] FALSE
D34V7, binary
                  cls
clus                 0   1
  NAP1L2 MUTATED     3   4
  NAP1L2 WILD-TYPE 135 369
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      3    4
  NAP1L2 WILD-TYPE  135  369
        clus
vv       NAP1L2 MUTATED NAP1L2 WILD-TYPE
  FEMALE              3              135
  MALE                4              369
[1] 2 2
[1] FALSE
D34V8, binary
                  cls
clus                 0   1
  NAP1L2 MUTATED     2   5
  NAP1L2 WILD-TYPE 155 288
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      2    5
  NAP1L2 WILD-TYPE  155  288
     clus
vv    NAP1L2 MUTATED NAP1L2 WILD-TYPE
  NO               2              155
  YES              5              288
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  NAP1L2 MUTATED                                     6
  NAP1L2 WILD-TYPE                                 494
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  NAP1L2 MUTATED                                                   1
  NAP1L2 WILD-TYPE                                                 9
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  NAP1L2 MUTATED                                                           0
  NAP1L2 WILD-TYPE                                                         1
D34V9, multiclass
                                                           clus
vv                                                          NAP1L2 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    6
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          NAP1L2 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    494
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, continuous
D34V11, continuous
D34V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NAP1L2 MUTATED                                  0     0
  NAP1L2 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NAP1L2 MUTATED                           0     6
  NAP1L2 WILD-TYPE                        47   431
D34V13, multiclass
                                  clus
vv                                 NAP1L2 MUTATED NAP1L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               47
  WHITE                                         6              431
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V14, binary
                  cls
clus                 0   1
  NAP1L2 MUTATED     3   3
  NAP1L2 WILD-TYPE  22 446
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      3    3
  NAP1L2 WILD-TYPE   22  446
                        clus
vv                       NAP1L2 MUTATED NAP1L2 WILD-TYPE
  HISPANIC OR LATINO                  3               22
  NOT HISPANIC OR LATINO              3              446
[1] 2 2
[1] FALSE

Clustering(35) Variable = CUL3 MUTATION ANALYSIS
D35V1, survival
                sevent
clus2              0   1
  CUL3 MUTATED     8   8
  CUL3 WILD-TYPE 281 212
  CUL3 MUTATED CUL3 WILD-TYPE 
            16            493 
  CUL3 MUTATED CUL3 WILD-TYPE 
             8            212 
$`CUL3 MUTATED`
TCGA-BA-6869 TCGA-BB-8601 TCGA-CN-5360 TCGA-CN-5369 TCGA-CN-6019 TCGA-CN-6989 
       21.17        20.52        71.31        12.49        34.13        32.22 
TCGA-CN-A497 TCGA-CR-6477 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-6960 TCGA-CV-7418 
       35.01        16.90       129.21        76.24        28.34        25.94 
TCGA-CV-A6JM TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-UF-A71B 
        6.38        14.76        12.20        49.51 

$`CUL3 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 
       17.10        23.84        65.59        15.52        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-A5HY 
        4.80         4.41        18.38        66.28        71.05        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 
       27.19        12.92         8.81         6.28        12.69        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       52.14        55.56        57.11        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       45.83        27.58        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
        8.58        12.39        69.70         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.84        11.57         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        48.00        23.90        47.44        28.04        19.07 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
        6.74        10.45        38.89         3.68        17.42        11.74 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       25.41        23.57        17.29        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 
       11.21         4.24        41.19        15.75        32.38        66.28 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 
       58.42        50.01        39.52        36.99        18.54        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       15.75         9.27        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58        24.79         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        5.95        35.41        29.95        48.39       139.43        17.16 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
      108.95        19.20        17.95       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6961 
       53.95        65.82        10.98         7.13         8.42         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        4.14        64.83       172.67       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       89.65        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       95.34         4.96        11.87        47.97         2.10        49.71 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       18.41        57.47        35.54       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
        0.46        22.85        25.08         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       14.89        56.48       156.49         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       19.76         7.17       153.86        16.64         6.38        22.19 
TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       35.93        30.48        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       48.20        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
       15.25         5.98        35.34        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        51.12        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
       23.05         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN 
       25.32        17.72        12.36        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        13.94        12.10        12.79        23.34        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 
       37.25        33.86        18.02        20.45        37.58        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       37.18        32.71        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        24.95         0.46        17.85        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       12.43        13.38        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 
        0.36        13.84         4.27         3.65         6.90        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
       33.57         5.29        13.68        13.84        19.04        15.48 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.27        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         6.25        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        71.74        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        21.47         9.34        12.72        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
       19.73        12.89         5.62        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.72        16.96         6.87        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       13.71         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       54.67         2.83        49.45        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  CUL3 MUTATED CUL3 WILD-TYPE 
          6.38           0.07 
  CUL3 MUTATED CUL3 WILD-TYPE 
        129.21         210.97 
  CUL3 MUTATED CUL3 WILD-TYPE 
         27.14          20.75 
[1] "6.4 - 129.2 (27.1)" "0.1 - 211.0 (20.8)"
[1] "hr=" "1"  
D35V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  CUL3 MUTATED         0        0         5         8         0         0
  CUL3 WILD-TYPE      25       75        75       245        11         1
D35V3, multiclass
           clus
vv          CUL3 MUTATED CUL3 WILD-TYPE
  STAGE I              0             25
  STAGE II             0             75
  STAGE III            5             75
  STAGE IVA            8            245
  STAGE IVB            0             11
  STAGE IVC            0              1
[1] 6 2
[1] 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
  CUL3 MUTATED       1   1   5   7
  CUL3 WILD-TYPE    46 136  94 165
D35V4, multiclass
       clus
vv      CUL3 MUTATED CUL3 WILD-TYPE
  T0+T1            1             46
  T2               1            136
  T3               5             94
  T4               7            165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CUL3 MUTATED     7   2   5   0
  CUL3 WILD-TYPE 168  65 163   7
D35V5, multiclass
    clus
vv   CUL3 MUTATED CUL3 WILD-TYPE
  N0            7            168
  N1            2             65
  N2            5            163
  N3            0              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"
D35V6, binary
                cls
clus               0   1
  CUL3 MUTATED     4   0
  CUL3 WILD-TYPE 187   1
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL3 MUTATED      4    0
  CUL3 WILD-TYPE  187    1
   clus
vv  CUL3 MUTATED CUL3 WILD-TYPE
  0            4            187
  1            0              1
[1] 2 2
[1] FALSE
D35V7, binary
                cls
clus               0   1
  CUL3 MUTATED     2  14
  CUL3 WILD-TYPE 136 359
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL3 MUTATED      2   14
  CUL3 WILD-TYPE  136  359
        clus
vv       CUL3 MUTATED CUL3 WILD-TYPE
  FEMALE            2            136
  MALE             14            359
[1] 2 2
[1] FALSE
D35V8, binary
                cls
clus               0   1
  CUL3 MUTATED     6   9
  CUL3 WILD-TYPE 151 284
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL3 MUTATED      6    9
  CUL3 WILD-TYPE  151  284
     clus
vv    CUL3 MUTATED CUL3 WILD-TYPE
  NO             6            151
  YES            9            284
[1] 2 2
[1] FALSE
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA
  CUL3 MUTATED                                    16
  CUL3 WILD-TYPE                                 484
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  CUL3 MUTATED                                                   0
  CUL3 WILD-TYPE                                                10
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  CUL3 MUTATED                                                           0
  CUL3 WILD-TYPE                                                         1
D35V9, multiclass
                                                           clus
vv                                                          CUL3 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                 16
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT            0
                                                           clus
vv                                                          CUL3 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  484
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, continuous
D35V11, continuous
D35V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CUL3 MUTATED                                  0     0
  CUL3 WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CUL3 MUTATED                           5    10
  CUL3 WILD-TYPE                        42   427
D35V13, multiclass
                                  clus
vv                                 CUL3 MUTATED CUL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   5             42
  WHITE                                      10            427
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V14, binary
                cls
clus               0   1
  CUL3 MUTATED     0  14
  CUL3 WILD-TYPE  25 435
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL3 MUTATED      0   14
  CUL3 WILD-TYPE   25  435
                        clus
vv                       CUL3 MUTATED CUL3 WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO           14            435
[1] 2 2
[1] FALSE

Clustering(36) Variable = CREBBP MUTATION ANALYSIS
D36V1, survival
                  sevent
clus2                0   1
  CREBBP MUTATED    19  15
  CREBBP WILD-TYPE 270 205
  CREBBP MUTATED CREBBP WILD-TYPE 
              34              475 
  CREBBP MUTATED CREBBP WILD-TYPE 
              15              205 
$`CREBBP MUTATED`
TCGA-CN-A6V3 TCGA-CR-6478 TCGA-UF-A71D TCGA-BA-4074 TCGA-BA-6869 TCGA-BA-A6D8 
       24.39         6.02        48.03        15.19        21.17        27.95 
TCGA-BB-A5HY TCGA-CN-4736 TCGA-CN-5369 TCGA-CN-6988 TCGA-CQ-5333 TCGA-CQ-7071 
       10.55        12.99        12.49        10.45        11.21        43.10 
TCGA-CQ-A4CI TCGA-CR-6481 TCGA-CV-5432 TCGA-CV-6951 TCGA-CV-6962 TCGA-CV-7429 
       31.23        10.22       129.21        30.08         4.14         3.52 
TCGA-CV-7434 TCGA-CV-7568 TCGA-CV-A45Z TCGA-CV-A6JE TCGA-DQ-7592 TCGA-F7-A624 
        7.17        30.48        48.20        35.34        37.58        12.43 
TCGA-H7-7774 TCGA-IQ-7631 TCGA-P3-A5QF TCGA-QK-A6IJ TCGA-RS-A6TO TCGA-T2-A6WX 
       13.38        38.53        10.85        12.72        12.72         6.87 
TCGA-T2-A6X2 TCGA-TN-A7HL TCGA-UF-A7JA TCGA-UF-A7JJ 
       32.45        20.35        74.47        18.05 

$`CREBBP WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-6221 
       11.08        35.05        32.48        19.82        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7082 TCGA-CX-7219 
       70.13        43.04        11.61        34.52         0.36        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       30.94        14.04        40.24        21.11        12.66        22.85 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
        2.96         3.35        13.64         9.07        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 
       42.35        57.93        17.10        23.84        65.59        15.52 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH 
       14.83        12.62         4.01        41.85        29.42        20.45 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 
        9.14         4.80         4.41        18.38        66.28        71.05 
TCGA-BB-8601 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       20.52        27.19        12.92         8.81         6.28        12.69 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       55.86        38.04         4.67        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 
       32.81        52.14        55.56        57.11        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       45.83        27.58        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 
        8.58        12.39        71.31        69.70         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.54        11.84        11.57         8.52        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 
       19.07        34.13         6.74        32.22        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       17.42        11.74        35.01        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        31.69        22.32        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       16.57         4.41        12.07         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       19.53        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 
       62.37        45.99        10.42         4.24        41.19        15.75 
TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.38        66.28        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 
       14.99        38.76        64.87        53.52        41.88        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       44.48        23.24        29.36        33.60        29.49        14.14 
TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       12.46        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       58.42        50.01        39.52        36.99        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       11.90        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       15.75         9.27        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58        24.79         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        5.95        35.41        29.95        48.39       139.43        17.16 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      108.95        76.24        19.20        17.95       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6952 
      140.78        19.79        12.03        42.38        15.09         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        2.50        64.83       172.67       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       89.65        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       95.34         4.96        11.87        47.97         2.10        49.71 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       18.41        57.47        35.54       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        0.46        22.85        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 
      100.57        14.89        56.48       156.49        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 
       19.76       153.86        16.64         6.38        22.19        35.93 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        21.01       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 
        1.05        45.96         6.51        88.87        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM 
        0.76        56.61         7.07        15.25         5.98         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       28.77         7.63        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        23.34        58.45        37.25        33.86        18.02 
TCGA-DQ-7591 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       20.45        41.59        37.18        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       11.80        20.25        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 
        0.36        13.84         4.27         3.65         6.90        15.95 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        37.71        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        6.25        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       15.78        71.74        51.25        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
        9.34        27.39        21.07        19.73        12.89         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP 
       14.76        12.20        17.82        15.32         8.32        16.96 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ 
       15.91         7.10        13.71         3.12        13.55        13.25 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
       64.80        54.67         2.83        49.51        49.45        44.65 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO 
       17.95        24.30        55.43        29.46        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  CREBBP MUTATED CREBBP WILD-TYPE 
            3.52             0.07 
  CREBBP MUTATED CREBBP WILD-TYPE 
          129.21           210.97 
  CREBBP MUTATED CREBBP WILD-TYPE 
           16.62            21.07 
[1] "3.5 - 129.2 (16.6)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.2"
D36V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  CREBBP MUTATED         0        4         6        18         0         0
  CREBBP WILD-TYPE      25       71        74       235        11         1
D36V3, multiclass
           clus
vv          CREBBP MUTATED CREBBP WILD-TYPE
  STAGE I                0               25
  STAGE II               4               71
  STAGE III              6               74
  STAGE IVA             18              235
  STAGE IVB              0               11
  STAGE IVC              0                1
[1] 6 2
[1] 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       2   7   6  14
  CREBBP WILD-TYPE    45 130  93 158
D36V4, multiclass
       clus
vv      CREBBP MUTATED CREBBP WILD-TYPE
  T0+T1              2               45
  T2                 7              130
  T3                 6               93
  T4                14              158
[1] 4 2
[1] TRUE
[1] "dimension of 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    10   5  10   0
  CREBBP WILD-TYPE 165  62 158   7
D36V5, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  N0             10              165
  N1              5               62
  N2             10              158
  N3              0                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"
D36V6, binary
                  cls
clus                 0   1
  CREBBP MUTATED    15   0
  CREBBP WILD-TYPE 176   1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     15    0
  CREBBP WILD-TYPE  176    1
   clus
vv  CREBBP MUTATED CREBBP WILD-TYPE
  0             15              176
  1              0                1
[1] 2 2
[1] FALSE
D36V7, binary
                  cls
clus                 0   1
  CREBBP MUTATED    11  23
  CREBBP WILD-TYPE 127 350
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     11   23
  CREBBP WILD-TYPE  127  350
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  FEMALE             11              127
  MALE               23              350
[1] 2 2
[1] FALSE
D36V8, binary
                  cls
clus                 0   1
  CREBBP MUTATED    10  20
  CREBBP WILD-TYPE 147 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     10   20
  CREBBP WILD-TYPE  147  273
     clus
vv    CREBBP MUTATED CREBBP WILD-TYPE
  NO              10              147
  YES             20              273
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  CREBBP MUTATED                                    33
  CREBBP WILD-TYPE                                 467
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  CREBBP MUTATED                                                   1
  CREBBP WILD-TYPE                                                 9
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  CREBBP MUTATED                                                           0
  CREBBP WILD-TYPE                                                         1
D36V9, multiclass
                                                           clus
vv                                                          CREBBP MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   33
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          CREBBP WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    467
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V10, continuous
D36V11, continuous
D36V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CREBBP MUTATED                                  1     0
  CREBBP WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CREBBP MUTATED                           1    31
  CREBBP WILD-TYPE                        46   406
D36V13, multiclass
                                  clus
vv                                 CREBBP MUTATED CREBBP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                1
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               46
  WHITE                                        31              406
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V14, binary
                  cls
clus                 0   1
  CREBBP MUTATED     1  29
  CREBBP WILD-TYPE  24 420
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED      1   29
  CREBBP WILD-TYPE   24  420
                        clus
vv                       CREBBP MUTATED CREBBP WILD-TYPE
  HISPANIC OR LATINO                  1               24
  NOT HISPANIC OR LATINO             29              420
[1] 2 2
[1] FALSE

Clustering(37) Variable = VEZF1 MUTATION ANALYSIS
D37V1, survival
                 sevent
clus2               0   1
  VEZF1 MUTATED     4   4
  VEZF1 WILD-TYPE 285 216
  VEZF1 MUTATED VEZF1 WILD-TYPE 
              8             501 
  VEZF1 MUTATED VEZF1 WILD-TYPE 
              4             216 
$`VEZF1 MUTATED`
TCGA-CN-4725 TCGA-CN-5356 TCGA-CN-5365 TCGA-CV-5436 TCGA-CV-6941 TCGA-D6-A6EP 
       38.04        46.32        11.54        19.20        11.24        13.94 
TCGA-MT-A67A TCGA-KU-A66S 
       30.05        13.35 

$`VEZF1 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 
        9.14         4.80         4.41        18.38        66.28        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       12.69        55.86         4.67        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       32.81        52.14        55.56        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 
        8.58        12.39        71.31        69.70         8.32        16.21 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.84        11.57        12.49         8.52        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
       19.07        34.13         6.74        10.45        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       17.29        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       70.45        62.37        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       41.19        15.75        32.38        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       11.34        11.64         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
      108.95        76.24        17.95       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 
       20.52         4.73        21.90        26.43       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       65.82        10.98         7.13         8.42        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        4.14        64.83       172.67       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       89.65        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       95.34         4.96        11.87        47.97         2.10        49.71 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       18.41        57.47        35.54       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        0.46        22.85        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 
      100.57        14.89        56.48       156.49         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       84.49        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       22.19        35.93        30.48        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
        7.07        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        22.59        24.95        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        37.25        33.86        18.02        20.45        37.58 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       31.13        18.94        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       20.25        12.43        13.38        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
       33.76        28.47        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         0.36        13.84         4.27         3.65         6.90 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
        0.07        33.57         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D 
       15.48        19.27        10.75        14.37         7.96         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         6.25        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        71.74        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        21.47         9.34        12.72        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       19.73        12.89         5.62        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       15.32         8.32        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ 
        7.10        32.45        13.71         3.12        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       20.35        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       18.05        13.94        20.75        22.36        32.65        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66T 
       20.55        14.56        18.15 

  VEZF1 MUTATED VEZF1 WILD-TYPE 
          11.24            0.07 
  VEZF1 MUTATED VEZF1 WILD-TYPE 
          46.32          210.97 
  VEZF1 MUTATED VEZF1 WILD-TYPE 
          16.57           21.01 
[1] "11.2 - 46.3 (16.6)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1.4"
D37V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  VEZF1 MUTATED         1        1         4         1         1         0
  VEZF1 WILD-TYPE      24       74        76       252        10         1
D37V3, multiclass
           clus
vv          VEZF1 MUTATED VEZF1 WILD-TYPE
  STAGE I               1              24
  STAGE II              1              74
  STAGE III             4              76
  STAGE IVA             1             252
  STAGE IVB             1              10
  STAGE IVC             0               1
[1] 6 2
[1] 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
  VEZF1 MUTATED       2   2   4   0
  VEZF1 WILD-TYPE    45 135  95 172
D37V4, multiclass
       clus
vv      VEZF1 MUTATED VEZF1 WILD-TYPE
  T0+T1             2              45
  T2                2             135
  T3                4              95
  T4                0             172
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  VEZF1 MUTATED     5   1   1   1
  VEZF1 WILD-TYPE 170  66 167   6
D37V5, multiclass
    clus
vv   VEZF1 MUTATED VEZF1 WILD-TYPE
  N0             5             170
  N1             1              66
  N2             1             167
  N3             1               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"
D37V6, binary
                 cls
clus                0   1
  VEZF1 MUTATED     1   0
  VEZF1 WILD-TYPE 190   1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEZF1 MUTATED      1    0
  VEZF1 WILD-TYPE  190    1
   clus
vv  VEZF1 MUTATED VEZF1 WILD-TYPE
  0             1             190
  1             0               1
[1] 2 2
[1] FALSE
D37V7, binary
                 cls
clus                0   1
  VEZF1 MUTATED     2   6
  VEZF1 WILD-TYPE 136 367
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEZF1 MUTATED      2    6
  VEZF1 WILD-TYPE  136  367
        clus
vv       VEZF1 MUTATED VEZF1 WILD-TYPE
  FEMALE             2             136
  MALE               6             367
[1] 2 2
[1] FALSE
D37V8, binary
                 cls
clus                0   1
  VEZF1 MUTATED     5   2
  VEZF1 WILD-TYPE 152 291
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEZF1 MUTATED      5    2
  VEZF1 WILD-TYPE  152  291
     clus
vv    VEZF1 MUTATED VEZF1 WILD-TYPE
  NO              5             152
  YES             2             291
[1] 2 2
[1] FALSE
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA
  VEZF1 MUTATED                                     7
  VEZF1 WILD-TYPE                                 493
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  VEZF1 MUTATED                                                   1
  VEZF1 WILD-TYPE                                                 9
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  VEZF1 MUTATED                                                           0
  VEZF1 WILD-TYPE                                                         1
D37V9, multiclass
                                                           clus
vv                                                          VEZF1 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   7
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             0
                                                           clus
vv                                                          VEZF1 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   493
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V10, continuous
D37V11, continuous
D37V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VEZF1 MUTATED                                  0     0
  VEZF1 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VEZF1 MUTATED                           0     7
  VEZF1 WILD-TYPE                        47   430
D37V13, multiclass
                                  clus
vv                                 VEZF1 MUTATED VEZF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              47
  WHITE                                        7             430
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V14, binary
                 cls
clus                0   1
  VEZF1 MUTATED     1   7
  VEZF1 WILD-TYPE  24 442
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEZF1 MUTATED      1    7
  VEZF1 WILD-TYPE   24  442
                        clus
vv                       VEZF1 MUTATED VEZF1 WILD-TYPE
  HISPANIC OR LATINO                 1              24
  NOT HISPANIC OR LATINO             7             442
[1] 2 2
[1] FALSE

Clustering(38) Variable = MLL4 MUTATION ANALYSIS
D38V1, survival
                sevent
clus2              0   1
  MLL4 MUTATED     9  10
  MLL4 WILD-TYPE 280 210
  MLL4 MUTATED MLL4 WILD-TYPE 
            19            490 
  MLL4 MUTATED MLL4 WILD-TYPE 
            10            210 
$`MLL4 MUTATED`
TCGA-BA-A4II TCGA-HD-8634 TCGA-BA-5151 TCGA-BA-A6DF TCGA-BA-A6DJ TCGA-CN-5360 
       30.18        12.66        23.74         7.82        13.38        71.31 
TCGA-CN-A499 TCGA-CN-A63T TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CR-7370 TCGA-CV-6938 
       23.57         7.40        11.21         4.24         3.45         4.73 
TCGA-CV-6948 TCGA-CV-7252 TCGA-CV-A45Q TCGA-D6-A6EN TCGA-F7-A622 TCGA-F7-A624 
       42.38         4.96       169.38        22.59        11.80        12.43 
TCGA-MT-A67A 
       30.05 

$`MLL4 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8635 
       34.36        30.94        14.04        40.24        21.11        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       48.03         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 
       26.50        42.35        57.93        17.10        23.84        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       15.52        21.17        14.83        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
       14.47         2.27        11.05        20.48        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 
      105.90         9.14         4.80         4.41        18.38        66.28 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       71.05        20.52        10.55        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
        6.28        12.69        55.86        38.04         4.67        56.68 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.81        52.14        55.56        57.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5361 
       13.05        42.02        46.32         8.58        12.39        69.70 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
        8.32        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        8.52        52.08        56.94        50.07        30.67        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       23.90        47.44        28.04        19.07        34.13         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       10.45        32.22        38.89         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U 
       35.01        25.41        17.29        29.72        21.21        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       23.44        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 
       54.58        70.45        62.37        45.99        10.42        41.19 
TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       15.75        32.38        66.28        46.95        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
        4.24        14.99        38.76        64.87        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        77.56        44.48        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.49        14.14        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
       47.18        39.16        47.34        40.93        35.84         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58        24.79         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        94.88        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       60.49         7.07        43.23        54.74        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
        9.60        90.12         2.14         9.70         5.46        20.52 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       21.90        26.43        11.24       140.78        19.79        12.03 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       15.09        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
        7.13         8.42        28.34         2.50         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      172.67       111.16        18.81        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        5.26         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       10.75       130.88        77.16         4.73        89.65        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 
       31.36        26.20        18.97        17.13        95.34        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       47.97         2.10        49.71        18.41        57.47        35.54 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
      210.97        89.33         9.67         0.46        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
       25.94         0.07        34.09       100.57        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
      156.49         3.52        16.27        84.49        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 
      153.86        16.64         6.38        22.19        35.93        30.48 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       27.98        21.01       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
       45.96         6.51        88.87        48.20        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        0.76        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       23.47        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       16.14        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       12.36        28.77         7.63        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        23.34        58.45        37.25        33.86        18.02 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       20.45        37.58        41.59        37.18        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       17.85        20.25        13.38        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
       33.76        28.47        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         0.36        13.84         4.27         3.65         6.90 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
        0.07        33.57         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D 
       15.48        19.27        10.75        14.37         7.96         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         6.25        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        71.74        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        21.47         9.34        12.72        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       19.73        12.89         5.62        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       15.32         8.32        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ 
        7.10        32.45        13.71         3.12        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       20.35        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       18.05        13.94        20.75        22.36        32.65        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.55        14.56        13.35        18.15 

  MLL4 MUTATED MLL4 WILD-TYPE 
          3.45           0.07 
  MLL4 MUTATED MLL4 WILD-TYPE 
        169.38         210.97 
  MLL4 MUTATED MLL4 WILD-TYPE 
         12.66          21.04 
[1] "3.5 - 169.4 (12.7)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1.4"
D38V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  MLL4 MUTATED         2        5         2         7         1         0
  MLL4 WILD-TYPE      23       70        78       246        10         1
D38V3, multiclass
           clus
vv          MLL4 MUTATED MLL4 WILD-TYPE
  STAGE I              2             23
  STAGE II             5             70
  STAGE III            2             78
  STAGE IVA            7            246
  STAGE IVB            1             10
  STAGE IVC            0              1
[1] 6 2
[1] 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
  MLL4 MUTATED       2   6   3   6
  MLL4 WILD-TYPE    45 131  96 166
D38V4, multiclass
       clus
vv      MLL4 MUTATED MLL4 WILD-TYPE
  T0+T1            2             45
  T2               6            131
  T3               3             96
  T4               6            166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MLL4 MUTATED     9   1   3   1
  MLL4 WILD-TYPE 166  66 165   6
D38V5, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  N0            9            166
  N1            1             66
  N2            3            165
  N3            1              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"
D38V6, binary
                cls
clus               0   1
  MLL4 MUTATED     7   0
  MLL4 WILD-TYPE 184   1
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED      7    0
  MLL4 WILD-TYPE  184    1
   clus
vv  MLL4 MUTATED MLL4 WILD-TYPE
  0            7            184
  1            0              1
[1] 2 2
[1] FALSE
D38V7, binary
                cls
clus               0   1
  MLL4 MUTATED     8  11
  MLL4 WILD-TYPE 130 362
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED      8   11
  MLL4 WILD-TYPE  130  362
        clus
vv       MLL4 MUTATED MLL4 WILD-TYPE
  FEMALE            8            130
  MALE             11            362
[1] 2 2
[1] FALSE
D38V8, binary
                cls
clus               0   1
  MLL4 MUTATED     8  10
  MLL4 WILD-TYPE 149 283
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED      8   10
  MLL4 WILD-TYPE  149  283
     clus
vv    MLL4 MUTATED MLL4 WILD-TYPE
  NO             8            149
  YES           10            283
[1] 2 2
[1] FALSE
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA
  MLL4 MUTATED                                    19
  MLL4 WILD-TYPE                                 481
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  MLL4 MUTATED                                                   0
  MLL4 WILD-TYPE                                                10
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  MLL4 MUTATED                                                           0
  MLL4 WILD-TYPE                                                         1
D38V9, multiclass
                                                           clus
vv                                                          MLL4 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                 19
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT            0
                                                           clus
vv                                                          MLL4 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  481
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, continuous
D38V11, continuous
D38V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL4 MUTATED                                  0     1
  MLL4 WILD-TYPE                                2     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MLL4 MUTATED                           1    17
  MLL4 WILD-TYPE                        46   420
D38V13, multiclass
                                  clus
vv                                 MLL4 MUTATED MLL4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             46
  WHITE                                      17            420
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V14, binary
                cls
clus               0   1
  MLL4 MUTATED     0  19
  MLL4 WILD-TYPE  25 430
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED      0   19
  MLL4 WILD-TYPE   25  430
                        clus
vv                       MLL4 MUTATED MLL4 WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO           19            430
[1] 2 2
[1] FALSE

Clustering(39) Variable = IRS4 MUTATION ANALYSIS
D39V1, survival
                sevent
clus2              0   1
  IRS4 MUTATED     9   8
  IRS4 WILD-TYPE 280 212
  IRS4 MUTATED IRS4 WILD-TYPE 
            17            492 
  IRS4 MUTATED IRS4 WILD-TYPE 
             8            212 
$`IRS4 MUTATED`
TCGA-DQ-7593 TCGA-BA-6868 TCGA-CN-4741 TCGA-CR-7388 TCGA-CR-7398 TCGA-CV-6953 
       40.24        15.52        73.61        27.06         5.13        53.95 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7427 TCGA-CV-7568 TCGA-CV-A468 
       26.20        17.13        47.97       156.49        30.48        15.25 
TCGA-F7-A50J TCGA-QK-A6IF TCGA-QK-A6V9 TCGA-TN-A7HL TCGA-UF-A7JJ 
       31.13        23.15        27.39        20.35        18.05 

$`IRS4 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-H7-A6C5 TCGA-HD-8634 
        0.36        34.36        30.94        14.04        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       23.84        65.59        21.17        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       41.85        29.42        20.45        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       20.48        16.41         6.15       105.90         9.14         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
        4.41        18.38        66.28        71.05        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 
       27.19        12.92         8.81         6.28        12.69        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       52.14        55.56        57.11        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       45.83        27.58        13.05        42.02        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       12.39        71.31        69.70         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.84        11.57        12.49         8.52        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
       19.07        34.13         6.74        10.45        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       17.29        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       70.45        62.37        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       41.19        15.75        32.38        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       11.34        11.64         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       47.01        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       44.25        30.58        24.79         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        94.88        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       60.49         7.07        43.23        54.74        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
        9.60        90.12         2.14         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6954 
       12.03        42.38        15.09        30.08         6.08        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       10.98         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       172.67       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        9.01         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        89.65 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       36.00        31.36        18.97        95.34         4.96        11.87 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 
        2.10        49.71        18.41        57.47        35.54       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 
       89.33         9.67         0.46        22.85        25.08        25.94 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7429 
        0.07        34.09       100.57        14.89        56.48         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 
       16.27        84.49        19.76         7.17       153.86        16.64 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
        6.38        22.19        35.93        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
        7.07         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        37.25        33.86        18.02        20.45        37.58 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        24.95         0.46        17.85        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       12.43        13.38        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 
        0.36        13.84         4.27         3.65         6.90        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
       33.57         5.29        13.68        13.84        19.04        15.48 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.27        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         6.25        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        71.74        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG 
       12.99        16.01        13.15        21.07        21.21         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
       21.47         9.34        12.72        21.07        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.72        16.96         6.87        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 
       13.71         3.12        13.55        13.25        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        2.83        49.51        49.45        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       24.30        55.43        29.46        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       32.65        17.03        20.55        14.56        13.35        18.15 

  IRS4 MUTATED IRS4 WILD-TYPE 
          5.13           0.07 
  IRS4 MUTATED IRS4 WILD-TYPE 
        156.49         210.97 
  IRS4 MUTATED IRS4 WILD-TYPE 
         27.06          20.65 
[1] "5.1 - 156.5 (27.1)" "0.1 - 211.0 (20.6)"
[1] "hr=" "1.1"
D39V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  IRS4 MUTATED         0        4         2         7         0         0
  IRS4 WILD-TYPE      25       71        78       246        11         1
D39V3, multiclass
           clus
vv          IRS4 MUTATED IRS4 WILD-TYPE
  STAGE I              0             25
  STAGE II             4             71
  STAGE III            2             78
  STAGE IVA            7            246
  STAGE IVB            0             11
  STAGE IVC            0              1
[1] 6 2
[1] 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
  IRS4 MUTATED       0   4   3   6
  IRS4 WILD-TYPE    47 133  96 166
D39V4, multiclass
       clus
vv      IRS4 MUTATED IRS4 WILD-TYPE
  T0+T1            0             47
  T2               4            133
  T3               3             96
  T4               6            166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  IRS4 MUTATED     6   0   3   0
  IRS4 WILD-TYPE 169  67 165   7
D39V5, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  N0            6            169
  N1            0             67
  N2            3            165
  N3            0              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"
D39V6, binary
                cls
clus               0   1
  IRS4 MUTATED     6   0
  IRS4 WILD-TYPE 185   1
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      6    0
  IRS4 WILD-TYPE  185    1
   clus
vv  IRS4 MUTATED IRS4 WILD-TYPE
  0            6            185
  1            0              1
[1] 2 2
[1] FALSE
D39V7, binary
                cls
clus               0   1
  IRS4 MUTATED     7  10
  IRS4 WILD-TYPE 131 363
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      7   10
  IRS4 WILD-TYPE  131  363
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  FEMALE            7            131
  MALE             10            363
[1] 2 2
[1] FALSE
D39V8, binary
                cls
clus               0   1
  IRS4 MUTATED     3  10
  IRS4 WILD-TYPE 154 283
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      3   10
  IRS4 WILD-TYPE  154  283
     clus
vv    IRS4 MUTATED IRS4 WILD-TYPE
  NO             3            154
  YES           10            283
[1] 2 2
[1] FALSE
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA
  IRS4 MUTATED                                    17
  IRS4 WILD-TYPE                                 483
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  IRS4 MUTATED                                                   0
  IRS4 WILD-TYPE                                                10
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  IRS4 MUTATED                                                           0
  IRS4 WILD-TYPE                                                         1
D39V9, multiclass
                                                           clus
vv                                                          IRS4 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                 17
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT            0
                                                           clus
vv                                                          IRS4 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  483
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, continuous
D39V11, continuous
D39V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IRS4 MUTATED                                  0     0
  IRS4 WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IRS4 MUTATED                           2    13
  IRS4 WILD-TYPE                        45   424
D39V13, multiclass
                                  clus
vv                                 IRS4 MUTATED IRS4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   2             45
  WHITE                                      13            424
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V14, binary
                cls
clus               0   1
  IRS4 MUTATED     2  13
  IRS4 WILD-TYPE  23 436
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      2   13
  IRS4 WILD-TYPE   23  436
                        clus
vv                       IRS4 MUTATED IRS4 WILD-TYPE
  HISPANIC OR LATINO                2             23
  NOT HISPANIC OR LATINO           13            436
[1] 2 2
[1] FALSE

Clustering(40) Variable = HUWE1 MUTATION ANALYSIS
D40V1, survival
                 sevent
clus2               0   1
  HUWE1 MUTATED    25  21
  HUWE1 WILD-TYPE 264 199
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             46             463 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             21             199 
$`HUWE1 MUTATED`
TCGA-BA-5557 TCGA-CQ-7068 TCGA-CR-6472 TCGA-BB-A6UO TCGA-CN-A63Y TCGA-CN-A642 
       20.48        43.04        34.52         8.81        16.57         2.70 
TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-7071 TCGA-CQ-A4CB TCGA-CR-5248 
       62.37        10.42         4.24        43.10        29.36        54.67 
TCGA-CR-6471 TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7374 TCGA-CV-5442 
       39.52        11.64        39.16         3.45         0.99        76.50 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7406 TCGA-CV-7425 TCGA-CV-7440 TCGA-CV-7568 
        2.50        64.83        57.47        56.48        22.19        30.48 
TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JZ TCGA-CV-A6K2 TCGA-D6-6516 
        0.76         7.07        15.25        23.47        10.42        25.41 
TCGA-D6-6824 TCGA-D6-A6EK TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-7596 TCGA-F7-A61W 
        2.53        28.77        58.45        37.25        41.59         0.46 
TCGA-HD-7832 TCGA-MT-A67F TCGA-P3-A5Q5 TCGA-P3-A6T5 TCGA-QK-A652 TCGA-QK-A6II 
       27.48        12.62        29.92        29.00        21.21         9.34 
TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-UF-A7JT 
       12.72         6.87        32.45        32.65 

$`HUWE1 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 
       70.13        11.61         6.02         0.36        34.36        30.94 
TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D 
       14.04        40.24        21.11        12.66        22.85        48.03 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 
        2.96         3.35        15.19        13.64         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 
       23.74        42.35        57.93        17.10        23.84        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       15.52        21.17        14.83        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.80         4.41 
TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ 
       18.38        66.28        71.05        20.52        10.55        27.19 
TCGA-BB-A6UM TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
       12.92         6.28        12.69        55.86        38.04         4.67 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       56.68        12.89        26.86        32.81        52.14        55.56 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       57.11        12.99        20.55        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       73.61        13.05        42.02        46.32         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       71.31        69.70         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.57        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        48.00        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 
       34.13         6.74        10.45        32.22        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       17.42        11.74        35.01        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        31.69        22.32        12.39 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
        4.41        12.07        23.44        20.88        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 
       21.50         2.93        54.58        70.45        45.99        11.21 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       41.19        15.75        32.38        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE 
       41.88        77.56        44.48        23.24        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 
       14.14        12.46        31.23        84.23        11.77        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       26.27        58.42        50.01        36.99        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       11.90        10.22        11.34         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       15.75         9.27        47.18        47.34        40.93        35.84 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        3.09        24.95        29.23        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58        24.79         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 
       19.20        17.95       107.51        94.88        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        7.07        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       90.12         2.14         9.70         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       21.90        26.43        11.24       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       42.38        15.09        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7090 
       10.98         7.13         8.42        28.34         4.14       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      111.16        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        1.84        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7410 
       47.97         2.10        49.71        18.41        35.54       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 
       89.33         9.67         0.46        22.85        25.08        25.94 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7429 
        0.07        34.09       100.57        14.89       156.49         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 
       16.27        84.49        19.76         7.17       153.86        16.64 
TCGA-CV-7438 TCGA-CV-7446 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
        6.38        35.93        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A6JD TCGA-CV-A6JE 
       48.20        60.43        67.86        56.61         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       19.92        22.52        10.55        18.84        51.12        13.25 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
        9.60        23.05        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       25.32        17.72        12.36         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5630 TCGA-DQ-5631 
       13.94        12.10        12.79        23.34        33.86        18.02 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       20.45        37.58        37.18        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 
        3.02        31.13        18.94        24.95        17.85        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       20.25        12.43        13.38        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-8224 TCGA-HD-8314 
       33.76        28.47        25.74        21.93        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 
        0.36        13.84         4.27         3.65         6.90        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
       33.57         5.29        13.68        13.84        19.04        15.48 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.27        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q6 
        6.25        15.42         7.13        16.08        17.98        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       75.55        18.97         2.04        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.07        23.15         7.30        21.47        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        19.73        12.89         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 
       17.82        15.32         8.32        16.96        15.91         7.10 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       13.71         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       20.75        22.36        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  HUWE1 MUTATED HUWE1 WILD-TYPE 
           0.46            0.07 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
          76.50          210.97 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
          24.44           20.55 
[1] "0.5 - 76.5 (24.4)"  "0.1 - 211.0 (20.6)"
[1] "hr=" "1.2"
D40V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  HUWE1 MUTATED         1        6         9        21         1         0
  HUWE1 WILD-TYPE      24       69        71       232        10         1
D40V3, multiclass
           clus
vv          HUWE1 MUTATED HUWE1 WILD-TYPE
  STAGE I               1              24
  STAGE II              6              69
  STAGE III             9              71
  STAGE IVA            21             232
  STAGE IVB             1              10
  STAGE IVC             0               1
[1] 6 2
[1] 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
  HUWE1 MUTATED       4  10   6  18
  HUWE1 WILD-TYPE    43 127  93 154
D40V4, multiclass
       clus
vv      HUWE1 MUTATED HUWE1 WILD-TYPE
  T0+T1             4              43
  T2               10             127
  T3                6              93
  T4               18             154
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HUWE1 MUTATED    17   6  11   1
  HUWE1 WILD-TYPE 158  61 157   6
D40V5, multiclass
    clus
vv   HUWE1 MUTATED HUWE1 WILD-TYPE
  N0            17             158
  N1             6              61
  N2            11             157
  N3             1               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"
D40V6, binary
                 cls
clus                0   1
  HUWE1 MUTATED    16   0
  HUWE1 WILD-TYPE 175   1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED     16    0
  HUWE1 WILD-TYPE  175    1
   clus
vv  HUWE1 MUTATED HUWE1 WILD-TYPE
  0            16             175
  1             0               1
[1] 2 2
[1] FALSE
D40V7, binary
                 cls
clus                0   1
  HUWE1 MUTATED    19  27
  HUWE1 WILD-TYPE 119 346
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED     19   27
  HUWE1 WILD-TYPE  119  346
        clus
vv       HUWE1 MUTATED HUWE1 WILD-TYPE
  FEMALE            19             119
  MALE              27             346
[1] 2 2
[1] FALSE
D40V8, binary
                 cls
clus                0   1
  HUWE1 MUTATED    14  25
  HUWE1 WILD-TYPE 143 268
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED     14   25
  HUWE1 WILD-TYPE  143  268
     clus
vv    HUWE1 MUTATED HUWE1 WILD-TYPE
  NO             14             143
  YES            25             268
[1] 2 2
[1] FALSE
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA
  HUWE1 MUTATED                                    45
  HUWE1 WILD-TYPE                                 455
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  HUWE1 MUTATED                                                   1
  HUWE1 WILD-TYPE                                                 9
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  HUWE1 MUTATED                                                           0
  HUWE1 WILD-TYPE                                                         1
D40V9, multiclass
                                                           clus
vv                                                          HUWE1 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  45
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             0
                                                           clus
vv                                                          HUWE1 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   455
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V10, continuous
D40V11, continuous
D40V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HUWE1 MUTATED                                  0     2
  HUWE1 WILD-TYPE                                2     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HUWE1 MUTATED                           0    41
  HUWE1 WILD-TYPE                        47   396
D40V13, multiclass
                                  clus
vv                                 HUWE1 MUTATED HUWE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        2               8
  BLACK OR AFRICAN AMERICAN                    0              47
  WHITE                                       41             396
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V14, binary
                 cls
clus                0   1
  HUWE1 MUTATED     4  40
  HUWE1 WILD-TYPE  21 409
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED      4   40
  HUWE1 WILD-TYPE   21  409
                        clus
vv                       HUWE1 MUTATED HUWE1 WILD-TYPE
  HISPANIC OR LATINO                 4              21
  NOT HISPANIC OR LATINO            40             409
[1] 2 2
[1] FALSE

Clustering(41) Variable = THSD7A MUTATION ANALYSIS
D41V1, survival
                  sevent
clus2                0   1
  THSD7A MUTATED    16  16
  THSD7A WILD-TYPE 273 204
  THSD7A MUTATED THSD7A WILD-TYPE 
              32              477 
  THSD7A MUTATED THSD7A WILD-TYPE 
              16              204 
$`THSD7A MUTATED`
TCGA-CN-6021 TCGA-BA-5149 TCGA-BB-A6UM TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-5360 
        9.07        26.50        12.92        14.33        73.61        71.31 
TCGA-CN-5373 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5326 
       52.08        35.01        25.41         7.40        12.39         2.93 
TCGA-CR-7367 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-7099 
       47.34        94.88        17.92         9.60        90.12         7.99 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7432 TCGA-CV-A45Z TCGA-CV-A6JN TCGA-CX-A4AQ 
       26.20        17.13        84.49        48.20        29.79        51.12 
TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-A74Q TCGA-F7-A624 TCGA-KU-A6H7 TCGA-MT-A67F 
       25.41        11.44        23.34        12.43        19.27        12.62 
TCGA-WA-A7GZ TCGA-KU-A66S 
       20.55        13.35 

$`THSD7A WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       30.18        25.71        51.29         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
        9.07        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       65.59        15.52        21.17        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       41.85        29.42        20.45        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       20.48        16.41         6.15       105.90         9.14         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
        4.41        18.38        66.28        71.05        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 
       27.19         8.81         6.28        12.69        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        4.67        56.68        12.89        26.86        32.81        52.14 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 
       55.56        57.11        12.99        20.55        45.83        27.58 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5361 
       13.05        42.02        46.32         8.58        12.39        69.70 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
        8.32        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
        8.52        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A499 
       32.22        38.89         3.68        17.42        11.74        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
       17.29        29.72        21.21        31.69        22.32        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       52.37        21.50        54.58        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 
       10.42        11.21         4.24        41.19        15.75        32.38 
TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       66.28        46.95        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       38.76        64.87        53.52        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       44.48        23.24        29.36        33.60        29.49        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       12.46        31.23        84.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
       26.27        58.42        50.01        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       16.90        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       12.46        22.78        15.75         9.27        47.18        39.16 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       40.93        35.84         3.45         3.09        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
        0.99        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       17.13        32.78        47.01        27.06        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       17.16       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 
      107.51        76.50        91.53        80.12        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
       21.07        62.43         2.14         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       65.82        10.98         7.13         8.42        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        4.14        64.83       172.67       111.16        18.81        12.66 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        9.01         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        89.65 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       36.00        31.36        18.97        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       47.97         2.10        49.71        18.41        57.47        35.54 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
      210.97        89.33         9.67         0.46        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
       25.94         0.07        34.09       100.57        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
      156.49         3.52        16.27        19.76         7.17       153.86 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O 
       16.64         6.38        22.19        35.93        30.48        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       21.01       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
       45.96         6.51        88.87        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       56.61         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6517 
       22.52        10.42        10.55        18.84        13.25         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
       23.05         2.53        16.14        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       13.94        12.10        12.79        58.45        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       18.02        20.45        37.58        41.59        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       21.63        20.25         3.02        31.13        18.94        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
        0.46        17.85        11.80        20.25        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.06        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        3.65         6.90        15.95        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        37.41         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.84        19.04        15.48        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
       30.05         1.84         6.25        15.42         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       17.98        29.92        15.78        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       36.82        47.01        19.00        75.55        18.97         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       29.00        12.99        16.01        13.15        21.07        21.21 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       23.15         7.30        21.47         9.34        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        19.73        12.89         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       17.82        15.32         8.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
       15.91         7.10        32.45        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.25        20.35        64.80        54.67         2.83        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.45        44.65        74.47        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       29.46        18.05        13.94        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66T 
       17.03        14.56        18.15 

  THSD7A MUTATED THSD7A WILD-TYPE 
            2.93             0.07 
  THSD7A MUTATED THSD7A WILD-TYPE 
           94.88           210.97 
  THSD7A MUTATED THSD7A WILD-TYPE 
          21.945           20.940 
[1] "2.9 - 94.9 (21.9)"  "0.1 - 211.0 (20.9)"
[1] "hr=" "1.1"
D41V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  THSD7A MUTATED         2        4         6        17         0         0
  THSD7A WILD-TYPE      23       71        74       236        11         1
D41V3, multiclass
           clus
vv          THSD7A MUTATED THSD7A WILD-TYPE
  STAGE I                2               23
  STAGE II               4               71
  STAGE III              6               74
  STAGE IVA             17              236
  STAGE IVB              0               11
  STAGE IVC              0                1
[1] 6 2
[1] 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
  THSD7A MUTATED       6   6   5  13
  THSD7A WILD-TYPE    41 131  94 159
D41V4, multiclass
       clus
vv      THSD7A MUTATED THSD7A WILD-TYPE
  T0+T1              6               41
  T2                 6              131
  T3                 5               94
  T4                13              159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  THSD7A MUTATED    13   5  10   0
  THSD7A WILD-TYPE 162  62 158   7
D41V5, multiclass
    clus
vv   THSD7A MUTATED THSD7A WILD-TYPE
  N0             13              162
  N1              5               62
  N2             10              158
  N3              0                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"
D41V6, binary
                  cls
clus                 0   1
  THSD7A MUTATED     9   0
  THSD7A WILD-TYPE 182   1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THSD7A MUTATED      9    0
  THSD7A WILD-TYPE  182    1
   clus
vv  THSD7A MUTATED THSD7A WILD-TYPE
  0              9              182
  1              0                1
[1] 2 2
[1] FALSE
D41V7, binary
                  cls
clus                 0   1
  THSD7A MUTATED    11  21
  THSD7A WILD-TYPE 127 352
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THSD7A MUTATED     11   21
  THSD7A WILD-TYPE  127  352
        clus
vv       THSD7A MUTATED THSD7A WILD-TYPE
  FEMALE             11              127
  MALE               21              352
[1] 2 2
[1] FALSE
D41V8, binary
                  cls
clus                 0   1
  THSD7A MUTATED     7  21
  THSD7A WILD-TYPE 150 272
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THSD7A MUTATED      7   21
  THSD7A WILD-TYPE  150  272
     clus
vv    THSD7A MUTATED THSD7A WILD-TYPE
  NO               7              150
  YES             21              272
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  THSD7A MUTATED                                    31
  THSD7A WILD-TYPE                                 469
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  THSD7A MUTATED                                                   1
  THSD7A WILD-TYPE                                                 9
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  THSD7A MUTATED                                                           0
  THSD7A WILD-TYPE                                                         1
D41V9, multiclass
                                                           clus
vv                                                          THSD7A MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   31
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          THSD7A WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    469
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, continuous
D41V11, continuous
D41V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  THSD7A MUTATED                                  0     0
  THSD7A WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  THSD7A MUTATED                           1    30
  THSD7A WILD-TYPE                        46   407
D41V13, multiclass
                                  clus
vv                                 THSD7A MUTATED THSD7A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               46
  WHITE                                        30              407
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V14, binary
                  cls
clus                 0   1
  THSD7A MUTATED     2  29
  THSD7A WILD-TYPE  23 420
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THSD7A MUTATED      2   29
  THSD7A WILD-TYPE   23  420
                        clus
vv                       THSD7A MUTATED THSD7A WILD-TYPE
  HISPANIC OR LATINO                  2               23
  NOT HISPANIC OR LATINO             29              420
[1] 2 2
[1] FALSE

Clustering(42) Variable = C3ORF59 MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  C3ORF59 MUTATED     6   4
  C3ORF59 WILD-TYPE 283 216
  C3ORF59 MUTATED C3ORF59 WILD-TYPE 
               10               499 
  C3ORF59 MUTATED C3ORF59 WILD-TYPE 
                4               216 
$`C3ORF59 MUTATED`
TCGA-CN-A6V3 TCGA-CR-7367 TCGA-CR-7371 TCGA-CR-7386 TCGA-CV-7406 TCGA-CV-7422 
       24.39        47.34         3.09        47.01        57.47        34.09 
TCGA-CV-A6JN TCGA-CV-A6K2 TCGA-F7-A624 TCGA-HD-A4C1 
       29.79        10.42        12.43         0.36 

$`C3ORF59 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-6221 
       11.08        35.05        32.48        19.82        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       23.84        65.59        15.52        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 
        4.80         4.41        18.38        66.28        71.05        20.52 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       10.55        27.19        12.92         8.81         6.28        12.69 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       55.86        38.04         4.67        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       32.81        52.14        55.56        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       46.32         8.58        12.39        71.31        69.70         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       16.21        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       32.22        38.89         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       25.41        23.57        17.29        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 
       11.21         4.24        41.19        15.75        32.38        66.28 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       58.42        50.01        39.52        36.99        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 
       22.78        15.75         9.27        47.18        39.16        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
       35.84         3.45        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       29.95        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       76.24        19.20        17.95       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        2.50         4.14        64.83       172.67       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 
       12.66         7.99         9.01         5.26         1.84        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
       12.92        21.80        71.21        10.75       130.88        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
        4.73        89.65        36.00        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       17.13        95.34         4.96        11.87        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       49.71        18.41        35.54       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7423 
        0.46        22.85        25.08        25.94         0.07       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       14.89        56.48       156.49         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       19.76         7.17       153.86        16.64         6.38        22.19 
TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       35.93        30.48        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       48.20        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT 
       15.25         5.98        35.34         6.38         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7085 
        3.62        21.24        23.47        19.92        22.52        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        51.12        13.25        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
        2.53        16.14        11.44        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 
       33.86        18.02        20.45        37.58        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-7774 
       24.95         0.46        17.85        11.80        20.25        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A633 TCGA-HD-A634 
       21.93        27.48        14.66        22.03        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        3.65         6.90        15.95        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        37.41         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       13.84        19.04        15.48        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       18.97         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        27.39        21.07        19.73        12.89         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       16.96         6.87        15.91         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        3.12        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        2.83        49.51        49.45        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  C3ORF59 MUTATED C3ORF59 WILD-TYPE 
             0.36              0.07 
  C3ORF59 MUTATED C3ORF59 WILD-TYPE 
            57.47            210.97 
  C3ORF59 MUTATED C3ORF59 WILD-TYPE 
            27.09             20.88 
[1] "0.4 - 57.5 (27.1)"  "0.1 - 211.0 (20.9)"
[1] "hr=" "1"  
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  C3ORF59 MUTATED         0        2         1         6         0         0
  C3ORF59 WILD-TYPE      25       73        79       247        11         1
D42V3, multiclass
           clus
vv          C3ORF59 MUTATED C3ORF59 WILD-TYPE
  STAGE I                 0                25
  STAGE II                2                73
  STAGE III               1                79
  STAGE IVA               6               247
  STAGE IVB               0                11
  STAGE IVC               0                 1
[1] 6 2
[1] 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
  C3ORF59 MUTATED       0   2   2   5
  C3ORF59 WILD-TYPE    47 135  97 167
D42V4, multiclass
       clus
vv      C3ORF59 MUTATED C3ORF59 WILD-TYPE
  T0+T1               0                47
  T2                  2               135
  T3                  2                97
  T4                  5               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C3ORF59 MUTATED     2   3   3   0
  C3ORF59 WILD-TYPE 173  64 165   7
D42V5, multiclass
    clus
vv   C3ORF59 MUTATED C3ORF59 WILD-TYPE
  N0               2               173
  N1               3                64
  N2               3               165
  N3               0                 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
  C3ORF59 MUTATED     6   0
  C3ORF59 WILD-TYPE 185   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF59 MUTATED      6    0
  C3ORF59 WILD-TYPE  185    1
   clus
vv  C3ORF59 MUTATED C3ORF59 WILD-TYPE
  0               6               185
  1               0                 1
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  C3ORF59 MUTATED     3   7
  C3ORF59 WILD-TYPE 135 366
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF59 MUTATED      3    7
  C3ORF59 WILD-TYPE  135  366
        clus
vv       C3ORF59 MUTATED C3ORF59 WILD-TYPE
  FEMALE               3               135
  MALE                 7               366
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  C3ORF59 MUTATED     1   7
  C3ORF59 WILD-TYPE 156 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF59 MUTATED      1    7
  C3ORF59 WILD-TYPE  156  286
     clus
vv    C3ORF59 MUTATED C3ORF59 WILD-TYPE
  NO                1               156
  YES               7               286
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  C3ORF59 MUTATED                                    10
  C3ORF59 WILD-TYPE                                 490
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  C3ORF59 MUTATED                                                   0
  C3ORF59 WILD-TYPE                                                10
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  C3ORF59 MUTATED                                                           0
  C3ORF59 WILD-TYPE                                                         1
D42V9, multiclass
                                                           clus
vv                                                          C3ORF59 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    10
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          C3ORF59 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     490
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V10, continuous
D42V11, continuous
D42V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C3ORF59 MUTATED                                  0     0
  C3ORF59 WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C3ORF59 MUTATED                           1     9
  C3ORF59 WILD-TYPE                        46   428
D42V13, multiclass
                                  clus
vv                                 C3ORF59 MUTATED C3ORF59 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                46
  WHITE                                          9               428
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V14, binary
                   cls
clus                  0   1
  C3ORF59 MUTATED     0  10
  C3ORF59 WILD-TYPE  25 439
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF59 MUTATED      0   10
  C3ORF59 WILD-TYPE   25  439
                        clus
vv                       C3ORF59 MUTATED C3ORF59 WILD-TYPE
  HISPANIC OR LATINO                   0                25
  NOT HISPANIC OR LATINO              10               439
[1] 2 2
[1] FALSE

Clustering(43) Variable = DYSF MUTATION ANALYSIS
D43V1, survival
                sevent
clus2              0   1
  DYSF MUTATED    11   9
  DYSF WILD-TYPE 278 211
  DYSF MUTATED DYSF WILD-TYPE 
            20            489 
  DYSF MUTATED DYSF WILD-TYPE 
             9            211 
$`DYSF MUTATED`
TCGA-CN-4727 TCGA-BA-6869 TCGA-BA-A6DA TCGA-BA-A6DF TCGA-BB-7870 TCGA-CN-6016 
       51.29        21.17        11.54         7.82        66.28        47.44 
TCGA-CN-6995 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6228 TCGA-CR-7364 TCGA-CR-7398 
        3.68        10.42        11.21        14.99        47.18         5.13 
TCGA-CR-7402 TCGA-CV-7242 TCGA-CV-A45U TCGA-CV-A461 TCGA-CV-A6JT TCGA-D6-6516 
       29.95        36.00        35.47        67.86        28.01        25.41 
TCGA-IQ-A61I TCGA-UF-A7JT 
        0.07        32.65 

$`DYSF WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       30.18        25.71         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       23.84        65.59        15.52        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD 
       41.85        29.42        20.45        27.95         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
       14.47         2.27        11.05        13.38        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15       105.90         9.14         4.80         4.41        18.38 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       71.05        20.52        10.55        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
        6.28        12.69        55.86        38.04         4.67        56.68 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.81        52.14        55.56        57.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        42.02        46.32         8.58        12.39        71.31 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       69.70         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
       12.49         8.52        52.08        56.94        50.07        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       48.00        23.90        28.04        19.07        34.13         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       10.45        32.22        38.89        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       25.41        23.57        17.29        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5334 
        2.93        54.58        70.45        62.37        45.99         4.24 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       41.19        15.75        32.38        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
       13.25         4.24        38.76        64.87        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        77.56        44.48        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.49        14.14        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       39.16        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 
       30.58        24.79         5.95        35.41        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       17.16       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       140.78        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       15.09        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
        7.13         8.42        28.34         2.50         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      172.67       111.16        18.81        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        5.26         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 
       10.75       130.88        77.16         4.73        89.65        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       47.97         2.10        49.71        18.41        57.47        35.54 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
      210.97        89.33         9.67         0.46        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
       25.94         0.07        34.09       100.57        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
      156.49         3.52        16.27        84.49        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 
      153.86        16.64         6.38        22.19        35.93        30.48 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V 
       27.98        21.01       169.38       180.16       159.65         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 
       45.96         6.51        88.87        48.20        60.43         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       56.61         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
       29.79         6.48         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        13.25 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        37.25        33.86        18.02        20.45        37.58 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       31.13        18.94        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       20.25        12.43        13.38        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
       33.76        28.47        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         0.36        13.84         4.27         3.65         6.90 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
       33.57         5.29        13.68        13.84        19.04        15.48 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.27        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         6.25        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        71.74        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        21.47         9.34        12.72        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       19.73        12.89         5.62        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       15.32         8.32        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ 
        7.10        32.45        13.71         3.12        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       20.35        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ 
       18.05        13.94        20.75        22.36        17.03        20.55 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  DYSF MUTATED DYSF WILD-TYPE 
          0.07           0.07 
  DYSF MUTATED DYSF WILD-TYPE 
         67.86         210.97 
  DYSF MUTATED DYSF WILD-TYPE 
         26.71          20.75 
[1] "0.1 - 67.9 (26.7)"  "0.1 - 211.0 (20.8)"
[1] "hr=" "1.1"
D43V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  DYSF MUTATED         1        4         3        10         0         0
  DYSF WILD-TYPE      24       71        77       243        11         1
D43V3, multiclass
           clus
vv          DYSF MUTATED DYSF WILD-TYPE
  STAGE I              1             24
  STAGE II             4             71
  STAGE III            3             77
  STAGE IVA           10            243
  STAGE IVB            0             11
  STAGE IVC            0              1
[1] 6 2
[1] 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
  DYSF MUTATED       3   4   3   8
  DYSF WILD-TYPE    44 133  96 164
D43V4, multiclass
       clus
vv      DYSF MUTATED DYSF WILD-TYPE
  T0+T1            3             44
  T2               4            133
  T3               3             96
  T4               8            164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  DYSF MUTATED    13   1   4   0
  DYSF WILD-TYPE 162  66 164   7
D43V5, multiclass
    clus
vv   DYSF MUTATED DYSF WILD-TYPE
  N0           13            162
  N1            1             66
  N2            4            164
  N3            0              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
  DYSF MUTATED     7   0
  DYSF WILD-TYPE 184   1
[1] "tbl2"
                cls
clus             [,1] [,2]
  DYSF MUTATED      7    0
  DYSF WILD-TYPE  184    1
   clus
vv  DYSF MUTATED DYSF WILD-TYPE
  0            7            184
  1            0              1
[1] 2 2
[1] FALSE
D43V7, binary
                cls
clus               0   1
  DYSF MUTATED     6  14
  DYSF WILD-TYPE 132 359
[1] "tbl2"
                cls
clus             [,1] [,2]
  DYSF MUTATED      6   14
  DYSF WILD-TYPE  132  359
        clus
vv       DYSF MUTATED DYSF WILD-TYPE
  FEMALE            6            132
  MALE             14            359
[1] 2 2
[1] FALSE
D43V8, binary
                cls
clus               0   1
  DYSF MUTATED     6  12
  DYSF WILD-TYPE 151 281
[1] "tbl2"
                cls
clus             [,1] [,2]
  DYSF MUTATED      6   12
  DYSF WILD-TYPE  151  281
     clus
vv    DYSF MUTATED DYSF WILD-TYPE
  NO             6            151
  YES           12            281
[1] 2 2
[1] FALSE
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA
  DYSF MUTATED                                    20
  DYSF WILD-TYPE                                 480
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DYSF MUTATED                                                   0
  DYSF WILD-TYPE                                                10
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DYSF MUTATED                                                           0
  DYSF WILD-TYPE                                                         1
D43V9, multiclass
                                                           clus
vv                                                          DYSF MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                 20
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT            0
                                                           clus
vv                                                          DYSF WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  480
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, continuous
D43V11, continuous
D43V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DYSF MUTATED                                  0     0
  DYSF WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DYSF MUTATED                           1    19
  DYSF WILD-TYPE                        46   418
D43V13, multiclass
                                  clus
vv                                 DYSF MUTATED DYSF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             46
  WHITE                                      19            418
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V14, binary
                cls
clus               0   1
  DYSF MUTATED     0  19
  DYSF WILD-TYPE  25 430
[1] "tbl2"
                cls
clus             [,1] [,2]
  DYSF MUTATED      0   19
  DYSF WILD-TYPE   25  430
                        clus
vv                       DYSF MUTATED DYSF WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO           19            430
[1] 2 2
[1] FALSE

Clustering(44) Variable = ZNF233 MUTATION ANALYSIS
D44V1, survival
                  sevent
clus2                0   1
  ZNF233 MUTATED     2   7
  ZNF233 WILD-TYPE 287 213
  ZNF233 MUTATED ZNF233 WILD-TYPE 
               9              500 
  ZNF233 MUTATED ZNF233 WILD-TYPE 
               7              213 
$`ZNF233 MUTATED`
TCGA-BA-A4IG TCGA-CN-A63V TCGA-CQ-5334 TCGA-CR-7388 TCGA-CV-5434 TCGA-CV-5435 
       28.11        22.32         4.24        27.06       108.95        76.24 
TCGA-CV-6936 TCGA-CV-7446 TCGA-CV-7568 
        5.46        35.93        30.48 

$`ZNF233 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4II 
        9.30        37.28        20.48        68.48         3.55        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       23.84        65.59        15.52        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 
        4.80         4.41        18.38        66.28        71.05        20.52 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       10.55        27.19        12.92         8.81         6.28        12.69 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       55.86        38.04         4.67        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       32.81        52.14        55.56        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       46.32         8.58        12.39        71.31        69.70         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       16.21        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       32.22        38.89         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       25.41        23.57        17.29        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       31.69        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       23.44        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       41.19        15.75        32.38        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       11.34        11.64         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       47.01        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5436 
       29.95        48.39       139.43        17.16       129.21        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       17.95       107.51        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        7.07        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
       90.12         2.14         9.70        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       140.78        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       15.09        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
        7.13         8.42        28.34         2.50         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      172.67       111.16        18.81        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        5.26         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       10.75       130.88        77.16         4.73        89.65        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       31.36        26.20        18.97        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
       11.87        47.97         2.10        49.71        18.41        57.47 
TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       35.54       210.97        89.33         9.67         0.46        22.85 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 
       25.08        25.94         0.07        34.09       100.57        14.89 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       56.48       156.49         3.52        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
        7.17       153.86        16.64         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       21.01       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
       45.96         6.51        88.87        48.20        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        0.76        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       23.47        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       16.14        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       12.36        28.77         7.63        22.59        24.95        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       12.10        12.79        23.34        58.45        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       18.02        20.45        37.58        41.59        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       21.63        20.25         3.02        31.13        18.94        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
        0.46        17.85        11.80        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       21.93        27.48        14.66        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65         6.90        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        27.39        21.07        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.72        16.96         6.87        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       13.71         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  ZNF233 MUTATED ZNF233 WILD-TYPE 
            4.24             0.07 
  ZNF233 MUTATED ZNF233 WILD-TYPE 
          108.95           210.97 
  ZNF233 MUTATED ZNF233 WILD-TYPE 
           28.11            20.65 
[1] "4.2 - 109.0 (28.1)" "0.1 - 211.0 (20.6)"
[1] "hr=" "1.5"
D44V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  ZNF233 MUTATED         0        0         0         7         0         0
  ZNF233 WILD-TYPE      25       75        80       246        11         1
D44V3, multiclass
           clus
vv          ZNF233 MUTATED ZNF233 WILD-TYPE
  STAGE I                0               25
  STAGE II               0               75
  STAGE III              0               80
  STAGE IVA              7              246
  STAGE IVB              0               11
  STAGE IVC              0                1
[1] 6 2
[1] 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
  ZNF233 MUTATED       1   1   1   5
  ZNF233 WILD-TYPE    46 136  98 167
D44V4, multiclass
       clus
vv      ZNF233 MUTATED ZNF233 WILD-TYPE
  T0+T1              1               46
  T2                 1              136
  T3                 1               98
  T4                 5              167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF233 MUTATED     1   0   5   0
  ZNF233 WILD-TYPE 174  67 163   7
D44V5, multiclass
    clus
vv   ZNF233 MUTATED ZNF233 WILD-TYPE
  N0              1              174
  N1              0               67
  N2              5              163
  N3              0                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"
D44V6, binary
                  cls
clus                 0   1
  ZNF233 MUTATED     0   0
  ZNF233 WILD-TYPE 191   1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF233 MUTATED      0    0
  ZNF233 WILD-TYPE  191    1
D44V7, binary
                  cls
clus                 0   1
  ZNF233 MUTATED     2   7
  ZNF233 WILD-TYPE 136 366
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF233 MUTATED      2    7
  ZNF233 WILD-TYPE  136  366
        clus
vv       ZNF233 MUTATED ZNF233 WILD-TYPE
  FEMALE              2              136
  MALE                7              366
[1] 2 2
[1] FALSE
D44V8, binary
                  cls
clus                 0   1
  ZNF233 MUTATED     2   5
  ZNF233 WILD-TYPE 155 288
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF233 MUTATED      2    5
  ZNF233 WILD-TYPE  155  288
     clus
vv    ZNF233 MUTATED ZNF233 WILD-TYPE
  NO               2              155
  YES              5              288
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  ZNF233 MUTATED                                     9
  ZNF233 WILD-TYPE                                 491
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  ZNF233 MUTATED                                                   0
  ZNF233 WILD-TYPE                                                10
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  ZNF233 MUTATED                                                           0
  ZNF233 WILD-TYPE                                                         1
D44V9, multiclass
                                                           clus
vv                                                          ZNF233 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    9
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          ZNF233 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    491
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V10, continuous
D44V11, continuous
D44V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF233 MUTATED                                  0     0
  ZNF233 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF233 MUTATED                           1     8
  ZNF233 WILD-TYPE                        46   429
D44V13, multiclass
                                  clus
vv                                 ZNF233 MUTATED ZNF233 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               46
  WHITE                                         8              429
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V14, binary
                  cls
clus                 0   1
  ZNF233 MUTATED     0   9
  ZNF233 WILD-TYPE  25 440
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF233 MUTATED      0    9
  ZNF233 WILD-TYPE   25  440
                        clus
vv                       ZNF233 MUTATED ZNF233 WILD-TYPE
  HISPANIC OR LATINO                  0               25
  NOT HISPANIC OR LATINO              9              440
[1] 2 2
[1] FALSE

Clustering(45) Variable = KIAA1267 MUTATION ANALYSIS
D45V1, survival
                    sevent
clus2                  0   1
  KIAA1267 MUTATED     7   4
  KIAA1267 WILD-TYPE 282 216
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                11                498 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                 4                216 
$`KIAA1267 MUTATED`
TCGA-CR-6472 TCGA-BA-5556 TCGA-CR-7373 TCGA-CR-7379 TCGA-CV-6962 TCGA-CV-7261 
       34.52        23.84        29.23        34.06         4.14        49.71 
TCGA-CV-A45Q TCGA-CV-A45V TCGA-CV-A468 TCGA-D6-8568 TCGA-F7-A624 
      169.38         1.05        15.25        24.95        12.43 

$`KIAA1267 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 
       32.88        70.13        43.04        11.61         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       65.59        15.52        21.17        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       41.85        29.42        20.45        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       20.48        16.41         6.15       105.90         9.14         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
        4.41        18.38        66.28        71.05        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 
       27.19        12.92         8.81         6.28        12.69        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       52.14        55.56        57.11        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       45.83        27.58        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 
        8.58        12.39        71.31        69.70         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       56.94        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       28.04        19.07        34.13         6.74        10.45        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       38.89         3.68        17.42        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       23.57        17.29        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       23.44        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 
        4.24        41.19        15.75        32.38        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       56.58        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       53.52        41.88        43.10        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       15.75         9.27        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 
       35.84         3.45         3.09        24.95         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
        9.17        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       29.95        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       76.24        19.20        17.95       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        2.50        64.83       172.67       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       89.65        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 
       95.34         4.96        11.87        47.97         2.10        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       57.47        35.54       210.97        89.33         9.67         0.46 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
       22.85        25.08        25.94         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       14.89        56.48       156.49         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       19.76         7.17       153.86        16.64         6.38        22.19 
TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T 
       35.93        30.48        27.98        21.01       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
       35.47        45.96         6.51        88.87        48.20        60.43 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A6JD TCGA-CV-A6JE 
       67.86         0.76        56.61         7.07         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       23.47        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       16.14        11.44        18.67        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       28.77         7.63        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        23.34        58.45        37.25        33.86        18.02 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       20.45        37.58        41.59        37.18        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       17.85        11.80        20.25        13.38        15.16        15.06 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       20.94        33.76        28.47        25.74        21.93        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       14.66        22.03         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        6.90        15.95        38.53        14.50        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       37.41         0.07        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       19.04        15.48        19.27        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       30.05         1.84        12.62         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
       16.08        17.98        29.92        15.78        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       10.85        36.82        47.01        19.00        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
        2.04        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.21        23.15         7.30        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       27.39        21.07        19.73        12.89         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        6.87        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       32.65        17.03        20.55        14.56        13.35        18.15 

  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
              1.05               0.07 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
            169.38             210.97 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
            24.950             20.815 
[1] "1.1 - 169.4 (24.9)" "0.1 - 211.0 (20.8)"
[1] "hr=" "1.5"
D45V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  KIAA1267 MUTATED         0        3         0         6         0         0
  KIAA1267 WILD-TYPE      25       72        80       247        11         1
D45V3, multiclass
           clus
vv          KIAA1267 MUTATED KIAA1267 WILD-TYPE
  STAGE I                  0                 25
  STAGE II                 3                 72
  STAGE III                0                 80
  STAGE IVA                6                247
  STAGE IVB                0                 11
  STAGE IVC                0                  1
[1] 6 2
[1] 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       0   3   0   6
  KIAA1267 WILD-TYPE    47 134  99 166
D45V4, multiclass
       clus
vv      KIAA1267 MUTATED KIAA1267 WILD-TYPE
  T0+T1                0                 47
  T2                   3                134
  T3                   0                 99
  T4                   6                166
[1] 4 2
[1] TRUE
[1] "dimension of 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     4   1   2   0
  KIAA1267 WILD-TYPE 171  66 166   7
D45V5, multiclass
    clus
vv   KIAA1267 MUTATED KIAA1267 WILD-TYPE
  N0                4                171
  N1                1                 66
  N2                2                166
  N3                0                  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"
D45V6, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED     6   0
  KIAA1267 WILD-TYPE 185   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED      6    0
  KIAA1267 WILD-TYPE  185    1
   clus
vv  KIAA1267 MUTATED KIAA1267 WILD-TYPE
  0                6                185
  1                0                  1
[1] 2 2
[1] FALSE
D45V7, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED     4   7
  KIAA1267 WILD-TYPE 134 366
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED      4    7
  KIAA1267 WILD-TYPE  134  366
        clus
vv       KIAA1267 MUTATED KIAA1267 WILD-TYPE
  FEMALE                4                134
  MALE                  7                366
[1] 2 2
[1] FALSE
D45V8, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED     3   8
  KIAA1267 WILD-TYPE 154 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED      3    8
  KIAA1267 WILD-TYPE  154  285
     clus
vv    KIAA1267 MUTATED KIAA1267 WILD-TYPE
  NO                 3                154
  YES                8                285
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  KIAA1267 MUTATED                                    11
  KIAA1267 WILD-TYPE                                 489
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  KIAA1267 MUTATED                                                   0
  KIAA1267 WILD-TYPE                                                10
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  KIAA1267 MUTATED                                                           0
  KIAA1267 WILD-TYPE                                                         1
D45V9, multiclass
                                                           clus
vv                                                          KIAA1267 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     11
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          KIAA1267 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      489
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, continuous
D45V11, continuous
D45V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1267 MUTATED                                  0     0
  KIAA1267 WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1267 MUTATED                           0    10
  KIAA1267 WILD-TYPE                        47   427
D45V13, multiclass
                                  clus
vv                                 KIAA1267 MUTATED KIAA1267 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 47
  WHITE                                          10                427
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V14, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED     2   9
  KIAA1267 WILD-TYPE  23 440
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED      2    9
  KIAA1267 WILD-TYPE   23  440
                        clus
vv                       KIAA1267 MUTATED KIAA1267 WILD-TYPE
  HISPANIC OR LATINO                    2                 23
  NOT HISPANIC OR LATINO                9                440
[1] 2 2
[1] FALSE

Clustering(46) Variable = ASXL1 MUTATION ANALYSIS
D46V1, survival
                 sevent
clus2               0   1
  ASXL1 MUTATED     6  10
  ASXL1 WILD-TYPE 283 210
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             16             493 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             10             210 
$`ASXL1 MUTATED`
TCGA-BA-A6D8 TCGA-CN-A498 TCGA-CR-7388 TCGA-CV-5439 TCGA-CV-5978 TCGA-CV-7089 
       27.95        25.41        27.06        17.95         7.07        64.83 
TCGA-CV-7177 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-A45U TCGA-CV-A6JY TCGA-D6-A6ES 
       21.80        84.49        19.76        35.47        21.24        12.79 
TCGA-DQ-5631 TCGA-DQ-7596 TCGA-HD-7832 TCGA-MT-A67F 
       18.02        41.59        27.48        12.62 

$`ASXL1 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6DA 
       12.62         4.01        41.85        29.42        20.45        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 
        4.80         4.41        18.38        66.28        71.05        20.52 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       10.55        27.19        12.92         8.81         6.28        12.69 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       55.86        38.04         4.67        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       32.81        52.14        55.56        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       46.32         8.58        12.39        71.31        69.70         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       16.21        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       32.22        38.89         3.68        17.42        11.74        35.01 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       23.57        17.29        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       23.44        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 
        4.24        41.19        15.75        32.38        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       56.58        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       53.52        41.88        43.10        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       15.75         9.27        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       32.78        47.01        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
      108.95        76.24        19.20       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       48.59        60.49        43.23        54.74        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
        9.60        90.12         2.14         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       65.82        10.98         7.13         8.42        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        4.14       172.67       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7178 
        9.01         5.26         1.84        52.31        12.92        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       10.75       130.88        77.16         4.73        89.65        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       31.36        26.20        18.97        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
       11.87        47.97         2.10        49.71        18.41        57.47 
TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       35.54       210.97        89.33         9.67         0.46        22.85 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 
       25.08        25.94         0.07        34.09       100.57        14.89 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7434 TCGA-CV-7435 
       56.48       156.49         3.52        16.27         7.17       153.86 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O 
       16.64         6.38        22.19        35.93        30.48        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W 
       21.01       169.38       180.16       159.65         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       56.61         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 
       29.79         6.48        28.01         3.62        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q 
        7.63        22.59        24.95        13.94        12.10        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 
       58.45        37.25        33.86        20.45        37.58        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       24.95         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       13.38        15.16        15.06        20.94        33.76        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       25.74        21.93        14.66        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65         6.90        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN 
       14.37         7.96        30.05         1.84         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       18.97         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        27.39        21.07        19.73        12.89         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       16.96         6.87        15.91         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        3.12        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        2.83        49.51        49.45        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  ASXL1 MUTATED ASXL1 WILD-TYPE 
           7.07            0.07 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
          84.49          210.97 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
         23.605          20.750 
[1] "7.1 - 84.5 (23.6)"  "0.1 - 211.0 (20.8)"
[1] "hr=" "1.4"
D46V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  ASXL1 MUTATED         0        2         1         9         1         0
  ASXL1 WILD-TYPE      25       73        79       244        10         1
D46V3, multiclass
           clus
vv          ASXL1 MUTATED ASXL1 WILD-TYPE
  STAGE I               0              25
  STAGE II              2              73
  STAGE III             1              79
  STAGE IVA             9             244
  STAGE IVB             1              10
  STAGE IVC             0               1
[1] 6 2
[1] 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
  ASXL1 MUTATED       0   2   2   9
  ASXL1 WILD-TYPE    47 135  97 163
D46V4, multiclass
       clus
vv      ASXL1 MUTATED ASXL1 WILD-TYPE
  T0+T1             0              47
  T2                2             135
  T3                2              97
  T4                9             163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ASXL1 MUTATED     6   0   5   1
  ASXL1 WILD-TYPE 169  67 163   6
D46V5, multiclass
    clus
vv   ASXL1 MUTATED ASXL1 WILD-TYPE
  N0             6             169
  N1             0              67
  N2             5             163
  N3             1               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"
D46V6, binary
                 cls
clus                0   1
  ASXL1 MUTATED     4   0
  ASXL1 WILD-TYPE 187   1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED      4    0
  ASXL1 WILD-TYPE  187    1
   clus
vv  ASXL1 MUTATED ASXL1 WILD-TYPE
  0             4             187
  1             0               1
[1] 2 2
[1] FALSE
D46V7, binary
                 cls
clus                0   1
  ASXL1 MUTATED     5  11
  ASXL1 WILD-TYPE 133 362
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED      5   11
  ASXL1 WILD-TYPE  133  362
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  FEMALE             5             133
  MALE              11             362
[1] 2 2
[1] FALSE
D46V8, binary
                 cls
clus                0   1
  ASXL1 MUTATED     0  13
  ASXL1 WILD-TYPE 157 280
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED      0   13
  ASXL1 WILD-TYPE  157  280
     clus
vv    ASXL1 MUTATED ASXL1 WILD-TYPE
  NO              0             157
  YES            13             280
[1] 2 2
[1] FALSE
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA
  ASXL1 MUTATED                                    16
  ASXL1 WILD-TYPE                                 484
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  ASXL1 MUTATED                                                   0
  ASXL1 WILD-TYPE                                                10
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  ASXL1 MUTATED                                                           0
  ASXL1 WILD-TYPE                                                         1
D46V9, multiclass
                                                           clus
vv                                                          ASXL1 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  16
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             0
                                                           clus
vv                                                          ASXL1 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   484
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V10, continuous
D46V11, continuous
D46V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASXL1 MUTATED                                  0     0
  ASXL1 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ASXL1 MUTATED                           2    14
  ASXL1 WILD-TYPE                        45   423
D46V13, multiclass
                                  clus
vv                                 ASXL1 MUTATED ASXL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              45
  WHITE                                       14             423
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V14, binary
                 cls
clus                0   1
  ASXL1 MUTATED     0  15
  ASXL1 WILD-TYPE  25 434
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED      0   15
  ASXL1 WILD-TYPE   25  434
                        clus
vv                       ASXL1 MUTATED ASXL1 WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO            15             434
[1] 2 2
[1] FALSE

Clustering(47) Variable = SMAD4 MUTATION ANALYSIS
D47V1, survival
                 sevent
clus2               0   1
  SMAD4 MUTATED     6   7
  SMAD4 WILD-TYPE 283 213
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             13             496 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              7             213 
$`SMAD4 MUTATED`
TCGA-CN-A6V1 TCGA-HD-8635 TCGA-BA-5555 TCGA-BB-A6UO TCGA-CN-4723 TCGA-CN-5364 
       19.82        22.85        17.10         8.81        55.86        16.21 
TCGA-CQ-6222 TCGA-CR-7365 TCGA-CV-7097 TCGA-CV-7406 TCGA-P3-A6T5 TCGA-P3-A6T7 
       66.28        39.16        12.66        57.47        29.00        16.01 
TCGA-UF-A7JC 
       17.95 

$`SMAD4 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       11.08        35.05        32.48        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       48.03         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 
       26.50        23.74        42.35        57.93        23.84        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       15.52        21.17        14.83        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.80         4.41 
TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ 
       18.38        66.28        71.05        20.52        10.55        27.19 
TCGA-BB-A6UM TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
       12.92         6.28        12.69        38.04         4.67        56.68 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.81        52.14        55.56        57.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        42.02        46.32         8.58        12.39        71.31 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
       69.70         8.32        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        8.52        52.08        56.94        50.07        30.67        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       23.90        47.44        28.04        19.07        34.13         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       10.45        32.22        38.89         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        31.69        22.32        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
       12.07         2.70        23.44        20.88        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 
       10.42        11.21         4.24        41.19        15.75        32.38 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       58.42        50.01        39.52        36.99        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
       22.78        15.75         9.27        47.18        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58        24.79         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        5.95        35.41        29.95        48.39       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
      129.21       108.95        76.24        19.20        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       54.74        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        9.70         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       140.78        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        8.42        28.34         2.50         4.14        64.83       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
      111.16        18.81         7.99         9.01         5.26         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
       52.31        12.92        21.80        71.21        10.75       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       77.16         4.73        89.65        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       18.97        17.13        95.34         4.96        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 
        2.10        49.71        18.41        35.54       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
        9.67         0.46        22.85        25.08        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 
       34.09       100.57        14.89        56.48       156.49         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 
       16.27        84.49        19.76         7.17       153.86        16.64 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P 
        6.38        22.19        35.93        30.48        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
      169.38       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       56.61         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       28.77         7.63        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        23.34        58.45        37.25        33.86        18.02 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       20.45        37.58        41.59        37.18        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       17.85        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.06        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        3.65         6.90        15.95        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        37.41         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       13.84        19.04        15.48        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       18.97         2.04        12.99        13.15        21.07        21.21 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       23.15         7.30        21.47         9.34        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        19.73        12.89         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       17.82        15.32         8.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
       15.91         7.10        32.45        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.25        20.35        64.80        54.67         2.83        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       49.45        44.65        74.47        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       18.05        13.94        20.75        22.36        32.65        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.55        14.56        13.35        18.15 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
           8.81            0.07 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          66.28          210.97 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
         19.820          20.975 
[1] "8.8 - 66.3 (19.8)"  "0.1 - 211.0 (21.0)"
[1] "hr=" "1.2"
D47V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  SMAD4 MUTATED         0        2         1        10         0         0
  SMAD4 WILD-TYPE      25       73        79       243        11         1
D47V3, multiclass
           clus
vv          SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE I               0              25
  STAGE II              2              73
  STAGE III             1              79
  STAGE IVA            10             243
  STAGE IVB             0              11
  STAGE IVC             0               1
[1] 6 2
[1] 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
  SMAD4 MUTATED       1   4   3   5
  SMAD4 WILD-TYPE    46 133  96 167
D47V4, multiclass
       clus
vv      SMAD4 MUTATED SMAD4 WILD-TYPE
  T0+T1             1              46
  T2                4             133
  T3                3              96
  T4                5             167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SMAD4 MUTATED     4   1   7   0
  SMAD4 WILD-TYPE 171  66 161   7
D47V5, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  N0             4             171
  N1             1              66
  N2             7             161
  N3             0               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
  SMAD4 MUTATED     3   0
  SMAD4 WILD-TYPE 188   1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      3    0
  SMAD4 WILD-TYPE  188    1
   clus
vv  SMAD4 MUTATED SMAD4 WILD-TYPE
  0             3             188
  1             0               1
[1] 2 2
[1] FALSE
D47V7, binary
                 cls
clus                0   1
  SMAD4 MUTATED     3  10
  SMAD4 WILD-TYPE 135 363
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      3   10
  SMAD4 WILD-TYPE  135  363
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  FEMALE             3             135
  MALE              10             363
[1] 2 2
[1] FALSE
D47V8, binary
                 cls
clus                0   1
  SMAD4 MUTATED     5   6
  SMAD4 WILD-TYPE 152 287
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      5    6
  SMAD4 WILD-TYPE  152  287
     clus
vv    SMAD4 MUTATED SMAD4 WILD-TYPE
  NO              5             152
  YES             6             287
[1] 2 2
[1] FALSE
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA
  SMAD4 MUTATED                                    13
  SMAD4 WILD-TYPE                                 487
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  SMAD4 MUTATED                                                   0
  SMAD4 WILD-TYPE                                                10
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  SMAD4 MUTATED                                                           0
  SMAD4 WILD-TYPE                                                         1
D47V9, multiclass
                                                           clus
vv                                                          SMAD4 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  13
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             0
                                                           clus
vv                                                          SMAD4 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   487
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, continuous
D47V11, continuous
D47V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMAD4 MUTATED                                  0     0
  SMAD4 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SMAD4 MUTATED                           1    12
  SMAD4 WILD-TYPE                        46   425
D47V13, multiclass
                                  clus
vv                                 SMAD4 MUTATED SMAD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              46
  WHITE                                       12             425
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V14, binary
                 cls
clus                0   1
  SMAD4 MUTATED     0  11
  SMAD4 WILD-TYPE  25 438
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      0   11
  SMAD4 WILD-TYPE   25  438
                        clus
vv                       SMAD4 MUTATED SMAD4 WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO            11             438
[1] 2 2
[1] FALSE

Clustering(48) Variable = GAGE2A MUTATION ANALYSIS
D48V1, survival
                  sevent
clus2                0   1
  GAGE2A MUTATED     1   3
  GAGE2A WILD-TYPE 288 217
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               4              505 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               3              217 
$`GAGE2A MUTATED`
TCGA-CQ-6221 TCGA-CV-5434 TCGA-CV-7430 TCGA-CV-A45W 
       32.88       108.95        16.27        45.96 

$`GAGE2A WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       23.84        65.59        15.52        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 
        4.80         4.41        18.38        66.28        71.05        20.52 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       10.55        27.19        12.92         8.81         6.28        12.69 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       55.86        38.04         4.67        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       32.81        52.14        55.56        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       46.32         8.58        12.39        71.31        69.70         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       16.21        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       32.22        38.89         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       25.41        23.57        17.29        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 
       11.21         4.24        41.19        15.75        32.38        66.28 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       58.42        50.01        39.52        36.99        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       22.78        15.75         9.27        47.18        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       40.93        35.84         3.45         3.09        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
        0.99        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       17.13        32.78        47.01        27.06        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
       17.16       129.21        76.24        19.20        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       54.74        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        9.70         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       140.78        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        8.42        28.34         2.50         4.14        64.83       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      111.16        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        1.84        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       47.97         2.10        49.71        18.41        57.47        35.54 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
      210.97        89.33         9.67         0.46        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
       25.94         0.07        34.09       100.57        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
      156.49         3.52        84.49        19.76         7.17       153.86 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O 
       16.64         6.38        22.19        35.93        30.48        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       21.01       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       56.61         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       28.77         7.63        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        23.34        58.45        37.25        33.86        18.02 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       20.45        37.58        41.59        37.18        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       17.85        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.06        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        3.65         6.90        15.95        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        37.41         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       13.84        19.04        15.48        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       18.97         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        27.39        21.07        19.73        12.89         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       16.96         6.87        15.91         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        3.12        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        2.83        49.51        49.45        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  GAGE2A MUTATED GAGE2A WILD-TYPE 
           16.27             0.07 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
          108.95           210.97 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
           39.42            20.88 
[1] "16.3 - 109.0 (39.4)" "0.1 - 211.0 (20.9)" 
[1] "hr=" "1.1"
D48V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  GAGE2A MUTATED         0        1         0         2         0         0
  GAGE2A WILD-TYPE      25       74        80       251        11         1
D48V3, multiclass
           clus
vv          GAGE2A MUTATED GAGE2A WILD-TYPE
  STAGE I                0               25
  STAGE II               1               74
  STAGE III              0               80
  STAGE IVA              2              251
  STAGE IVB              0               11
  STAGE IVC              0                1
[1] 6 2
[1] 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
  GAGE2A MUTATED       0   2   0   2
  GAGE2A WILD-TYPE    47 135  99 170
D48V4, multiclass
       clus
vv      GAGE2A MUTATED GAGE2A WILD-TYPE
  T0+T1              0               47
  T2                 2              135
  T3                 0               99
  T4                 2              170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GAGE2A MUTATED     2   0   1   0
  GAGE2A WILD-TYPE 173  67 167   7
D48V5, multiclass
    clus
vv   GAGE2A MUTATED GAGE2A WILD-TYPE
  N0              2              173
  N1              0               67
  N2              1              167
  N3              0                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"
D48V6, binary
                  cls
clus                 0   1
  GAGE2A MUTATED     1   0
  GAGE2A WILD-TYPE 190   1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      1    0
  GAGE2A WILD-TYPE  190    1
   clus
vv  GAGE2A MUTATED GAGE2A WILD-TYPE
  0              1              190
  1              0                1
[1] 2 2
[1] FALSE
D48V7, binary
                  cls
clus                 0   1
  GAGE2A MUTATED     0   4
  GAGE2A WILD-TYPE 138 369
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      0    4
  GAGE2A WILD-TYPE  138  369
        clus
vv       GAGE2A MUTATED GAGE2A WILD-TYPE
  FEMALE              0              138
  MALE                4              369
[1] 2 2
[1] FALSE
D48V8, binary
                  cls
clus                 0   1
  GAGE2A MUTATED     2   1
  GAGE2A WILD-TYPE 155 292
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      2    1
  GAGE2A WILD-TYPE  155  292
     clus
vv    GAGE2A MUTATED GAGE2A WILD-TYPE
  NO               2              155
  YES              1              292
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  GAGE2A MUTATED                                     4
  GAGE2A WILD-TYPE                                 496
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  GAGE2A MUTATED                                                   0
  GAGE2A WILD-TYPE                                                10
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  GAGE2A MUTATED                                                           0
  GAGE2A WILD-TYPE                                                         1
D48V9, multiclass
                                                           clus
vv                                                          GAGE2A MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    4
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          GAGE2A WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    496
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V10, continuous
[1] "Remove cluster labels:" "GAGE2A MUTATED"        
clus
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               2              288 
      TCGA-BA-4075       TCGA-BA-4077       TCGA-BA-6871       TCGA-BA-A4II 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-4727       TCGA-CN-6021       TCGA-CN-6023       TCGA-CN-6024 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-6992       TCGA-CN-6997       TCGA-CN-A6V3       TCGA-CQ-5323 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-7063       TCGA-CQ-A4C7       TCGA-CX-7082       TCGA-CX-7219 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-DQ-5629       TCGA-DQ-7588       TCGA-DQ-7593       TCGA-H7-A6C4 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-H7-A6C5       TCGA-HD-8634       TCGA-HD-8635       TCGA-UF-A71D 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BA-4074       TCGA-BA-4076       TCGA-BA-4078       TCGA-BA-5149 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BA-5151       TCGA-BA-5555       TCGA-BA-5556       TCGA-BA-6868 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BA-6869       TCGA-BA-6870       TCGA-BA-6872       TCGA-BA-6873 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BA-7269       TCGA-BA-A4IF       TCGA-BA-A4IH       TCGA-BA-A6D8 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BA-A6DA       TCGA-BA-A6DD       TCGA-BA-A6DE       TCGA-BA-A6DG 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BA-A6DI       TCGA-BA-A6DJ       TCGA-BA-A6DL       TCGA-BA-A8YP 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BB-4217       TCGA-BB-4225       TCGA-BB-4227       TCGA-BB-4228 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BB-7870       TCGA-BB-8596       TCGA-BB-A5HY       TCGA-BB-A6UM 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BB-A6UO       TCGA-CN-4726       TCGA-CN-4728       TCGA-CN-4729 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-4730       TCGA-CN-4731       TCGA-CN-4735       TCGA-CN-4736 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-4738       TCGA-CN-4739       TCGA-CN-4740       TCGA-CN-4741 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-4742       TCGA-CN-5355       TCGA-CN-5358       TCGA-CN-5359 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-5360       TCGA-CN-5361       TCGA-CN-5363       TCGA-CN-5365 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-5366       TCGA-CN-5367       TCGA-CN-5373       TCGA-CN-5374 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-6010       TCGA-CN-6011       TCGA-CN-6012       TCGA-CN-6016 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-6017       TCGA-CN-6019       TCGA-CN-6988       TCGA-CN-6989 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-6994       TCGA-CN-6998       TCGA-CN-A498       TCGA-CN-A49B 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-A49C       TCGA-CN-A63T       TCGA-CN-A63U       TCGA-CN-A63V 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-A641       TCGA-CN-A642       TCGA-CN-A6UY       TCGA-CN-A6V6 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-5324       TCGA-CQ-5325       TCGA-CQ-5326       TCGA-CQ-5330 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-5331       TCGA-CQ-5332       TCGA-CQ-5333       TCGA-CQ-6218 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-6219       TCGA-CQ-6222       TCGA-CQ-6223       TCGA-CQ-6224 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-6227       TCGA-CQ-6228       TCGA-CQ-7072       TCGA-CQ-A4C6 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-A4C9       TCGA-CQ-A4CA       TCGA-CQ-A4CB       TCGA-CQ-A4CG 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-A4CI       TCGA-CR-5247       TCGA-CR-5248       TCGA-CR-5250 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-6467       TCGA-CR-6471       TCGA-CR-6473       TCGA-CR-6474 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-6482       TCGA-CR-6487       TCGA-CR-6491       TCGA-CR-6492 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-6493       TCGA-CR-7364       TCGA-CR-7367       TCGA-CR-7368 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7369       TCGA-CR-7370       TCGA-CR-7371       TCGA-CR-7373 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7374       TCGA-CR-7376       TCGA-CR-7377       TCGA-CR-7379 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7383       TCGA-CR-7385       TCGA-CR-7386       TCGA-CR-7388 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7389       TCGA-CR-7390       TCGA-CR-7392       TCGA-CR-7394 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7395       TCGA-CR-7398       TCGA-CR-7399       TCGA-CR-7401 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7402       TCGA-CV-6436       TCGA-CV-6441       TCGA-CV-6933 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-6934       TCGA-CV-6940       TCGA-CV-6941       TCGA-CV-6945 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-6952       TCGA-CV-6961       TCGA-CV-7095       TCGA-CV-7097 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7235       TCGA-CV-7242       TCGA-CV-7245       TCGA-CV-7248 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7250       TCGA-CV-7254       TCGA-CV-7261       TCGA-CV-7263 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7406       TCGA-CV-7410       TCGA-CV-7418       TCGA-CV-7422 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7424       TCGA-CV-7427       TCGA-CV-7432       TCGA-CV-7433 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7434       TCGA-CV-7440       TCGA-CV-7446       TCGA-CV-7568 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-A45Y       TCGA-CV-A45Z       TCGA-CV-A460       TCGA-CV-A464 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-A468       TCGA-CV-A6JD       TCGA-CV-A6JN       TCGA-CV-A6JO 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-A6JU       TCGA-CV-A6JZ       TCGA-CV-A6K1       TCGA-CV-A6K2 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CX-7085       TCGA-CX-7086       TCGA-CX-A4AQ       TCGA-D6-6516 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-D6-6517       TCGA-D6-6823       TCGA-D6-6824       TCGA-D6-6825 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-D6-6827       TCGA-D6-8568       TCGA-D6-8569       TCGA-D6-A4Z9 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-D6-A4ZB       TCGA-D6-A6EK       TCGA-D6-A6EP       TCGA-DQ-5625 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-DQ-5630       TCGA-DQ-5631       TCGA-DQ-7591       TCGA-DQ-7592 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-F7-7848       TCGA-F7-8298       TCGA-F7-8489       TCGA-F7-A50G 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-F7-A50I       TCGA-F7-A50J       TCGA-F7-A61S       TCGA-F7-A61V 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-F7-A61W       TCGA-F7-A620       TCGA-F7-A623       TCGA-H7-7774 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-H7-8502       TCGA-HD-7753       TCGA-HD-7754       TCGA-HD-7832 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-HD-A634       TCGA-HD-A6I0       TCGA-IQ-7631       TCGA-IQ-7632 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-IQ-A61E       TCGA-IQ-A61G       TCGA-IQ-A61H       TCGA-IQ-A61K 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-IQ-A6SH       TCGA-KU-A6H7       TCGA-KU-A6H8       TCGA-MT-A51W 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-MT-A51X       TCGA-MT-A67D       TCGA-MZ-A6I9       TCGA-MZ-A7D7 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-P3-A5Q5       TCGA-P3-A5Q6       TCGA-P3-A6SW       TCGA-P3-A6SX 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-P3-A6T0       TCGA-P3-A6T4       TCGA-P3-A6T5       TCGA-P3-A6T7 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-P3-A6T8       TCGA-QK-A6IG       TCGA-QK-A6II       TCGA-QK-A6IJ 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-QK-A8Z7       TCGA-QK-A8Z8       TCGA-QK-A8Z9       TCGA-QK-A8ZA 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-RS-A6TP       TCGA-T2-A6WZ       TCGA-T2-A6X0       TCGA-T2-A6X2 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-T3-A92M       TCGA-T3-A92N       TCGA-TN-A7HI       TCGA-TN-A7HL 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-UF-A718       TCGA-UF-A71B       TCGA-UF-A7J9       TCGA-UF-A7JC 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-UF-A7JD       TCGA-UF-A7JF       TCGA-UF-A7JH       TCGA-UF-A7JJ 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-UF-A7JS       TCGA-WA-A7GZ       TCGA-WA-A7H4       TCGA-KU-A66S 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
D48V11, continuous
[1] "Remove cluster labels:" "GAGE2A MUTATED"        
clus
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               2              274 
      TCGA-BA-4075       TCGA-BA-4077       TCGA-BA-6871       TCGA-CN-4727 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-6021       TCGA-CN-6023       TCGA-CN-6024       TCGA-CN-6992 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-6997       TCGA-CN-A6V3       TCGA-CQ-5323       TCGA-CQ-7063 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-A4C7       TCGA-CR-6478       TCGA-CX-7219       TCGA-DQ-5629 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-DQ-7588       TCGA-DQ-7593       TCGA-H7-A6C4       TCGA-H7-A6C5 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-HD-8634       TCGA-HD-8635       TCGA-UF-A71D       TCGA-BA-4074 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BA-4076       TCGA-BA-4078       TCGA-BA-5149       TCGA-BA-5151 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BA-5556       TCGA-BA-6868       TCGA-BA-6869       TCGA-BA-6870 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BA-6872       TCGA-BA-6873       TCGA-BA-7269       TCGA-BA-A6DA 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BA-A6DG       TCGA-BA-A8YP       TCGA-BB-4225       TCGA-BB-4228 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BB-8596       TCGA-BB-A5HY       TCGA-BB-A6UM       TCGA-BB-A6UO 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-4728       TCGA-CN-4730       TCGA-CN-4736       TCGA-CN-4738 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-4739       TCGA-CN-4741       TCGA-CN-4742       TCGA-CN-5358 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-5359       TCGA-CN-5360       TCGA-CN-5361       TCGA-CN-5363 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-5365       TCGA-CN-5366       TCGA-CN-5367       TCGA-CN-5370 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-6010       TCGA-CN-6011       TCGA-CN-6012       TCGA-CN-6016 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-6017       TCGA-CN-6989       TCGA-CN-6994       TCGA-CN-6998 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-A498       TCGA-CN-A49B       TCGA-CN-A49C       TCGA-CN-A63T 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-A63U       TCGA-CN-A63V       TCGA-CN-A641       TCGA-CN-A6UY 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-A6V6       TCGA-CQ-5324       TCGA-CQ-5325       TCGA-CQ-5330 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-5331       TCGA-CQ-5333       TCGA-CQ-6218       TCGA-CQ-6219 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-6222       TCGA-CQ-6223       TCGA-CQ-6224       TCGA-CQ-6227 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-6228       TCGA-CQ-7072       TCGA-CQ-A4C6       TCGA-CQ-A4C9 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-A4CA       TCGA-CQ-A4CB       TCGA-CQ-A4CI       TCGA-CR-5247 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-5248       TCGA-CR-5250       TCGA-CR-6467       TCGA-CR-6471 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-6473       TCGA-CR-6474       TCGA-CR-6477       TCGA-CR-6482 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-6487       TCGA-CR-6491       TCGA-CR-6492       TCGA-CR-6493 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7364       TCGA-CR-7365       TCGA-CR-7367       TCGA-CR-7368 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7369       TCGA-CR-7370       TCGA-CR-7371       TCGA-CR-7373 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7374       TCGA-CR-7376       TCGA-CR-7377       TCGA-CR-7383 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7385       TCGA-CR-7386       TCGA-CR-7388       TCGA-CR-7389 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7390       TCGA-CR-7391       TCGA-CR-7392       TCGA-CR-7394 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7395       TCGA-CR-7397       TCGA-CR-7399       TCGA-CR-7401 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7402       TCGA-CV-5430       TCGA-CV-5431       TCGA-CV-5432 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-5435       TCGA-CV-5436       TCGA-CV-5440       TCGA-CV-5443 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-5966       TCGA-CV-5970       TCGA-CV-5976       TCGA-CV-6433 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-6436       TCGA-CV-6441       TCGA-CV-6934       TCGA-CV-6935 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-6936       TCGA-CV-6940       TCGA-CV-6941       TCGA-CV-6943 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-6945       TCGA-CV-6952       TCGA-CV-6954       TCGA-CV-6960 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-6961       TCGA-CV-7091       TCGA-CV-7095       TCGA-CV-7097 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7099       TCGA-CV-7100       TCGA-CV-7101       TCGA-CV-7102 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7180       TCGA-CV-7183       TCGA-CV-7235       TCGA-CV-7242 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7245       TCGA-CV-7248       TCGA-CV-7250       TCGA-CV-7254 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7261       TCGA-CV-7406       TCGA-CV-7410       TCGA-CV-7418 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7422       TCGA-CV-7424       TCGA-CV-7427       TCGA-CV-7432 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7433       TCGA-CV-7434       TCGA-CV-7435       TCGA-CV-7440 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7446       TCGA-CV-7568       TCGA-CV-A45Q       TCGA-CV-A45Y 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-A45Z       TCGA-CV-A460       TCGA-CV-A461       TCGA-CV-A464 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-A468       TCGA-CV-A6JD       TCGA-CV-A6JE       TCGA-CV-A6JN 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-A6JO       TCGA-CV-A6JU       TCGA-CV-A6JY       TCGA-CV-A6JZ 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-A6K1       TCGA-CV-A6K2       TCGA-CX-7086       TCGA-D6-6516 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-D6-6517       TCGA-D6-6823       TCGA-D6-6824       TCGA-D6-6825 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-D6-6827       TCGA-D6-8568       TCGA-D6-8569       TCGA-D6-A4Z9 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-D6-A4ZB       TCGA-D6-A6EK       TCGA-D6-A6EP       TCGA-D6-A74Q 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-DQ-5625       TCGA-DQ-5630       TCGA-DQ-5631       TCGA-DQ-7591 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-DQ-7592       TCGA-F7-7848       TCGA-F7-8298       TCGA-F7-8489 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-F7-A50G       TCGA-F7-A50I       TCGA-F7-A50J       TCGA-F7-A61S 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-F7-A61V       TCGA-F7-A61W       TCGA-F7-A620       TCGA-F7-A623 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-H7-7774       TCGA-H7-8502       TCGA-H7-A76A       TCGA-HD-A634 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-HD-A6I0       TCGA-IQ-7631       TCGA-IQ-7632       TCGA-IQ-A61E 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-IQ-A61G       TCGA-IQ-A6SH       TCGA-KU-A6H7       TCGA-KU-A6H8 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-MT-A51W       TCGA-MT-A51X       TCGA-MT-A67D       TCGA-MZ-A6I9 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-MZ-A7D7       TCGA-P3-A6SX       TCGA-P3-A6T0       TCGA-P3-A6T4 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-P3-A6T8       TCGA-QK-A6IG       TCGA-QK-A6II       TCGA-QK-A6IJ 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-QK-A8Z7       TCGA-QK-A8ZA       TCGA-RS-A6TP       TCGA-T3-A92N 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-TN-A7HI       TCGA-TN-A7HL       TCGA-UF-A718       TCGA-UF-A71B 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-UF-A7J9       TCGA-UF-A7JC       TCGA-UF-A7JD       TCGA-UF-A7JF 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-UF-A7JH       TCGA-UF-A7JJ       TCGA-UF-A7JS       TCGA-WA-A7GZ 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-WA-A7H4       TCGA-KU-A66S 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
D48V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAGE2A MUTATED                                  0     0
  GAGE2A WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GAGE2A MUTATED                           1     3
  GAGE2A WILD-TYPE                        46   434
D48V13, multiclass
                                  clus
vv                                 GAGE2A MUTATED GAGE2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               46
  WHITE                                         3              434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V14, binary
                  cls
clus                 0   1
  GAGE2A MUTATED     0   4
  GAGE2A WILD-TYPE  25 445
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      0    4
  GAGE2A WILD-TYPE   25  445
                        clus
vv                       GAGE2A MUTATED GAGE2A WILD-TYPE
  HISPANIC OR LATINO                  0               25
  NOT HISPANIC OR LATINO              4              445
[1] 2 2
[1] FALSE

Clustering(49) Variable = EMG1 MUTATION ANALYSIS
D49V1, survival
                sevent
clus2              0   1
  EMG1 MUTATED     2   1
  EMG1 WILD-TYPE 287 219
  EMG1 MUTATED EMG1 WILD-TYPE 
             3            506 
  EMG1 MUTATED EMG1 WILD-TYPE 
             1            219 
$`EMG1 MUTATED`
TCGA-CN-5369 TCGA-CR-7367 TCGA-CV-6003 
       12.49        47.34        54.74 

$`EMG1 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 
        9.14         4.80         4.41        18.38        66.28        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       12.69        55.86        38.04         4.67        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
       26.86        32.81        52.14        55.56        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        45.83        27.58        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 
       42.02        46.32         8.58        12.39        71.31        69.70 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 
        8.32        16.21        11.54        11.84        11.57         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       32.22        38.89         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       25.41        23.57        17.29        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 
       11.21         4.24        41.19        15.75        32.38        66.28 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       58.42        50.01        39.52        36.99        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 
       22.78        15.75         9.27        47.18        39.16        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58        24.79         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        5.95        35.41        29.95        48.39       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
      129.21       108.95        76.24        19.20        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      140.78        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
        6.08        53.95        65.82        10.98         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
       28.34         2.50         4.14        64.83       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
       18.81        12.66         7.99         9.01         5.26         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
       52.31        12.92        21.80        71.21        10.75       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       77.16         4.73        89.65        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       18.97        17.13        95.34         4.96        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 
        2.10        49.71        18.41        57.47        35.54       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 
       89.33         9.67         0.46        22.85        25.08        25.94 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
        0.07        34.09       100.57        14.89        56.48       156.49 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        3.52        16.27        84.49        19.76         7.17       153.86 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O 
       16.64         6.38        22.19        35.93        30.48        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       21.01       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
       45.96         6.51        88.87        48.20        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        0.76        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       23.47        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       16.14        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       12.36        28.77         7.63        22.59        24.95        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       12.10        12.79        23.34        58.45        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       18.02        20.45        37.58        41.59        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       21.63        20.25         3.02        31.13        18.94        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
        0.46        17.85        11.80        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       21.93        27.48        14.66        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65         6.90        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        27.39        21.07        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.72        16.96         6.87        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       13.71         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  EMG1 MUTATED EMG1 WILD-TYPE 
         12.49           0.07 
  EMG1 MUTATED EMG1 WILD-TYPE 
         54.74         210.97 
  EMG1 MUTATED EMG1 WILD-TYPE 
         47.34          20.91 
[1] "12.5 - 54.7 (47.3)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1.5"
D49V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  EMG1 MUTATED         0        0         1         2         0         0
  EMG1 WILD-TYPE      25       75        79       251        11         1
D49V3, multiclass
           clus
vv          EMG1 MUTATED EMG1 WILD-TYPE
  STAGE I              0             25
  STAGE II             0             75
  STAGE III            1             79
  STAGE IVA            2            251
  STAGE IVB            0             11
  STAGE IVC            0              1
[1] 6 2
[1] 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
  EMG1 MUTATED       0   1   0   2
  EMG1 WILD-TYPE    47 136  99 170
D49V4, multiclass
       clus
vv      EMG1 MUTATED EMG1 WILD-TYPE
  T0+T1            0             47
  T2               1            136
  T3               0             99
  T4               2            170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  EMG1 MUTATED     1   2   0   0
  EMG1 WILD-TYPE 174  65 168   7
D49V5, multiclass
    clus
vv   EMG1 MUTATED EMG1 WILD-TYPE
  N0            1            174
  N1            2             65
  N2            0            168
  N3            0              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
  EMG1 MUTATED     2   0
  EMG1 WILD-TYPE 189   1
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      2    0
  EMG1 WILD-TYPE  189    1
   clus
vv  EMG1 MUTATED EMG1 WILD-TYPE
  0            2            189
  1            0              1
[1] 2 2
[1] FALSE
D49V7, binary
                cls
clus               0   1
  EMG1 MUTATED     2   1
  EMG1 WILD-TYPE 136 372
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      2    1
  EMG1 WILD-TYPE  136  372
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  FEMALE            2            136
  MALE              1            372
[1] 2 2
[1] FALSE
D49V8, binary
                cls
clus               0   1
  EMG1 MUTATED     2   1
  EMG1 WILD-TYPE 155 292
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      2    1
  EMG1 WILD-TYPE  155  292
     clus
vv    EMG1 MUTATED EMG1 WILD-TYPE
  NO             2            155
  YES            1            292
[1] 2 2
[1] FALSE
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA
  EMG1 MUTATED                                     3
  EMG1 WILD-TYPE                                 497
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  EMG1 MUTATED                                                   0
  EMG1 WILD-TYPE                                                10
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  EMG1 MUTATED                                                           0
  EMG1 WILD-TYPE                                                         1
D49V9, multiclass
                                                           clus
vv                                                          EMG1 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  3
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT            0
                                                           clus
vv                                                          EMG1 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  497
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V10, continuous
[1] "Remove cluster labels:" "EMG1 MUTATED"          
clus
  EMG1 MUTATED EMG1 WILD-TYPE 
             1            289 
    TCGA-BA-4075     TCGA-BA-4077     TCGA-BA-6871     TCGA-BA-A4II 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-4727     TCGA-CN-6021     TCGA-CN-6023     TCGA-CN-6024 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-6992     TCGA-CN-6997     TCGA-CN-A6V3     TCGA-CQ-5323 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-6221     TCGA-CQ-7063     TCGA-CQ-A4C7     TCGA-CX-7082 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CX-7219     TCGA-DQ-5629     TCGA-DQ-7588     TCGA-DQ-7593 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-H7-A6C4     TCGA-H7-A6C5     TCGA-HD-8634     TCGA-HD-8635 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-UF-A71D     TCGA-BA-4074     TCGA-BA-4076     TCGA-BA-4078 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-5149     TCGA-BA-5151     TCGA-BA-5555     TCGA-BA-5556 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-6868     TCGA-BA-6869     TCGA-BA-6870     TCGA-BA-6872 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-6873     TCGA-BA-7269     TCGA-BA-A4IF     TCGA-BA-A4IH 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-A6D8     TCGA-BA-A6DA     TCGA-BA-A6DD     TCGA-BA-A6DE 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-A6DG     TCGA-BA-A6DI     TCGA-BA-A6DJ     TCGA-BA-A6DL 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-A8YP     TCGA-BB-4217     TCGA-BB-4225     TCGA-BB-4227 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BB-4228     TCGA-BB-7870     TCGA-BB-8596     TCGA-BB-A5HY 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BB-A6UM     TCGA-BB-A6UO     TCGA-CN-4726     TCGA-CN-4728 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-4729     TCGA-CN-4730     TCGA-CN-4731     TCGA-CN-4735 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-4736     TCGA-CN-4738     TCGA-CN-4739     TCGA-CN-4740 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-4741     TCGA-CN-4742     TCGA-CN-5355     TCGA-CN-5358 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-5359     TCGA-CN-5360     TCGA-CN-5361     TCGA-CN-5363 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-5365     TCGA-CN-5366     TCGA-CN-5367     TCGA-CN-5373 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-5374     TCGA-CN-6010     TCGA-CN-6011     TCGA-CN-6012 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-6016     TCGA-CN-6017     TCGA-CN-6019     TCGA-CN-6988 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-6989     TCGA-CN-6994     TCGA-CN-6998     TCGA-CN-A498 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-A49B     TCGA-CN-A49C     TCGA-CN-A63T     TCGA-CN-A63U 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-A63V     TCGA-CN-A641     TCGA-CN-A642     TCGA-CN-A6UY 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-A6V6     TCGA-CQ-5324     TCGA-CQ-5325     TCGA-CQ-5326 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-5330     TCGA-CQ-5331     TCGA-CQ-5332     TCGA-CQ-5333 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-6218     TCGA-CQ-6219     TCGA-CQ-6222     TCGA-CQ-6223 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-6224     TCGA-CQ-6227     TCGA-CQ-6228     TCGA-CQ-7072 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-A4C6     TCGA-CQ-A4C9     TCGA-CQ-A4CA     TCGA-CQ-A4CB 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-A4CG     TCGA-CQ-A4CI     TCGA-CR-5247     TCGA-CR-5248 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-5250     TCGA-CR-6467     TCGA-CR-6471     TCGA-CR-6473 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-6474     TCGA-CR-6482     TCGA-CR-6487     TCGA-CR-6491 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-6492     TCGA-CR-6493     TCGA-CR-7364     TCGA-CR-7368 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7369     TCGA-CR-7370     TCGA-CR-7371     TCGA-CR-7373 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7374     TCGA-CR-7376     TCGA-CR-7377     TCGA-CR-7379 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7383     TCGA-CR-7385     TCGA-CR-7386     TCGA-CR-7388 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7389     TCGA-CR-7390     TCGA-CR-7392     TCGA-CR-7394 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7395     TCGA-CR-7398     TCGA-CR-7399     TCGA-CR-7401 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7402     TCGA-CV-6436     TCGA-CV-6441     TCGA-CV-6933 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-6934     TCGA-CV-6940     TCGA-CV-6941     TCGA-CV-6945 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-6952     TCGA-CV-6961     TCGA-CV-7095     TCGA-CV-7097 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7235     TCGA-CV-7242     TCGA-CV-7245     TCGA-CV-7248 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7250     TCGA-CV-7254     TCGA-CV-7261     TCGA-CV-7263 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7406     TCGA-CV-7410     TCGA-CV-7418     TCGA-CV-7422 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7424     TCGA-CV-7427     TCGA-CV-7430     TCGA-CV-7432 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7433     TCGA-CV-7434     TCGA-CV-7440     TCGA-CV-7446 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7568     TCGA-CV-A45Y     TCGA-CV-A45Z     TCGA-CV-A460 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-A464     TCGA-CV-A468     TCGA-CV-A6JD     TCGA-CV-A6JN 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-A6JO     TCGA-CV-A6JU     TCGA-CV-A6JZ     TCGA-CV-A6K1 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-A6K2     TCGA-CX-7085     TCGA-CX-7086     TCGA-CX-A4AQ 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-D6-6516     TCGA-D6-6517     TCGA-D6-6823     TCGA-D6-6824 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-D6-6825     TCGA-D6-6827     TCGA-D6-8568     TCGA-D6-8569 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-D6-A4Z9     TCGA-D6-A4ZB     TCGA-D6-A6EK     TCGA-D6-A6EP 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-DQ-5625     TCGA-DQ-5630     TCGA-DQ-5631     TCGA-DQ-7591 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-DQ-7592     TCGA-F7-7848     TCGA-F7-8298     TCGA-F7-8489 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-F7-A50G     TCGA-F7-A50I     TCGA-F7-A50J     TCGA-F7-A61S 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-F7-A61V     TCGA-F7-A61W     TCGA-F7-A620     TCGA-F7-A623 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-H7-7774     TCGA-H7-8502     TCGA-HD-7753     TCGA-HD-7754 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HD-7832     TCGA-HD-A634     TCGA-HD-A6I0     TCGA-IQ-7631 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-IQ-7632     TCGA-IQ-A61E     TCGA-IQ-A61G     TCGA-IQ-A61H 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-IQ-A61K     TCGA-IQ-A6SH     TCGA-KU-A6H7     TCGA-KU-A6H8 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-MT-A51W     TCGA-MT-A51X     TCGA-MT-A67D     TCGA-MZ-A6I9 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-MZ-A7D7     TCGA-P3-A5Q5     TCGA-P3-A5Q6     TCGA-P3-A6SW 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-P3-A6SX     TCGA-P3-A6T0     TCGA-P3-A6T4     TCGA-P3-A6T5 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-P3-A6T7     TCGA-P3-A6T8     TCGA-QK-A6IG     TCGA-QK-A6II 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-QK-A6IJ     TCGA-QK-A8Z7     TCGA-QK-A8Z8     TCGA-QK-A8Z9 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-QK-A8ZA     TCGA-RS-A6TP     TCGA-T2-A6WZ     TCGA-T2-A6X0 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-T2-A6X2     TCGA-T3-A92M     TCGA-T3-A92N     TCGA-TN-A7HI 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-TN-A7HL     TCGA-UF-A718     TCGA-UF-A71B     TCGA-UF-A7J9 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-UF-A7JC     TCGA-UF-A7JD     TCGA-UF-A7JF     TCGA-UF-A7JH 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-UF-A7JJ     TCGA-UF-A7JS     TCGA-WA-A7GZ     TCGA-WA-A7H4 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KU-A66S 
"EMG1 WILD-TYPE" 
D49V11, continuous
[1] "Remove cluster labels:" "EMG1 MUTATED"          
clus
  EMG1 MUTATED EMG1 WILD-TYPE 
             1            275 
    TCGA-BA-4075     TCGA-BA-4077     TCGA-BA-6871     TCGA-CN-4727 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-6021     TCGA-CN-6023     TCGA-CN-6024     TCGA-CN-6992 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-6997     TCGA-CN-A6V3     TCGA-CQ-5323     TCGA-CQ-6221 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-7063     TCGA-CQ-A4C7     TCGA-CR-6478     TCGA-CX-7219 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-DQ-5629     TCGA-DQ-7588     TCGA-DQ-7593     TCGA-H7-A6C4 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-H7-A6C5     TCGA-HD-8634     TCGA-HD-8635     TCGA-UF-A71D 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-4074     TCGA-BA-4076     TCGA-BA-4078     TCGA-BA-5149 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-5151     TCGA-BA-5556     TCGA-BA-6868     TCGA-BA-6869 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-6870     TCGA-BA-6872     TCGA-BA-6873     TCGA-BA-7269 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-A6DA     TCGA-BA-A6DG     TCGA-BA-A8YP     TCGA-BB-4225 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BB-4228     TCGA-BB-8596     TCGA-BB-A5HY     TCGA-BB-A6UM 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BB-A6UO     TCGA-CN-4728     TCGA-CN-4730     TCGA-CN-4736 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-4738     TCGA-CN-4739     TCGA-CN-4741     TCGA-CN-4742 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-5358     TCGA-CN-5359     TCGA-CN-5360     TCGA-CN-5361 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-5363     TCGA-CN-5365     TCGA-CN-5366     TCGA-CN-5367 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-5370     TCGA-CN-6010     TCGA-CN-6011     TCGA-CN-6012 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-6016     TCGA-CN-6017     TCGA-CN-6989     TCGA-CN-6994 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-6998     TCGA-CN-A498     TCGA-CN-A49B     TCGA-CN-A49C 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-A63T     TCGA-CN-A63U     TCGA-CN-A63V     TCGA-CN-A641 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-A6UY     TCGA-CN-A6V6     TCGA-CQ-5324     TCGA-CQ-5325 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-5330     TCGA-CQ-5331     TCGA-CQ-5333     TCGA-CQ-6218 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-6219     TCGA-CQ-6222     TCGA-CQ-6223     TCGA-CQ-6224 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-6227     TCGA-CQ-6228     TCGA-CQ-7072     TCGA-CQ-A4C6 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-A4C9     TCGA-CQ-A4CA     TCGA-CQ-A4CB     TCGA-CQ-A4CI 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-5247     TCGA-CR-5248     TCGA-CR-5250     TCGA-CR-6467 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-6471     TCGA-CR-6473     TCGA-CR-6474     TCGA-CR-6477 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-6482     TCGA-CR-6487     TCGA-CR-6491     TCGA-CR-6492 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-6493     TCGA-CR-7364     TCGA-CR-7365     TCGA-CR-7368 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7369     TCGA-CR-7370     TCGA-CR-7371     TCGA-CR-7373 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7374     TCGA-CR-7376     TCGA-CR-7377     TCGA-CR-7383 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7385     TCGA-CR-7386     TCGA-CR-7388     TCGA-CR-7389 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7390     TCGA-CR-7391     TCGA-CR-7392     TCGA-CR-7394 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7395     TCGA-CR-7397     TCGA-CR-7399     TCGA-CR-7401 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7402     TCGA-CV-5430     TCGA-CV-5431     TCGA-CV-5432 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-5435     TCGA-CV-5436     TCGA-CV-5440     TCGA-CV-5443 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-5966     TCGA-CV-5970     TCGA-CV-5976     TCGA-CV-6433 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-6436     TCGA-CV-6441     TCGA-CV-6934     TCGA-CV-6935 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-6936     TCGA-CV-6940     TCGA-CV-6941     TCGA-CV-6943 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-6945     TCGA-CV-6952     TCGA-CV-6954     TCGA-CV-6960 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-6961     TCGA-CV-7091     TCGA-CV-7095     TCGA-CV-7097 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7099     TCGA-CV-7100     TCGA-CV-7101     TCGA-CV-7102 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7180     TCGA-CV-7183     TCGA-CV-7235     TCGA-CV-7242 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7245     TCGA-CV-7248     TCGA-CV-7250     TCGA-CV-7254 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7261     TCGA-CV-7406     TCGA-CV-7410     TCGA-CV-7418 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7422     TCGA-CV-7424     TCGA-CV-7427     TCGA-CV-7430 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7432     TCGA-CV-7433     TCGA-CV-7434     TCGA-CV-7435 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7440     TCGA-CV-7446     TCGA-CV-7568     TCGA-CV-A45Q 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-A45Y     TCGA-CV-A45Z     TCGA-CV-A460     TCGA-CV-A461 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-A464     TCGA-CV-A468     TCGA-CV-A6JD     TCGA-CV-A6JE 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-A6JN     TCGA-CV-A6JO     TCGA-CV-A6JU     TCGA-CV-A6JY 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-A6JZ     TCGA-CV-A6K1     TCGA-CV-A6K2     TCGA-CX-7086 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-D6-6516     TCGA-D6-6517     TCGA-D6-6823     TCGA-D6-6824 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-D6-6825     TCGA-D6-6827     TCGA-D6-8568     TCGA-D6-8569 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-D6-A4Z9     TCGA-D6-A4ZB     TCGA-D6-A6EK     TCGA-D6-A6EP 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-D6-A74Q     TCGA-DQ-5625     TCGA-DQ-5630     TCGA-DQ-5631 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-DQ-7591     TCGA-DQ-7592     TCGA-F7-7848     TCGA-F7-8298 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-F7-8489     TCGA-F7-A50G     TCGA-F7-A50I     TCGA-F7-A50J 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-F7-A61S     TCGA-F7-A61V     TCGA-F7-A61W     TCGA-F7-A620 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-F7-A623     TCGA-H7-7774     TCGA-H7-8502     TCGA-H7-A76A 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HD-A634     TCGA-HD-A6I0     TCGA-IQ-7631     TCGA-IQ-7632 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-IQ-A61E     TCGA-IQ-A61G     TCGA-IQ-A6SH     TCGA-KU-A6H7 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KU-A6H8     TCGA-MT-A51W     TCGA-MT-A51X     TCGA-MT-A67D 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-MZ-A6I9     TCGA-MZ-A7D7     TCGA-P3-A6SX     TCGA-P3-A6T0 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-P3-A6T4     TCGA-P3-A6T8     TCGA-QK-A6IG     TCGA-QK-A6II 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-QK-A6IJ     TCGA-QK-A8Z7     TCGA-QK-A8ZA     TCGA-RS-A6TP 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-T3-A92N     TCGA-TN-A7HI     TCGA-TN-A7HL     TCGA-UF-A718 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-UF-A71B     TCGA-UF-A7J9     TCGA-UF-A7JC     TCGA-UF-A7JD 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-UF-A7JF     TCGA-UF-A7JH     TCGA-UF-A7JJ     TCGA-UF-A7JS 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-WA-A7GZ     TCGA-WA-A7H4     TCGA-KU-A66S 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
D49V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EMG1 MUTATED                                  0     0
  EMG1 WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EMG1 MUTATED                           0     3
  EMG1 WILD-TYPE                        47   434
D49V13, multiclass
                                  clus
vv                                 EMG1 MUTATED EMG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             47
  WHITE                                       3            434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V14, binary
                cls
clus               0   1
  EMG1 MUTATED     0   3
  EMG1 WILD-TYPE  25 446
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      0    3
  EMG1 WILD-TYPE   25  446
                        clus
vv                       EMG1 MUTATED EMG1 WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO            3            446
[1] 2 2
[1] FALSE

Clustering(50) Variable = PIK3R1 MUTATION ANALYSIS
D50V1, survival
                  sevent
clus2                0   1
  PIK3R1 MUTATED     7   1
  PIK3R1 WILD-TYPE 282 219
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               8              501 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               1              219 
$`PIK3R1 MUTATED`
TCGA-BB-7870 TCGA-CN-4729 TCGA-CN-A49C TCGA-CR-5248 TCGA-CR-6492 TCGA-DQ-5625 
       66.28        12.89        21.21        54.67        15.75        37.25 
TCGA-DQ-7596 TCGA-QK-A6VB 
       41.59        21.07 

$`PIK3R1 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-8596 TCGA-BB-8601 
        9.14         4.80         4.41        18.38        71.05        20.52 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       10.55        27.19        12.92         8.81         6.28        12.69 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 
       55.86        38.04         4.67        56.68        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       52.14        55.56        57.11        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       45.83        27.58        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 
        8.58        12.39        71.31        69.70         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       56.94        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       28.04        19.07        34.13         6.74        10.45        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       38.89         3.68        17.42        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       23.57        17.29        29.72         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       70.45        62.37        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       41.19        15.75        32.38        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       11.77        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 
       11.64         7.69        12.46        22.78         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       39.16        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58        24.79         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        94.88        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       60.49         7.07        43.23        54.74        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
        9.60        90.12         2.14         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       65.82        10.98         7.13         8.42        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        4.14        64.83       172.67       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       89.65        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       95.34         4.96        11.87        47.97         2.10        49.71 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       18.41        57.47        35.54       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        0.46        22.85        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 
      100.57        14.89        56.48       156.49         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       84.49        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       22.19        35.93        30.48        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
        7.07        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        7.63        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       23.34        58.45        33.86        18.02        20.45        37.58 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       37.18        32.71        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        24.95         0.46        17.85        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       12.43        13.38        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 
        0.36        13.84         4.27         3.65         6.90        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
       33.57         5.29        13.68        13.84        19.04        15.48 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.27        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         6.25        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        71.74        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC 
        7.30        21.47         9.34        12.72        27.39        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       12.89         5.62        14.76        12.20        17.82        15.32 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
        8.32        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       32.45        13.71         3.12        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
       64.80        54.67         2.83        49.51        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       74.47        17.95        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       13.94        20.75        22.36        32.65        17.03        20.55 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           12.89             0.07 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           66.28           210.97 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           29.23            20.75 
[1] "12.9 - 66.3 (29.2)" "0.1 - 211.0 (20.8)"
[1] "hr=" "4.1"
D50V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  PIK3R1 MUTATED         0        0         2         2         0         0
  PIK3R1 WILD-TYPE      25       75        78       251        11         1
D50V3, multiclass
           clus
vv          PIK3R1 MUTATED PIK3R1 WILD-TYPE
  STAGE I                0               25
  STAGE II               0               75
  STAGE III              2               78
  STAGE IVA              2              251
  STAGE IVB              0               11
  STAGE IVC              0                1
[1] 6 2
[1] 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
  PIK3R1 MUTATED       0   2   0   2
  PIK3R1 WILD-TYPE    47 135  99 170
D50V4, multiclass
       clus
vv      PIK3R1 MUTATED PIK3R1 WILD-TYPE
  T0+T1              0               47
  T2                 2              135
  T3                 0               99
  T4                 2              170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PIK3R1 MUTATED     2   2   0   0
  PIK3R1 WILD-TYPE 173  65 168   7
D50V5, multiclass
    clus
vv   PIK3R1 MUTATED PIK3R1 WILD-TYPE
  N0              2              173
  N1              2               65
  N2              0              168
  N3              0                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"
D50V6, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     2   0
  PIK3R1 WILD-TYPE 189   1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      2    0
  PIK3R1 WILD-TYPE  189    1
   clus
vv  PIK3R1 MUTATED PIK3R1 WILD-TYPE
  0              2              189
  1              0                1
[1] 2 2
[1] FALSE
D50V7, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     1   7
  PIK3R1 WILD-TYPE 137 366
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      1    7
  PIK3R1 WILD-TYPE  137  366
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  FEMALE              1              137
  MALE                7              366
[1] 2 2
[1] FALSE
D50V8, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     2   6
  PIK3R1 WILD-TYPE 155 287
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      2    6
  PIK3R1 WILD-TYPE  155  287
     clus
vv    PIK3R1 MUTATED PIK3R1 WILD-TYPE
  NO               2              155
  YES              6              287
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  PIK3R1 MUTATED                                     8
  PIK3R1 WILD-TYPE                                 492
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  PIK3R1 MUTATED                                                   0
  PIK3R1 WILD-TYPE                                                10
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  PIK3R1 MUTATED                                                           0
  PIK3R1 WILD-TYPE                                                         1
D50V9, multiclass
                                                           clus
vv                                                          PIK3R1 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    8
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          PIK3R1 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    492
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, continuous
D50V11, continuous
D50V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3R1 MUTATED                                  0     0
  PIK3R1 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3R1 MUTATED                           0     8
  PIK3R1 WILD-TYPE                        47   429
D50V13, multiclass
                                  clus
vv                                 PIK3R1 MUTATED PIK3R1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               47
  WHITE                                         8              429
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V14, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     0   8
  PIK3R1 WILD-TYPE  25 441
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      0    8
  PIK3R1 WILD-TYPE   25  441
                        clus
vv                       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  HISPANIC OR LATINO                  0               25
  NOT HISPANIC OR LATINO              8              441
[1] 2 2
[1] FALSE

Clustering(51) Variable = KRTAP5-7 MUTATION ANALYSIS
D51V1, survival
                    sevent
clus2                  0   1
  KRTAP5-7 MUTATED     5   0
  KRTAP5-7 WILD-TYPE 284 220
  KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE 
                 5                504 
  KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE 
                 0                220 
$`KRTAP5-7 MUTATED`
TCGA-CN-4730 TCGA-CQ-5331 TCGA-CR-6484 TCGA-CR-7399 TCGA-F7-8298 
       26.86        45.99        11.64         5.95        32.71 

$`KRTAP5-7 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 
        9.14         4.80         4.41        18.38        66.28        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       12.69        55.86        38.04         4.67        56.68        12.89 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       32.81        52.14        55.56        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       46.32         8.58        12.39        71.31        69.70         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       16.21        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       32.22        38.89         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       25.41        23.57        17.29        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 
        2.93        54.58        70.45        62.37        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 
        4.24        41.19        15.75        32.38        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       56.58        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       53.52        41.88        43.10        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       10.22        11.34         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 
       32.65        44.25        30.58        24.79         5.13        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       29.95        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       76.24        19.20        17.95       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        2.50         4.14        64.83       172.67       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 
       12.66         7.99         9.01         5.26         1.84        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
       12.92        21.80        71.21        10.75       130.88        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
        4.73        89.65        36.00        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       17.13        95.34         4.96        11.87        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 
       49.71        18.41        57.47        35.54       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
        9.67         0.46        22.85        25.08        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 
       34.09       100.57        14.89        56.48       156.49         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 
       16.27        84.49        19.76         7.17       153.86        16.64 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P 
        6.38        22.19        35.93        30.48        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
      169.38       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       56.61         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       28.77         7.63        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        23.34        58.45        37.25        33.86        18.02 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       20.45        37.58        41.59        37.18        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       20.94        33.76        28.47        25.74        21.93        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       14.66        22.03         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        6.90        15.95        38.53        14.50        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       37.41         0.07        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       19.04        15.48        19.27        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       30.05         1.84        12.62         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
       16.08        17.98        29.92        15.78        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       10.85        36.82        47.01        19.00        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
        2.04        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.21        23.15         7.30        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       27.39        21.07        19.73        12.89         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        6.87        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       32.65        17.03        20.55        14.56        13.35        18.15 

  KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE 
              5.95               0.07 
  KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE 
             45.99             210.97 
  KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE 
             26.86              20.91 
[1] "6.0 - 46.0 (26.9)"  "0.1 - 211.0 (20.9)"
[1] "hr="     "3300000"
D51V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  KRTAP5-7 MUTATED         1        0         0         3         0         0
  KRTAP5-7 WILD-TYPE      24       75        80       250        11         1
D51V3, multiclass
           clus
vv          KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE
  STAGE I                  1                 24
  STAGE II                 0                 75
  STAGE III                0                 80
  STAGE IVA                3                250
  STAGE IVB                0                 11
  STAGE IVC                0                  1
[1] 6 2
[1] 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
  KRTAP5-7 MUTATED       1   1   1   2
  KRTAP5-7 WILD-TYPE    46 136  98 170
D51V4, multiclass
       clus
vv      KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE
  T0+T1                1                 46
  T2                   1                136
  T3                   1                 98
  T4                   2                170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KRTAP5-7 MUTATED     1   1   2   0
  KRTAP5-7 WILD-TYPE 174  66 166   7
D51V5, multiclass
    clus
vv   KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE
  N0                1                174
  N1                1                 66
  N2                2                166
  N3                0                  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"
D51V6, binary
                    cls
clus                   0   1
  KRTAP5-7 MUTATED     3   0
  KRTAP5-7 WILD-TYPE 188   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-7 MUTATED      3    0
  KRTAP5-7 WILD-TYPE  188    1
   clus
vv  KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE
  0                3                188
  1                0                  1
[1] 2 2
[1] FALSE
D51V7, binary
                    cls
clus                   0   1
  KRTAP5-7 MUTATED     3   2
  KRTAP5-7 WILD-TYPE 135 371
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-7 MUTATED      3    2
  KRTAP5-7 WILD-TYPE  135  371
        clus
vv       KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE
  FEMALE                3                135
  MALE                  2                371
[1] 2 2
[1] FALSE
D51V8, binary
                    cls
clus                   0   1
  KRTAP5-7 MUTATED     3   2
  KRTAP5-7 WILD-TYPE 154 291
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-7 MUTATED      3    2
  KRTAP5-7 WILD-TYPE  154  291
     clus
vv    KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE
  NO                 3                154
  YES                2                291
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA
  KRTAP5-7 MUTATED                                     5
  KRTAP5-7 WILD-TYPE                                 495
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  KRTAP5-7 MUTATED                                                   0
  KRTAP5-7 WILD-TYPE                                                10
                    vv
clus                 HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  KRTAP5-7 MUTATED                                                           0
  KRTAP5-7 WILD-TYPE                                                         1
D51V9, multiclass
                                                           clus
vv                                                          KRTAP5-7 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      5
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                0
                                                           clus
vv                                                          KRTAP5-7 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                      495
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V10, continuous
D51V11, continuous
D51V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRTAP5-7 MUTATED                                  0     1
  KRTAP5-7 WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KRTAP5-7 MUTATED                           0     4
  KRTAP5-7 WILD-TYPE                        47   433
D51V13, multiclass
                                  clus
vv                                 KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       0                 47
  WHITE                                           4                433
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V14, binary
                    cls
clus                   0   1
  KRTAP5-7 MUTATED     0   5
  KRTAP5-7 WILD-TYPE  25 444
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-7 MUTATED      0    5
  KRTAP5-7 WILD-TYPE   25  444
                        clus
vv                       KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE
  HISPANIC OR LATINO                    0                 25
  NOT HISPANIC OR LATINO                5                444
[1] 2 2
[1] FALSE

Clustering(52) Variable = SLC9A6 MUTATION ANALYSIS
D52V1, survival
                  sevent
clus2                0   1
  SLC9A6 MUTATED     1   4
  SLC9A6 WILD-TYPE 288 216
  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
               5              504 
  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
               4              216 
$`SLC9A6 MUTATED`
TCGA-CN-4742 TCGA-CV-6952 TCGA-CV-7438 TCGA-IQ-A61J TCGA-P3-A6T7 
       13.05         6.08         6.38        33.57        16.01 

$`SLC9A6 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 
        9.14         4.80         4.41        18.38        66.28        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       12.69        55.86        38.04         4.67        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
       26.86        32.81        52.14        55.56        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 
       20.55        14.33        45.83        27.58        73.61        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       46.32         8.58        12.39        71.31        69.70         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       16.21        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       32.22        38.89         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       25.41        23.57        17.29        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 
       11.21         4.24        41.19        15.75        32.38        66.28 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       58.42        50.01        39.52        36.99        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       22.78        15.75         9.27        47.18        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       40.93        35.84         3.45         3.09        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
        0.99        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       17.13        32.78        47.01        27.06        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       17.16       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       140.78        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       15.09        30.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        8.42        28.34         2.50         4.14        64.83       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      111.16        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        1.84        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       47.97         2.10        49.71        18.41        57.47        35.54 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
      210.97        89.33         9.67         0.46        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
       25.94         0.07        34.09       100.57        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
      156.49         3.52        16.27        84.49        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O 
      153.86        16.64        22.19        35.93        30.48        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       21.01       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
       45.96         6.51        88.87        48.20        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        0.76        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       23.47        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       16.14        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       12.36        28.77         7.63        22.59        24.95        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       12.10        12.79        23.34        58.45        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       18.02        20.45        37.58        41.59        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       21.63        20.25         3.02        31.13        18.94        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
        0.46        17.85        11.80        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       21.93        27.48        14.66        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65         6.90        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L 
       37.71        11.84        37.41         0.07         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       13.84        19.04        15.48        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A64Z 
       18.97         2.04        29.00        12.99        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.21        23.15         7.30        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       27.39        21.07        19.73        12.89         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        6.87        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       32.65        17.03        20.55        14.56        13.35        18.15 

  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
            6.08             0.07 
  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
           33.57           210.97 
  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
           13.05            21.04 
[1] "6.1 - 33.6 (13.1)"  "0.1 - 211.0 (21.0)"
[1] "hr=" "3.3"
D52V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  SLC9A6 MUTATED         1        0         0         4         0         0
  SLC9A6 WILD-TYPE      24       75        80       249        11         1
D52V3, multiclass
           clus
vv          SLC9A6 MUTATED SLC9A6 WILD-TYPE
  STAGE I                1               24
  STAGE II               0               75
  STAGE III              0               80
  STAGE IVA              4              249
  STAGE IVB              0               11
  STAGE IVC              0                1
[1] 6 2
[1] 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
  SLC9A6 MUTATED       1   1   2   1
  SLC9A6 WILD-TYPE    46 136  97 171
D52V4, multiclass
       clus
vv      SLC9A6 MUTATED SLC9A6 WILD-TYPE
  T0+T1              1               46
  T2                 1              136
  T3                 2               97
  T4                 1              171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SLC9A6 MUTATED     0   0   4   0
  SLC9A6 WILD-TYPE 175  67 164   7
D52V5, multiclass
    clus
vv   SLC9A6 MUTATED SLC9A6 WILD-TYPE
  N0              0              175
  N1              0               67
  N2              4              164
  N3              0                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"
D52V6, binary
                  cls
clus                 0   1
  SLC9A6 MUTATED     2   0
  SLC9A6 WILD-TYPE 189   1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A6 MUTATED      2    0
  SLC9A6 WILD-TYPE  189    1
   clus
vv  SLC9A6 MUTATED SLC9A6 WILD-TYPE
  0              2              189
  1              0                1
[1] 2 2
[1] FALSE
D52V7, binary
                  cls
clus                 0   1
  SLC9A6 MUTATED     3   2
  SLC9A6 WILD-TYPE 135 371
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A6 MUTATED      3    2
  SLC9A6 WILD-TYPE  135  371
        clus
vv       SLC9A6 MUTATED SLC9A6 WILD-TYPE
  FEMALE              3              135
  MALE                2              371
[1] 2 2
[1] FALSE
D52V8, binary
                  cls
clus                 0   1
  SLC9A6 MUTATED     1   4
  SLC9A6 WILD-TYPE 156 289
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A6 MUTATED      1    4
  SLC9A6 WILD-TYPE  156  289
     clus
vv    SLC9A6 MUTATED SLC9A6 WILD-TYPE
  NO               1              156
  YES              4              289
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  SLC9A6 MUTATED                                     5
  SLC9A6 WILD-TYPE                                 495
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  SLC9A6 MUTATED                                                   0
  SLC9A6 WILD-TYPE                                                10
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  SLC9A6 MUTATED                                                           0
  SLC9A6 WILD-TYPE                                                         1
D52V9, multiclass
                                                           clus
vv                                                          SLC9A6 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    5
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          SLC9A6 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    495
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V10, continuous
D52V11, continuous
[1] "Remove cluster labels:" "SLC9A6 MUTATED"        
clus
  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
               2              274 
      TCGA-BA-4075       TCGA-BA-4077       TCGA-BA-6871       TCGA-CN-4727 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CN-6021       TCGA-CN-6023       TCGA-CN-6024       TCGA-CN-6992 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CN-6997       TCGA-CN-A6V3       TCGA-CQ-5323       TCGA-CQ-6221 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CQ-7063       TCGA-CQ-A4C7       TCGA-CR-6478       TCGA-CX-7219 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-DQ-5629       TCGA-DQ-7588       TCGA-DQ-7593       TCGA-H7-A6C4 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-H7-A6C5       TCGA-HD-8634       TCGA-HD-8635       TCGA-UF-A71D 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-BA-4074       TCGA-BA-4076       TCGA-BA-4078       TCGA-BA-5149 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-BA-5151       TCGA-BA-5556       TCGA-BA-6868       TCGA-BA-6869 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-BA-6870       TCGA-BA-6872       TCGA-BA-6873       TCGA-BA-7269 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-BA-A6DA       TCGA-BA-A6DG       TCGA-BA-A8YP       TCGA-BB-4225 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-BB-4228       TCGA-BB-8596       TCGA-BB-A5HY       TCGA-BB-A6UM 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-BB-A6UO       TCGA-CN-4728       TCGA-CN-4730       TCGA-CN-4736 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CN-4738       TCGA-CN-4739       TCGA-CN-4741       TCGA-CN-5358 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CN-5359       TCGA-CN-5360       TCGA-CN-5361       TCGA-CN-5363 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CN-5365       TCGA-CN-5366       TCGA-CN-5367       TCGA-CN-5370 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CN-6010       TCGA-CN-6011       TCGA-CN-6012       TCGA-CN-6016 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CN-6017       TCGA-CN-6989       TCGA-CN-6994       TCGA-CN-6998 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CN-A498       TCGA-CN-A49B       TCGA-CN-A49C       TCGA-CN-A63T 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CN-A63U       TCGA-CN-A63V       TCGA-CN-A641       TCGA-CN-A6UY 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CN-A6V6       TCGA-CQ-5324       TCGA-CQ-5325       TCGA-CQ-5330 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CQ-5331       TCGA-CQ-5333       TCGA-CQ-6218       TCGA-CQ-6219 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CQ-6222       TCGA-CQ-6223       TCGA-CQ-6224       TCGA-CQ-6227 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CQ-6228       TCGA-CQ-7072       TCGA-CQ-A4C6       TCGA-CQ-A4C9 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CQ-A4CA       TCGA-CQ-A4CB       TCGA-CQ-A4CI       TCGA-CR-5247 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-5248       TCGA-CR-5250       TCGA-CR-6467       TCGA-CR-6471 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-6473       TCGA-CR-6474       TCGA-CR-6477       TCGA-CR-6482 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-6487       TCGA-CR-6491       TCGA-CR-6492       TCGA-CR-6493 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-7364       TCGA-CR-7365       TCGA-CR-7367       TCGA-CR-7368 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-7369       TCGA-CR-7370       TCGA-CR-7371       TCGA-CR-7373 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-7374       TCGA-CR-7376       TCGA-CR-7377       TCGA-CR-7383 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-7385       TCGA-CR-7386       TCGA-CR-7388       TCGA-CR-7389 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-7390       TCGA-CR-7391       TCGA-CR-7392       TCGA-CR-7394 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-7395       TCGA-CR-7397       TCGA-CR-7399       TCGA-CR-7401 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-7402       TCGA-CV-5430       TCGA-CV-5431       TCGA-CV-5432 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-5435       TCGA-CV-5436       TCGA-CV-5440       TCGA-CV-5443 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-5966       TCGA-CV-5970       TCGA-CV-5976       TCGA-CV-6433 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-6436       TCGA-CV-6441       TCGA-CV-6934       TCGA-CV-6935 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-6936       TCGA-CV-6940       TCGA-CV-6941       TCGA-CV-6943 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-6945       TCGA-CV-6954       TCGA-CV-6960       TCGA-CV-6961 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7091       TCGA-CV-7095       TCGA-CV-7097       TCGA-CV-7099 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7100       TCGA-CV-7101       TCGA-CV-7102       TCGA-CV-7180 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7183       TCGA-CV-7235       TCGA-CV-7242       TCGA-CV-7245 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7248       TCGA-CV-7250       TCGA-CV-7254       TCGA-CV-7261 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7406       TCGA-CV-7410       TCGA-CV-7418       TCGA-CV-7422 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7424       TCGA-CV-7427       TCGA-CV-7430       TCGA-CV-7432 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7433       TCGA-CV-7434       TCGA-CV-7435       TCGA-CV-7440 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7446       TCGA-CV-7568       TCGA-CV-A45Q       TCGA-CV-A45Y 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-A45Z       TCGA-CV-A460       TCGA-CV-A461       TCGA-CV-A464 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-A468       TCGA-CV-A6JD       TCGA-CV-A6JE       TCGA-CV-A6JN 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-A6JO       TCGA-CV-A6JU       TCGA-CV-A6JY       TCGA-CV-A6JZ 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-A6K1       TCGA-CV-A6K2       TCGA-CX-7086       TCGA-D6-6516 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-D6-6517       TCGA-D6-6823       TCGA-D6-6824       TCGA-D6-6825 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-D6-6827       TCGA-D6-8568       TCGA-D6-8569       TCGA-D6-A4Z9 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-D6-A4ZB       TCGA-D6-A6EK       TCGA-D6-A6EP       TCGA-D6-A74Q 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-DQ-5625       TCGA-DQ-5630       TCGA-DQ-5631       TCGA-DQ-7591 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-DQ-7592       TCGA-F7-7848       TCGA-F7-8298       TCGA-F7-8489 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-F7-A50G       TCGA-F7-A50I       TCGA-F7-A50J       TCGA-F7-A61S 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-F7-A61V       TCGA-F7-A61W       TCGA-F7-A620       TCGA-F7-A623 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-H7-7774       TCGA-H7-8502       TCGA-H7-A76A       TCGA-HD-A634 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-HD-A6I0       TCGA-IQ-7631       TCGA-IQ-7632       TCGA-IQ-A61E 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-IQ-A61G       TCGA-IQ-A6SH       TCGA-KU-A6H7       TCGA-KU-A6H8 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-MT-A51W       TCGA-MT-A51X       TCGA-MT-A67D       TCGA-MZ-A6I9 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-MZ-A7D7       TCGA-P3-A6SX       TCGA-P3-A6T0       TCGA-P3-A6T4 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-P3-A6T8       TCGA-QK-A6IG       TCGA-QK-A6II       TCGA-QK-A6IJ 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-QK-A8Z7       TCGA-QK-A8ZA       TCGA-RS-A6TP       TCGA-T3-A92N 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-TN-A7HI       TCGA-TN-A7HL       TCGA-UF-A718       TCGA-UF-A71B 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-UF-A7J9       TCGA-UF-A7JC       TCGA-UF-A7JD       TCGA-UF-A7JF 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-UF-A7JH       TCGA-UF-A7JJ       TCGA-UF-A7JS       TCGA-WA-A7GZ 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-WA-A7H4       TCGA-KU-A66S 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
D52V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC9A6 MUTATED                                  0     0
  SLC9A6 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLC9A6 MUTATED                           0     5
  SLC9A6 WILD-TYPE                        47   432
D52V13, multiclass
                                  clus
vv                                 SLC9A6 MUTATED SLC9A6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               47
  WHITE                                         5              432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V14, binary
                  cls
clus                 0   1
  SLC9A6 MUTATED     0   5
  SLC9A6 WILD-TYPE  25 444
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A6 MUTATED      0    5
  SLC9A6 WILD-TYPE   25  444
                        clus
vv                       SLC9A6 MUTATED SLC9A6 WILD-TYPE
  HISPANIC OR LATINO                  0               25
  NOT HISPANIC OR LATINO              5              444
[1] 2 2
[1] FALSE

Clustering(53) Variable = ELF4 MUTATION ANALYSIS
D53V1, survival
                sevent
clus2              0   1
  ELF4 MUTATED     5   2
  ELF4 WILD-TYPE 284 218
  ELF4 MUTATED ELF4 WILD-TYPE 
             7            502 
  ELF4 MUTATED ELF4 WILD-TYPE 
             2            218 
$`ELF4 MUTATED`
TCGA-CQ-5324 TCGA-CR-5248 TCGA-CR-7376 TCGA-CV-7099 TCGA-CV-7406 TCGA-F7-8298 
       52.37        54.67        31.96         7.99        57.47        32.71 
TCGA-F7-A61V 
       24.95 

$`ELF4 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 
        9.14         4.80         4.41        18.38        66.28        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       12.69        55.86        38.04         4.67        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
       26.86        32.81        52.14        55.56        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        45.83        27.58        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 
       42.02        46.32         8.58        12.39        71.31        69.70 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
        8.32        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        8.52        52.08        56.94        50.07        30.67        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       23.90        47.44        28.04        19.07        34.13         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       10.45        32.22        38.89         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        31.69        22.32        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5325 
       12.07         2.70        23.44        20.88        19.53        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 
       11.21         4.24        41.19        15.75        32.38        66.28 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       31.23        84.23        11.77        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       15.75         9.27        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      108.95        76.24        19.20        17.95       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      140.78        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
        6.08        53.95        65.82        10.98         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
       28.34         2.50         4.14        64.83       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 
       18.81        12.66         9.01         5.26         1.84        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
       12.92        21.80        71.21        10.75       130.88        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
        4.73        89.65        36.00        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       17.13        95.34         4.96        11.87        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       49.71        18.41        35.54       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        0.46        22.85        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 
      100.57        14.89        56.48       156.49         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       84.49        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       22.19        35.93        30.48        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
        7.07        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        7.63        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 
       23.34        58.45        37.25        33.86        18.02        20.45 
TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       37.58        41.59        37.18        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       31.13        18.94         0.46        17.85        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       12.43        13.38        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 
        0.36        13.84         4.27         3.65         6.90        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
       33.57         5.29        13.68        13.84        19.04        15.48 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.27        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         6.25        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        71.74        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        21.47         9.34        12.72        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       19.73        12.89         5.62        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       15.32         8.32        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ 
        7.10        32.45        13.71         3.12        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       20.35        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       18.05        13.94        20.75        22.36        32.65        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.55        14.56        13.35        18.15 

  ELF4 MUTATED ELF4 WILD-TYPE 
          7.99           0.07 
  ELF4 MUTATED ELF4 WILD-TYPE 
         57.47         210.97 
  ELF4 MUTATED ELF4 WILD-TYPE 
         32.71          20.65 
[1] "8.0 - 57.5 (32.7)"  "0.1 - 211.0 (20.6)"
[1] "hr=" "1.9"
D53V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  ELF4 MUTATED         1        3         2         0         0         0
  ELF4 WILD-TYPE      24       72        78       253        11         1
D53V3, multiclass
           clus
vv          ELF4 MUTATED ELF4 WILD-TYPE
  STAGE I              1             24
  STAGE II             3             72
  STAGE III            2             78
  STAGE IVA            0            253
  STAGE IVB            0             11
  STAGE IVC            0              1
[1] 6 2
[1] 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
  ELF4 MUTATED       1   4   1   0
  ELF4 WILD-TYPE    46 133  98 172
D53V4, multiclass
       clus
vv      ELF4 MUTATED ELF4 WILD-TYPE
  T0+T1            1             46
  T2               4            133
  T3               1             98
  T4               0            172
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ELF4 MUTATED     4   1   0   0
  ELF4 WILD-TYPE 171  66 168   7
D53V5, multiclass
    clus
vv   ELF4 MUTATED ELF4 WILD-TYPE
  N0            4            171
  N1            1             66
  N2            0            168
  N3            0              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"
D53V6, binary
                cls
clus               0   1
  ELF4 MUTATED     3   0
  ELF4 WILD-TYPE 188   1
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF4 MUTATED      3    0
  ELF4 WILD-TYPE  188    1
   clus
vv  ELF4 MUTATED ELF4 WILD-TYPE
  0            3            188
  1            0              1
[1] 2 2
[1] FALSE
D53V7, binary
                cls
clus               0   1
  ELF4 MUTATED     1   6
  ELF4 WILD-TYPE 137 367
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF4 MUTATED      1    6
  ELF4 WILD-TYPE  137  367
        clus
vv       ELF4 MUTATED ELF4 WILD-TYPE
  FEMALE            1            137
  MALE              6            367
[1] 2 2
[1] FALSE
D53V8, binary
                cls
clus               0   1
  ELF4 MUTATED     5   1
  ELF4 WILD-TYPE 152 292
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF4 MUTATED      5    1
  ELF4 WILD-TYPE  152  292
     clus
vv    ELF4 MUTATED ELF4 WILD-TYPE
  NO             5            152
  YES            1            292
[1] 2 2
[1] FALSE
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA
  ELF4 MUTATED                                     7
  ELF4 WILD-TYPE                                 493
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  ELF4 MUTATED                                                   0
  ELF4 WILD-TYPE                                                10
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  ELF4 MUTATED                                                           0
  ELF4 WILD-TYPE                                                         1
D53V9, multiclass
                                                           clus
vv                                                          ELF4 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  7
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT            0
                                                           clus
vv                                                          ELF4 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  493
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V10, continuous
D53V11, continuous
D53V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ELF4 MUTATED                                  0     0
  ELF4 WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ELF4 MUTATED                           0     7
  ELF4 WILD-TYPE                        47   430
D53V13, multiclass
                                  clus
vv                                 ELF4 MUTATED ELF4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             47
  WHITE                                       7            430
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V14, binary
                cls
clus               0   1
  ELF4 MUTATED     0   6
  ELF4 WILD-TYPE  25 443
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF4 MUTATED      0    6
  ELF4 WILD-TYPE   25  443
                        clus
vv                       ELF4 MUTATED ELF4 WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO            6            443
[1] 2 2
[1] FALSE

Clustering(54) Variable = CTCF MUTATION ANALYSIS
D54V1, survival
                sevent
clus2              0   1
  CTCF MUTATED     7   8
  CTCF WILD-TYPE 282 212
  CTCF MUTATED CTCF WILD-TYPE 
            15            494 
  CTCF MUTATED CTCF WILD-TYPE 
             8            212 
$`CTCF MUTATED`
TCGA-BA-5151 TCGA-BA-A6DF TCGA-CQ-5327 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6228 
       23.74         7.82        54.58        11.21         4.24        14.99 
TCGA-CR-7382 TCGA-CV-6938 TCGA-CV-7102 TCGA-CV-7242 TCGA-CV-7253 TCGA-CV-A45V 
       26.17         4.73         1.84        36.00        11.87         1.05 
TCGA-F7-A624 TCGA-H7-7774 TCGA-QK-A6IH 
       12.43        13.38        21.47 

$`CTCF WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
       13.64         9.07        26.50        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       23.84        65.59        15.52        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        7.10         5.69        14.47         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       20.48        16.41         6.15       105.90         9.14         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
        4.41        18.38        66.28        71.05        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 
       27.19        12.92         8.81         6.28        12.69        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       52.14        55.56        57.11        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       45.83        27.58        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 
        8.58        12.39        71.31        69.70         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       56.94        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       28.04        19.07        34.13         6.74        10.45        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       38.89         3.68        17.42        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       23.57        17.29        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       23.44        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6219 
       70.45        62.37        45.99        10.42        41.19        15.75 
TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.38        66.28        46.95        56.58        13.25         4.24 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       38.76        64.87        53.52        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       44.48        23.24        29.36        33.60        29.49        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       12.46        31.23        84.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
       26.27        58.42        50.01        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       16.90        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       12.46        22.78        15.75         9.27        47.18        39.16 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
       47.34        40.93        35.84         3.45         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       29.23         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       17.13        32.78        47.01        27.06        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       17.16       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6940 
        2.14         9.70         5.46        20.52        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       140.78        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        8.42        28.34         2.50         4.14        64.83       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      111.16        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
       52.31        12.92        21.80        71.21        10.75       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
       77.16         4.73        89.65        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       17.13        95.34         4.96        47.97         2.10        49.71 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       18.41        57.47        35.54       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        0.46        22.85        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 
      100.57        14.89        56.48       156.49         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       84.49        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       22.19        35.93        30.48        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      180.16       159.65        35.47        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       48.20        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        37.25        33.86        18.02        20.45        37.58 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       31.13        18.94        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       20.25        15.16        15.06        20.94        33.76        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       25.74        21.93        27.48        14.66        22.03         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         3.65         6.90        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        37.71        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        6.25        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       15.78        71.74        51.25        10.85        36.82        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       19.00        75.55        18.97         2.04        29.00        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       16.01        13.15        21.07        21.21        23.15         7.30 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        27.39        21.07        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.72        16.96         6.87        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       13.71         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  CTCF MUTATED CTCF WILD-TYPE 
          1.05           0.07 
  CTCF MUTATED CTCF WILD-TYPE 
         54.58         210.97 
  CTCF MUTATED CTCF WILD-TYPE 
         12.43          21.07 
[1] "1.1 - 54.6 (12.4)"  "0.1 - 211.0 (21.1)"
[1] "hr=" "2.1"
D54V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  CTCF MUTATED         0        4         0        10         1         0
  CTCF WILD-TYPE      25       71        80       243        10         1
D54V3, multiclass
           clus
vv          CTCF MUTATED CTCF WILD-TYPE
  STAGE I              0             25
  STAGE II             4             71
  STAGE III            0             80
  STAGE IVA           10            243
  STAGE IVB            1             10
  STAGE IVC            0              1
[1] 6 2
[1] 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
  CTCF MUTATED       1   5   3   6
  CTCF WILD-TYPE    46 132  96 166
D54V4, multiclass
       clus
vv      CTCF MUTATED CTCF WILD-TYPE
  T0+T1            1             46
  T2               5            132
  T3               3             96
  T4               6            166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CTCF MUTATED     7   0   6   0
  CTCF WILD-TYPE 168  67 162   7
D54V5, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  N0            7            168
  N1            0             67
  N2            6            162
  N3            0              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"
D54V6, binary
                cls
clus               0   1
  CTCF MUTATED     5   0
  CTCF WILD-TYPE 186   1
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED      5    0
  CTCF WILD-TYPE  186    1
   clus
vv  CTCF MUTATED CTCF WILD-TYPE
  0            5            186
  1            0              1
[1] 2 2
[1] FALSE
D54V7, binary
                cls
clus               0   1
  CTCF MUTATED     8   7
  CTCF WILD-TYPE 130 366
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED      8    7
  CTCF WILD-TYPE  130  366
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  FEMALE            8            130
  MALE              7            366
[1] 2 2
[1] FALSE
D54V8, binary
                cls
clus               0   1
  CTCF MUTATED     5   8
  CTCF WILD-TYPE 152 285
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED      5    8
  CTCF WILD-TYPE  152  285
     clus
vv    CTCF MUTATED CTCF WILD-TYPE
  NO             5            152
  YES            8            285
[1] 2 2
[1] FALSE
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA
  CTCF MUTATED                                    15
  CTCF WILD-TYPE                                 485
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  CTCF MUTATED                                                   0
  CTCF WILD-TYPE                                                10
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  CTCF MUTATED                                                           0
  CTCF WILD-TYPE                                                         1
D54V9, multiclass
                                                           clus
vv                                                          CTCF MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                 15
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT            0
                                                           clus
vv                                                          CTCF WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  485
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V10, continuous
D54V11, continuous
D54V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTCF MUTATED                                  0     1
  CTCF WILD-TYPE                                2     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CTCF MUTATED                           1    13
  CTCF WILD-TYPE                        46   424
D54V13, multiclass
                                  clus
vv                                 CTCF MUTATED CTCF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             46
  WHITE                                      13            424
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V14, binary
                cls
clus               0   1
  CTCF MUTATED     0  15
  CTCF WILD-TYPE  25 434
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED      0   15
  CTCF WILD-TYPE   25  434
                        clus
vv                       CTCF MUTATED CTCF WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO           15            434
[1] 2 2
[1] FALSE

Clustering(55) Variable = HNRNPL MUTATION ANALYSIS
D55V1, survival
                  sevent
clus2                0   1
  HNRNPL MUTATED     4   7
  HNRNPL WILD-TYPE 285 213
  HNRNPL MUTATED HNRNPL WILD-TYPE 
              11              498 
  HNRNPL MUTATED HNRNPL WILD-TYPE 
               7              213 
$`HNRNPL MUTATED`
TCGA-CN-4729 TCGA-CN-6018 TCGA-CR-7377 TCGA-CV-6948 TCGA-CV-6952 TCGA-CV-6953 
       12.89        19.07         9.17        42.38         6.08        53.95 
TCGA-CV-A45Q TCGA-DQ-5631 TCGA-P3-A6T8 TCGA-QK-A6VB TCGA-QK-A8Z7 
      169.38        18.02        13.15        21.07        12.89 

$`HNRNPL WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 
        9.14         4.80         4.41        18.38        66.28        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 
       12.69        55.86        38.04         4.67        56.68        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       32.81        52.14        55.56        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       46.32         8.58        12.39        71.31        69.70         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       16.21        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       47.44        28.04        34.13         6.74        10.45        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       38.89         3.68        17.42        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       23.57        17.29        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       23.44        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 
        4.24        41.19        15.75        32.38        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       56.58        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       53.52        41.88        43.10        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       15.75         9.27        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
       31.96        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58        24.79         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      108.95        76.24        19.20        17.95       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6954 
      140.78        19.79        12.03        15.09        30.08        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       10.98         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       172.67       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        9.01         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        89.65 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 
       36.00        31.36        26.20        18.97        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 
        4.96        11.87        47.97         2.10        49.71        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       57.47        35.54       210.97        89.33         9.67         0.46 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
       22.85        25.08        25.94         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       14.89        56.48       156.49         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       19.76         7.17       153.86        16.64         6.38        22.19 
TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T 
       35.93        30.48        27.98        21.01       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
       35.47         1.05        45.96         6.51        88.87        48.20 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       60.43        67.86         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        51.12        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
       23.05         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN 
       25.32        17.72        12.36        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        13.94        12.10        12.79        23.34        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 
       37.25        33.86        20.45        37.58        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       24.95         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       13.38        15.16        15.06        20.94        33.76        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       25.74        21.93        27.48        14.66        22.03         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         3.65         6.90        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        37.71        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        6.25        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       15.78        71.74        51.25        10.85        36.82        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       19.00        75.55        18.97         2.04        29.00        12.99 
TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       16.01        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 
        9.34        12.72        27.39        19.73         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        6.87        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       32.65        17.03        20.55        14.56        13.35        18.15 

  HNRNPL MUTATED HNRNPL WILD-TYPE 
            6.08             0.07 
  HNRNPL MUTATED HNRNPL WILD-TYPE 
          169.38           210.97 
  HNRNPL MUTATED HNRNPL WILD-TYPE 
           18.02            21.04 
[1] "6.1 - 169.4 (18.0)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1.3"
D55V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  HNRNPL MUTATED         0        0         2         6         1         0
  HNRNPL WILD-TYPE      25       75        78       247        10         1
D55V3, multiclass
           clus
vv          HNRNPL MUTATED HNRNPL WILD-TYPE
  STAGE I                0               25
  STAGE II               0               75
  STAGE III              2               78
  STAGE IVA              6              247
  STAGE IVB              1               10
  STAGE IVC              0                1
[1] 6 2
[1] 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
  HNRNPL MUTATED       0   1   2   6
  HNRNPL WILD-TYPE    47 136  97 166
D55V4, multiclass
       clus
vv      HNRNPL MUTATED HNRNPL WILD-TYPE
  T0+T1              0               47
  T2                 1              136
  T3                 2               97
  T4                 6              166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  HNRNPL MUTATED     2   1   5   1
  HNRNPL WILD-TYPE 173  66 163   6
D55V5, multiclass
    clus
vv   HNRNPL MUTATED HNRNPL WILD-TYPE
  N0              2              173
  N1              1               66
  N2              5              163
  N3              1                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"
D55V6, binary
                  cls
clus                 0   1
  HNRNPL MUTATED     3   0
  HNRNPL WILD-TYPE 188   1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPL MUTATED      3    0
  HNRNPL WILD-TYPE  188    1
   clus
vv  HNRNPL MUTATED HNRNPL WILD-TYPE
  0              3              188
  1              0                1
[1] 2 2
[1] FALSE
D55V7, binary
                  cls
clus                 0   1
  HNRNPL MUTATED     5   6
  HNRNPL WILD-TYPE 133 367
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPL MUTATED      5    6
  HNRNPL WILD-TYPE  133  367
        clus
vv       HNRNPL MUTATED HNRNPL WILD-TYPE
  FEMALE              5              133
  MALE                6              367
[1] 2 2
[1] FALSE
D55V8, binary
                  cls
clus                 0   1
  HNRNPL MUTATED     4   7
  HNRNPL WILD-TYPE 153 286
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPL MUTATED      4    7
  HNRNPL WILD-TYPE  153  286
     clus
vv    HNRNPL MUTATED HNRNPL WILD-TYPE
  NO               4              153
  YES              7              286
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  HNRNPL MUTATED                                    10
  HNRNPL WILD-TYPE                                 490
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  HNRNPL MUTATED                                                   1
  HNRNPL WILD-TYPE                                                 9
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  HNRNPL MUTATED                                                           0
  HNRNPL WILD-TYPE                                                         1
D55V9, multiclass
                                                           clus
vv                                                          HNRNPL MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   10
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          HNRNPL WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    490
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V10, continuous
D55V11, continuous
D55V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNRNPL MUTATED                                  0     0
  HNRNPL WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HNRNPL MUTATED                           1    10
  HNRNPL WILD-TYPE                        46   427
D55V13, multiclass
                                  clus
vv                                 HNRNPL MUTATED HNRNPL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               46
  WHITE                                        10              427
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V14, binary
                  cls
clus                 0   1
  HNRNPL MUTATED     0  11
  HNRNPL WILD-TYPE  25 438
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPL MUTATED      0   11
  HNRNPL WILD-TYPE   25  438
                        clus
vv                       HNRNPL MUTATED HNRNPL WILD-TYPE
  HISPANIC OR LATINO                  0               25
  NOT HISPANIC OR LATINO             11              438
[1] 2 2
[1] FALSE

Clustering(56) Variable = ZFP36L2 MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  ZFP36L2 MUTATED     2   6
  ZFP36L2 WILD-TYPE 287 214
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                8               501 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                6               214 
$`ZFP36L2 MUTATED`
TCGA-BB-A6UO TCGA-CN-4723 TCGA-CN-4731 TCGA-CN-A63U TCGA-CV-6940 TCGA-CV-6962 
        8.81        55.86        32.81        31.69        26.43         4.14 
TCGA-P3-A6SX TCGA-T2-A6WZ 
       47.01        15.91 

$`ZFP36L2 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 
        9.14         4.80         4.41        18.38        66.28        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-C9-A47Z TCGA-C9-A480 
       20.52        10.55        27.19        12.92         6.28        12.69 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4733 
       38.04         4.67        56.68        12.89        26.86        52.14 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       55.56        57.11        12.99        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        73.61        13.05        42.02        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       12.39        71.31        69.70         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.84        11.57        12.49         8.52        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
       19.07        34.13         6.74        10.45        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W 
       17.29        29.72        21.21         7.40        22.32        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       16.57         4.41        12.07         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       19.53        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       15.75        32.38        66.28        46.95        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
        4.24        14.99        38.76        64.87        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        77.56        44.48        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.49        14.14        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       47.18        39.16        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.09        24.95        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       29.95        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       76.24        19.20        17.95       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
       20.52         4.73        21.90        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       65.82        10.98         7.13         8.42        28.34         2.50 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       172.67       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        9.01         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        89.65 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 
       36.00        31.36        26.20        18.97        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 
        4.96        11.87        47.97         2.10        49.71        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       57.47        35.54       210.97        89.33         9.67         0.46 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
       22.85        25.08        25.94         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       14.89        56.48       156.49         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       19.76         7.17       153.86        16.64         6.38        22.19 
TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       35.93        30.48        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       48.20        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        37.25        33.86        18.02        20.45        37.58 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       31.13        18.94        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       20.25        12.43        13.38        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
       33.76        28.47        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         0.36        13.84         4.27         3.65         6.90 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
        0.07        33.57         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       15.48        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
        1.84        12.62         6.25        15.42         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       17.98        29.92        15.78        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       36.82        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        21.47         9.34        12.72        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       19.73        12.89         5.62        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
       15.32         8.32        12.72        16.96         6.87         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       32.45        13.71         3.12        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
       64.80        54.67         2.83        49.51        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       74.47        17.95        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       13.94        20.75        22.36        32.65        17.03        20.55 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
             4.14              0.07 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
            55.86            210.97 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
            29.06             20.88 
[1] "4.1 - 55.9 (29.1)"  "0.1 - 211.0 (20.9)"
[1] "hr=" "1.9"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  ZFP36L2 MUTATED         0        0         2         5         0         0
  ZFP36L2 WILD-TYPE      25       75        78       248        11         1
D56V3, multiclass
           clus
vv          ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  STAGE I                 0                25
  STAGE II                0                75
  STAGE III               2                78
  STAGE IVA               5               248
  STAGE IVB               0                11
  STAGE IVC               0                 1
[1] 6 2
[1] 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
  ZFP36L2 MUTATED       0   2   2   4
  ZFP36L2 WILD-TYPE    47 135  97 168
D56V4, multiclass
       clus
vv      ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  T0+T1               0                47
  T2                  2               135
  T3                  2                97
  T4                  4               168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  ZFP36L2 MUTATED     1   2   4   0
  ZFP36L2 WILD-TYPE 174  65 164   7
D56V5, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  N0               1               174
  N1               2                65
  N2               4               164
  N3               0                 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"
D56V6, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     0   0
  ZFP36L2 WILD-TYPE 191   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      0    0
  ZFP36L2 WILD-TYPE  191    1
D56V7, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     3   5
  ZFP36L2 WILD-TYPE 135 368
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      3    5
  ZFP36L2 WILD-TYPE  135  368
        clus
vv       ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  FEMALE               3               135
  MALE                 5               368
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     3   5
  ZFP36L2 WILD-TYPE 154 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      3    5
  ZFP36L2 WILD-TYPE  154  288
     clus
vv    ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  NO                3               154
  YES               5               288
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  ZFP36L2 MUTATED                                     8
  ZFP36L2 WILD-TYPE                                 492
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  ZFP36L2 MUTATED                                                   0
  ZFP36L2 WILD-TYPE                                                10
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  ZFP36L2 MUTATED                                                           0
  ZFP36L2 WILD-TYPE                                                         1
D56V9, multiclass
                                                           clus
vv                                                          ZFP36L2 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     8
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          ZFP36L2 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     492
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V10, continuous
D56V11, continuous
D56V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFP36L2 MUTATED                                  0     0
  ZFP36L2 WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZFP36L2 MUTATED                           0     8
  ZFP36L2 WILD-TYPE                        47   429
D56V13, multiclass
                                  clus
vv                                 ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                47
  WHITE                                          8               429
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V14, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     1   7
  ZFP36L2 WILD-TYPE  24 442
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      1    7
  ZFP36L2 WILD-TYPE   24  442
                        clus
vv                       ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  HISPANIC OR LATINO                   1                24
  NOT HISPANIC OR LATINO               7               442
[1] 2 2
[1] FALSE

Clustering(57) Variable = MYH9 MUTATION ANALYSIS
D57V1, survival
                sevent
clus2              0   1
  MYH9 MUTATED    11  10
  MYH9 WILD-TYPE 278 210
  MYH9 MUTATED MYH9 WILD-TYPE 
            21            488 
  MYH9 MUTATED MYH9 WILD-TYPE 
            10            210 
$`MYH9 MUTATED`
TCGA-BA-5153 TCGA-BA-A4IH TCGA-BA-A6DJ TCGA-CN-4728 TCGA-CN-6013 TCGA-CN-A6V6 
       57.93        20.45        13.38        56.68        23.90        20.88 
TCGA-CR-7386 TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7437 
       47.01        30.08        53.95        28.34         2.50        16.64 
TCGA-CV-A45Q TCGA-CV-A463 TCGA-CV-A6JT TCGA-F7-A620 TCGA-IQ-7630 TCGA-P3-A6T2 
      169.38         0.76        28.01        17.85        15.95        75.55 
TCGA-QK-A6VB TCGA-T2-A6X2 TCGA-UF-A7JJ 
       21.07        32.45        18.05 

$`MYH9 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5555 
       13.64         9.07        26.50        23.74        42.35        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       23.84        65.59        15.52        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
        4.01        41.85        29.42        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL 
        5.69        14.47         7.82         2.27        11.05        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.80         4.41 
TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ 
       18.38        66.28        71.05        20.52        10.55        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 
       12.92         8.81         6.28        12.69        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
        4.67        12.89        26.86        32.81        52.14        55.56 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       57.11        12.99        20.55        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       73.61        13.05        42.02        46.32         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       71.31        69.70         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.57        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       30.67        48.00        47.44        28.04        19.07        34.13 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
        6.74        10.45        32.22        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 
        4.41        12.07         2.70        23.44        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 
       10.42        11.21         4.24        41.19        15.75        32.38 
TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       66.28        46.95        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       38.76        64.87        53.52        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       44.48        23.24        29.36        33.60        29.49        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       12.46        31.23        84.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
       26.27        58.42        50.01        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       16.90        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       12.46        22.78        15.75         9.27        47.18        39.16 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
       47.34        40.93        35.84         3.45         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       29.23         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       26.17        17.13        32.78        27.06        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       17.16       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       140.78        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
       15.09         6.08        65.82        10.98         7.13         8.42 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        4.14        64.83       172.67       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       89.65        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       95.34         4.96        11.87        47.97         2.10        49.71 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       18.41        57.47        35.54       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        0.46        22.85        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 
      100.57        14.89        56.48       156.49         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7440 
       84.49        19.76         7.17       153.86         6.38        22.19 
TCGA-CV-7446 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T 
       35.93        30.48        27.98        21.01       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
       35.47         1.05        45.96         6.51        88.87        48.20 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       60.43        67.86        56.61         7.07        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JU TCGA-CV-A6JY 
       35.34         6.38        29.79         6.48         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       23.47        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       16.14        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       12.36        28.77         7.63        22.59        24.95        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       12.10        12.79        23.34        58.45        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       18.02        20.45        37.58        41.59        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       21.63        20.25         3.02        31.13        18.94        24.95 
TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
        0.46        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.06        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        3.65         6.90        38.53        14.50        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       37.41         0.07        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       19.04        15.48        19.27        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       30.05         1.84        12.62         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
       16.08        17.98        29.92        15.78        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 
       10.85        36.82        47.01        19.00        18.97         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       29.00        12.99        16.01        13.15        21.07        21.21 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       23.15         7.30        21.47         9.34        12.72        27.39 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       19.73        12.89         5.62        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       15.32         8.32        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
        7.10        13.71         3.12        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
       64.80        54.67         2.83        49.51        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK 
       74.47        17.95        24.30        55.43        29.46        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  MYH9 MUTATED MYH9 WILD-TYPE 
          0.76           0.07 
  MYH9 MUTATED MYH9 WILD-TYPE 
        169.38         210.97 
  MYH9 MUTATED MYH9 WILD-TYPE 
         23.90          20.65 
[1] "0.8 - 169.4 (23.9)" "0.1 - 211.0 (20.6)"
[1] "hr=" "1.1"
D57V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  MYH9 MUTATED         0        4         4        10         0         0
  MYH9 WILD-TYPE      25       71        76       243        11         1
D57V3, multiclass
           clus
vv          MYH9 MUTATED MYH9 WILD-TYPE
  STAGE I              0             25
  STAGE II             4             71
  STAGE III            4             76
  STAGE IVA           10            243
  STAGE IVB            0             11
  STAGE IVC            0              1
[1] 6 2
[1] 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
  MYH9 MUTATED       0   7   6   7
  MYH9 WILD-TYPE    47 130  93 165
D57V4, multiclass
       clus
vv      MYH9 MUTATED MYH9 WILD-TYPE
  T0+T1            0             47
  T2               7            130
  T3               6             93
  T4               7            165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MYH9 MUTATED     9   2   7   0
  MYH9 WILD-TYPE 166  65 161   7
D57V5, multiclass
    clus
vv   MYH9 MUTATED MYH9 WILD-TYPE
  N0            9            166
  N1            2             65
  N2            7            161
  N3            0              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
  MYH9 MUTATED     9   0
  MYH9 WILD-TYPE 182   1
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH9 MUTATED      9    0
  MYH9 WILD-TYPE  182    1
   clus
vv  MYH9 MUTATED MYH9 WILD-TYPE
  0            9            182
  1            0              1
[1] 2 2
[1] FALSE
D57V7, binary
                cls
clus               0   1
  MYH9 MUTATED     3  18
  MYH9 WILD-TYPE 135 355
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH9 MUTATED      3   18
  MYH9 WILD-TYPE  135  355
        clus
vv       MYH9 MUTATED MYH9 WILD-TYPE
  FEMALE            3            135
  MALE             18            355
[1] 2 2
[1] FALSE
D57V8, binary
                cls
clus               0   1
  MYH9 MUTATED     5  14
  MYH9 WILD-TYPE 152 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH9 MUTATED      5   14
  MYH9 WILD-TYPE  152  279
     clus
vv    MYH9 MUTATED MYH9 WILD-TYPE
  NO             5            152
  YES           14            279
[1] 2 2
[1] FALSE
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA
  MYH9 MUTATED                                    20
  MYH9 WILD-TYPE                                 480
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  MYH9 MUTATED                                                   1
  MYH9 WILD-TYPE                                                 9
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  MYH9 MUTATED                                                           0
  MYH9 WILD-TYPE                                                         1
D57V9, multiclass
                                                           clus
vv                                                          MYH9 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                 20
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT            0
                                                           clus
vv                                                          MYH9 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  480
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V10, continuous
D57V11, continuous
D57V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYH9 MUTATED                                  0     1
  MYH9 WILD-TYPE                                2     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MYH9 MUTATED                           1    17
  MYH9 WILD-TYPE                        46   420
D57V13, multiclass
                                  clus
vv                                 MYH9 MUTATED MYH9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             46
  WHITE                                      17            420
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V14, binary
                cls
clus               0   1
  MYH9 MUTATED     2  16
  MYH9 WILD-TYPE  23 433
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH9 MUTATED      2   16
  MYH9 WILD-TYPE   23  433
                        clus
vv                       MYH9 MUTATED MYH9 WILD-TYPE
  HISPANIC OR LATINO                2             23
  NOT HISPANIC OR LATINO           16            433
[1] 2 2
[1] FALSE

Clustering(58) Variable = NOTCH2 MUTATION ANALYSIS
D58V1, survival
                  sevent
clus2                0   1
  NOTCH2 MUTATED     8  13
  NOTCH2 WILD-TYPE 281 207
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
              21              488 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
              13              207 
$`NOTCH2 MUTATED`
TCGA-CN-4727 TCGA-CN-6021 TCGA-BA-6870 TCGA-CN-4726 TCGA-CN-6018 TCGA-CN-6989 
       51.29         9.07        14.83         4.67        19.07        32.22 
TCGA-CN-A498 TCGA-CR-7364 TCGA-CR-7383 TCGA-CR-7394 TCGA-CV-6003 TCGA-CV-6937 
       25.41        47.18        17.13        44.25        54.74        20.52 
TCGA-CV-7178 TCGA-CV-7427 TCGA-CV-7568 TCGA-CV-A45P TCGA-CX-A4AQ TCGA-DQ-5631 
       71.21       156.49        30.48        21.01        51.12        18.02 
TCGA-MT-A67A TCGA-P3-A6SX TCGA-P3-A6T0 
       30.05        47.01        19.00 

$`NOTCH2 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 
       30.18        25.71         9.24        52.08        11.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       32.48        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 
       43.04        11.61        34.52         6.02         0.36        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       30.94        14.04        40.24        21.11        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       48.03         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       65.59        15.52        21.17        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.80         4.41 
TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ 
       18.38        66.28        71.05        20.52        10.55        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 
       12.92         8.81         6.28        12.69        55.86        38.04 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       56.68        12.89        26.86        32.81        52.14        55.56 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       57.11        12.99        20.55        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       73.61        13.05        42.02        46.32         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       71.31        69.70         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.57        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
       30.67        48.00        23.90        47.44        28.04        34.13 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
        6.74        10.45        38.89         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       35.01        23.57        17.29        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 
       11.21         4.24        41.19        15.75        32.38        66.28 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       58.42        50.01        39.52        36.99        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       22.78        15.75         9.27        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 
       31.96         9.17        34.06        19.92        26.17        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        49.58        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       32.65        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       29.95        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       76.24        19.20        17.95       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
       48.59        60.49         7.07        43.23        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 
        9.60        90.12         2.14         9.70         5.46         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       21.90        26.43        11.24       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       42.38        15.09        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       10.98         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       172.67       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        9.01         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       10.75       130.88        77.16         4.73        89.65        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       31.36        26.20        18.97        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
       11.87        47.97         2.10        49.71        18.41        57.47 
TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       35.54       210.97        89.33         9.67         0.46        22.85 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 
       25.08        25.94         0.07        34.09       100.57        14.89 
TCGA-CV-7425 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
       56.48         3.52        16.27        84.49        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A45O 
      153.86        16.64         6.38        22.19        35.93        27.98 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
      169.38       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       56.61         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 
       19.92        22.52        10.42        10.55        18.84        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        7.63        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7591 TCGA-DQ-7592 
       23.34        58.45        37.25        33.86        20.45        37.58 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       31.13        18.94        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       20.25        12.43        13.38        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
       33.76        28.47        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         0.36        13.84         4.27         3.65         6.90 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
        0.07        33.57         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D 
       15.48        19.27        10.75        14.37         7.96         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         6.25        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        71.74        51.25        10.85        36.82 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        27.39        21.07        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.72        16.96         6.87        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       13.71         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        32.65        17.03        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
            4.67             0.07 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
          156.49           210.97 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
           30.05            20.65 
[1] "4.7 - 156.5 (30.1)" "0.1 - 211.0 (20.6)"
[1] "hr=" "1.2"
D58V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  NOTCH2 MUTATED         3        2         4         9         0         0
  NOTCH2 WILD-TYPE      22       73        76       244        11         1
D58V3, multiclass
           clus
vv          NOTCH2 MUTATED NOTCH2 WILD-TYPE
  STAGE I                3               22
  STAGE II               2               73
  STAGE III              4               76
  STAGE IVA              9              244
  STAGE IVB              0               11
  STAGE IVC              0                1
[1] 6 2
[1] 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
  NOTCH2 MUTATED       3   5   4   6
  NOTCH2 WILD-TYPE    44 132  95 166
D58V4, multiclass
       clus
vv      NOTCH2 MUTATED NOTCH2 WILD-TYPE
  T0+T1              3               44
  T2                 5              132
  T3                 4               95
  T4                 6              166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  NOTCH2 MUTATED     9   2   5   0
  NOTCH2 WILD-TYPE 166  65 163   7
D58V5, multiclass
    clus
vv   NOTCH2 MUTATED NOTCH2 WILD-TYPE
  N0              9              166
  N1              2               65
  N2              5              163
  N3              0                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"
D58V6, binary
                  cls
clus                 0   1
  NOTCH2 MUTATED     5   0
  NOTCH2 WILD-TYPE 186   1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      5    0
  NOTCH2 WILD-TYPE  186    1
   clus
vv  NOTCH2 MUTATED NOTCH2 WILD-TYPE
  0              5              186
  1              0                1
[1] 2 2
[1] FALSE
D58V7, binary
                  cls
clus                 0   1
  NOTCH2 MUTATED    12   9
  NOTCH2 WILD-TYPE 126 364
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED     12    9
  NOTCH2 WILD-TYPE  126  364
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  FEMALE             12              126
  MALE                9              364
[1] 2 2
[1] FALSE
D58V8, binary
                  cls
clus                 0   1
  NOTCH2 MUTATED     7  10
  NOTCH2 WILD-TYPE 150 283
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      7   10
  NOTCH2 WILD-TYPE  150  283
     clus
vv    NOTCH2 MUTATED NOTCH2 WILD-TYPE
  NO               7              150
  YES             10              283
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  NOTCH2 MUTATED                                    21
  NOTCH2 WILD-TYPE                                 479
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  NOTCH2 MUTATED                                                   0
  NOTCH2 WILD-TYPE                                                10
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  NOTCH2 MUTATED                                                           0
  NOTCH2 WILD-TYPE                                                         1
D58V9, multiclass
                                                           clus
vv                                                          NOTCH2 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   21
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          NOTCH2 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    479
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V10, continuous
D58V11, continuous
D58V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOTCH2 MUTATED                                  0     0
  NOTCH2 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NOTCH2 MUTATED                           1    20
  NOTCH2 WILD-TYPE                        46   417
D58V13, multiclass
                                  clus
vv                                 NOTCH2 MUTATED NOTCH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               46
  WHITE                                        20              417
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V14, binary
                  cls
clus                 0   1
  NOTCH2 MUTATED     0  21
  NOTCH2 WILD-TYPE  25 428
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      0   21
  NOTCH2 WILD-TYPE   25  428
                        clus
vv                       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  HISPANIC OR LATINO                  0               25
  NOT HISPANIC OR LATINO             21              428
[1] 2 2
[1] FALSE

Clustering(59) Variable = NCOR1 MUTATION ANALYSIS
D59V1, survival
                 sevent
clus2               0   1
  NCOR1 MUTATED    10   7
  NCOR1 WILD-TYPE 279 213
  NCOR1 MUTATED NCOR1 WILD-TYPE 
             17             492 
  NCOR1 MUTATED NCOR1 WILD-TYPE 
              7             213 
$`NCOR1 MUTATED`
TCGA-CN-6992 TCGA-CQ-5331 TCGA-CQ-A4CD TCGA-CR-6481 TCGA-CV-5444 TCGA-CV-6441 
       35.05        45.99        33.60        10.22        80.12         9.60 
TCGA-CV-7245 TCGA-CV-7252 TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7427 TCGA-CV-7568 
       26.20         4.96        35.54         0.46       156.49        30.48 
TCGA-CV-A6JM TCGA-F7-A624 TCGA-MT-A67F TCGA-MZ-A7D7 TCGA-QK-A6VB 
        6.38        12.43        12.62        17.98        21.07 

$`NCOR1 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       11.08        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       23.84        65.59        15.52        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 
        4.80         4.41        18.38        66.28        71.05        20.52 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       10.55        27.19        12.92         8.81         6.28        12.69 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       55.86        38.04         4.67        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       32.81        52.14        55.56        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       46.32         8.58        12.39        71.31        69.70         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       16.21        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       32.22        38.89         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       25.41        23.57        17.29        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 
        2.93        54.58        70.45        62.37        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 
        4.24        41.19        15.75        32.38        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       56.58        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       53.52        41.88        43.10        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       29.36        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6482 
       39.52        36.99        18.54        16.90        11.90        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       47.18        39.16        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.09        24.95        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       29.95        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       76.24        19.20        17.95       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       91.53        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       60.49         7.07        43.23        54.74        21.07        62.43 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       90.12         2.14         9.70         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       21.90        26.43        11.24       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       42.38        15.09        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       10.98         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       172.67       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        9.01         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        89.65 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 
       36.00        31.36        18.97        17.13        95.34        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7410 
       47.97         2.10        49.71        18.41        57.47       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
       89.33         9.67        22.85        25.08        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7429 TCGA-CV-7430 
       34.09       100.57        14.89        56.48         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       84.49        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       22.19        35.93        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       48.20        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
       15.25         5.98        35.34        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        51.12        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
       23.05         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN 
       25.32        17.72        12.36        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        13.94        12.10        12.79        23.34        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 
       37.25        33.86        18.02        20.45        37.58        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       37.18        32.71        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        24.95         0.46        17.85        11.80        20.25 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       13.38        15.16        15.06        20.94        33.76        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       25.74        21.93        27.48        14.66        22.03         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         3.65         6.90        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        37.71        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G 
       10.75        14.37         7.96        30.05         1.84         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
       15.42         7.13        16.08        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       18.97         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       12.72        27.39        19.73        12.89         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        6.87        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       32.65        17.03        20.55        14.56        13.35        18.15 

  NCOR1 MUTATED NCOR1 WILD-TYPE 
           0.46            0.07 
  NCOR1 MUTATED NCOR1 WILD-TYPE 
         156.49          210.97 
  NCOR1 MUTATED NCOR1 WILD-TYPE 
          21.07           20.91 
[1] "0.5 - 156.5 (21.1)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1.1"
D59V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  NCOR1 MUTATED         0        3         1        10         0         0
  NCOR1 WILD-TYPE      25       72        79       243        11         1
D59V3, multiclass
           clus
vv          NCOR1 MUTATED NCOR1 WILD-TYPE
  STAGE I               0              25
  STAGE II              3              72
  STAGE III             1              79
  STAGE IVA            10             243
  STAGE IVB             0              11
  STAGE IVC             0               1
[1] 6 2
[1] 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
  NCOR1 MUTATED       0   4   3   8
  NCOR1 WILD-TYPE    47 133  96 164
D59V4, multiclass
       clus
vv      NCOR1 MUTATED NCOR1 WILD-TYPE
  T0+T1             0              47
  T2                4             133
  T3                3              96
  T4                8             164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NCOR1 MUTATED     6   1   3   0
  NCOR1 WILD-TYPE 169  66 165   7
D59V5, multiclass
    clus
vv   NCOR1 MUTATED NCOR1 WILD-TYPE
  N0             6             169
  N1             1              66
  N2             3             165
  N3             0               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
  NCOR1 MUTATED     3   0
  NCOR1 WILD-TYPE 188   1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOR1 MUTATED      3    0
  NCOR1 WILD-TYPE  188    1
   clus
vv  NCOR1 MUTATED NCOR1 WILD-TYPE
  0             3             188
  1             0               1
[1] 2 2
[1] FALSE
D59V7, binary
                 cls
clus                0   1
  NCOR1 MUTATED     6  11
  NCOR1 WILD-TYPE 132 362
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOR1 MUTATED      6   11
  NCOR1 WILD-TYPE  132  362
        clus
vv       NCOR1 MUTATED NCOR1 WILD-TYPE
  FEMALE             6             132
  MALE              11             362
[1] 2 2
[1] FALSE
D59V8, binary
                 cls
clus                0   1
  NCOR1 MUTATED     6   7
  NCOR1 WILD-TYPE 151 286
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOR1 MUTATED      6    7
  NCOR1 WILD-TYPE  151  286
     clus
vv    NCOR1 MUTATED NCOR1 WILD-TYPE
  NO              6             151
  YES             7             286
[1] 2 2
[1] FALSE
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA
  NCOR1 MUTATED                                    17
  NCOR1 WILD-TYPE                                 483
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  NCOR1 MUTATED                                                   0
  NCOR1 WILD-TYPE                                                10
                 vv
clus              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  NCOR1 MUTATED                                                           0
  NCOR1 WILD-TYPE                                                         1
D59V9, multiclass
                                                           clus
vv                                                          NCOR1 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  17
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             0
                                                           clus
vv                                                          NCOR1 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                   483
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, continuous
D59V11, continuous
D59V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCOR1 MUTATED                                  0     0
  NCOR1 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NCOR1 MUTATED                           2    15
  NCOR1 WILD-TYPE                        45   422
D59V13, multiclass
                                  clus
vv                                 NCOR1 MUTATED NCOR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              45
  WHITE                                       15             422
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V14, binary
                 cls
clus                0   1
  NCOR1 MUTATED     2  15
  NCOR1 WILD-TYPE  23 434
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOR1 MUTATED      2   15
  NCOR1 WILD-TYPE   23  434
                        clus
vv                       NCOR1 MUTATED NCOR1 WILD-TYPE
  HISPANIC OR LATINO                 2              23
  NOT HISPANIC OR LATINO            15             434
[1] 2 2
[1] FALSE

Clustering(60) Variable = AK5 MUTATION ANALYSIS
D60V1, survival
               sevent
clus2             0   1
  AK5 MUTATED     4   9
  AK5 WILD-TYPE 285 211
  AK5 MUTATED AK5 WILD-TYPE 
           13           496 
  AK5 MUTATED AK5 WILD-TYPE 
            9           211 
$`AK5 MUTATED`
TCGA-BA-A6DF TCGA-CN-A63U TCGA-CR-7398 TCGA-CV-5970 TCGA-CV-6441 TCGA-CV-7104 
        7.82        31.69         5.13        13.35         9.60        12.92 
TCGA-CV-7263 TCGA-CV-A45V TCGA-CV-A6K2 TCGA-D6-A6EQ TCGA-QK-A8Z9 TCGA-UF-A7JJ 
       18.41         1.05        10.42        12.10        14.76        18.05 
TCGA-UF-A7JT 
       32.65 

$`AK5 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DI 
       11.54         7.10         5.69        14.47         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 
        4.80         4.41        18.38        66.28        71.05        20.52 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       10.55        27.19        12.92         8.81         6.28        12.69 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       55.86        38.04         4.67        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       32.81        52.14        55.56        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       46.32         8.58        12.39        71.31        69.70         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       16.21        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       32.22        38.89         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       25.41        23.57        17.29        29.72        21.21         7.40 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       23.44        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 
        4.24        41.19        15.75        32.38        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       56.58        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       53.52        41.88        43.10        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       15.75         9.27        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 
       46.85        32.65        44.25        30.58        24.79         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      108.95        76.24        19.20        17.95       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 
       76.50        91.53        80.12        17.92        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
       62.43        90.12         2.14         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       65.82        10.98         7.13         8.42        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        4.14        64.83       172.67       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7177 
        7.99         9.01         5.26         1.84        52.31        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        89.65 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 
       36.00        31.36        26.20        18.97        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7406 
        4.96        11.87        47.97         2.10        49.71        57.47 
TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       35.54       210.97        89.33         9.67         0.46        22.85 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 
       25.08        25.94         0.07        34.09       100.57        14.89 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       56.48       156.49         3.52        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 
        7.17       153.86        16.64         6.38        22.19        35.93 
TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
       30.48        27.98        21.01       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
       35.47        45.96         6.51        88.87        48.20        60.43 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       67.86         0.76        56.61         7.07        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       35.34         6.38        29.79         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7085 TCGA-CX-7086 
       21.24        23.47        19.92        22.52        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       16.14        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       12.36        28.77         7.63        22.59        24.95        13.94 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        23.34        58.45        37.25        33.86        18.02 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       20.45        37.58        41.59        37.18        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       17.85        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.06        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        3.65         6.90        15.95        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        37.41         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       13.84        19.04        15.48        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       18.97         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        27.39        21.07        19.73        12.89         5.62 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        6.87        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UP-A6WW 
       55.43        29.46        13.94        20.75        22.36        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.55        14.56        13.35        18.15 

  AK5 MUTATED AK5 WILD-TYPE 
         1.05          0.07 
  AK5 MUTATED AK5 WILD-TYPE 
        32.65        210.97 
  AK5 MUTATED AK5 WILD-TYPE 
        12.92         21.09 
[1] "1.1 - 32.6 (12.9)"  "0.1 - 211.0 (21.1)"
[1] "hr=" "3"  
D60V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  AK5 MUTATED         0        2         1        10         0         0
  AK5 WILD-TYPE      25       73        79       243        11         1
D60V3, multiclass
           clus
vv          AK5 MUTATED AK5 WILD-TYPE
  STAGE I             0            25
  STAGE II            2            73
  STAGE III           1            79
  STAGE IVA          10           243
  STAGE IVB           0            11
  STAGE IVC           0             1
[1] 6 2
[1] 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
  AK5 MUTATED       0   3   2   8
  AK5 WILD-TYPE    47 134  97 164
D60V4, multiclass
       clus
vv      AK5 MUTATED AK5 WILD-TYPE
  T0+T1           0            47
  T2              3           134
  T3              2            97
  T4              8           164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  AK5 MUTATED     7   1   4   0
  AK5 WILD-TYPE 168  66 164   7
D60V5, multiclass
    clus
vv   AK5 MUTATED AK5 WILD-TYPE
  N0           7           168
  N1           1            66
  N2           4           164
  N3           0             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
  AK5 MUTATED     7   0
  AK5 WILD-TYPE 184   1
[1] "tbl2"
               cls
clus            [,1] [,2]
  AK5 MUTATED      7    0
  AK5 WILD-TYPE  184    1
   clus
vv  AK5 MUTATED AK5 WILD-TYPE
  0           7           184
  1           0             1
[1] 2 2
[1] FALSE
D60V7, binary
               cls
clus              0   1
  AK5 MUTATED     5   8
  AK5 WILD-TYPE 133 365
[1] "tbl2"
               cls
clus            [,1] [,2]
  AK5 MUTATED      5    8
  AK5 WILD-TYPE  133  365
        clus
vv       AK5 MUTATED AK5 WILD-TYPE
  FEMALE           5           133
  MALE             8           365
[1] 2 2
[1] FALSE
D60V8, binary
               cls
clus              0   1
  AK5 MUTATED     4   7
  AK5 WILD-TYPE 153 286
[1] "tbl2"
               cls
clus            [,1] [,2]
  AK5 MUTATED      4    7
  AK5 WILD-TYPE  153  286
     clus
vv    AK5 MUTATED AK5 WILD-TYPE
  NO            4           153
  YES           7           286
[1] 2 2
[1] FALSE
               vv
clus            HEAD & NECK SQUAMOUS CELL CARCINOMA
  AK5 MUTATED                                    13
  AK5 WILD-TYPE                                 487
               vv
clus            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AK5 MUTATED                                                   0
  AK5 WILD-TYPE                                                10
               vv
clus            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AK5 MUTATED                                                           0
  AK5 WILD-TYPE                                                         1
D60V9, multiclass
                                                           clus
vv                                                          AK5 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                13
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                   0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT           0
                                                           clus
vv                                                          AK5 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                 487
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V10, continuous
D60V11, continuous
D60V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AK5 MUTATED                                  0     0
  AK5 WILD-TYPE                                2    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  AK5 MUTATED                           2    10
  AK5 WILD-TYPE                        45   427
D60V13, multiclass
                                  clus
vv                                 AK5 MUTATED AK5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  2            45
  WHITE                                     10           427
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V14, binary
               cls
clus              0   1
  AK5 MUTATED     2   8
  AK5 WILD-TYPE  23 441
[1] "tbl2"
               cls
clus            [,1] [,2]
  AK5 MUTATED      2    8
  AK5 WILD-TYPE   23  441
                        clus
vv                       AK5 MUTATED AK5 WILD-TYPE
  HISPANIC OR LATINO               2            23
  NOT HISPANIC OR LATINO           8           441
[1] 2 2
[1] FALSE

Clustering(61) Variable = SPTY2D1 MUTATION ANALYSIS
D61V1, survival
                   sevent
clus2                 0   1
  SPTY2D1 MUTATED     5   5
  SPTY2D1 WILD-TYPE 284 215
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
               10               499 
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
                5               215 
$`SPTY2D1 MUTATED`
TCGA-BA-5559 TCGA-DQ-7588 TCGA-BA-4078 TCGA-CN-4723 TCGA-CN-4736 TCGA-CR-7374 
       68.48        14.04         9.07        55.86        12.99         0.99 
TCGA-CR-7402 TCGA-CV-5436 TCGA-F7-A624 TCGA-KU-A6H7 
       29.95        19.20        12.43        19.27 

$`SPTY2D1 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       34.36        30.94        40.24        21.11        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5149 
       48.03         2.96         3.35        15.19        13.64        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 
       23.74        42.35        57.93        17.10        23.84        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       15.52        21.17        14.83        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.80         4.41 
TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ 
       18.38        66.28        71.05        20.52        10.55        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 
       12.92         8.81         6.28        12.69        38.04         4.67 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       56.68        12.89        26.86        32.81        52.14        55.56 
TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       57.11        20.55        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        42.02        46.32         8.58        12.39        71.31 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       69.70         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
       12.49         8.52        52.08        56.94        50.07        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       48.00        23.90        47.44        28.04        19.07        34.13 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
        6.74        10.45        32.22        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 
       45.99        10.42        11.21         4.24        41.19        15.75 
TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.38        66.28        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       14.99        38.76        64.87        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       77.56        44.48        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       14.14        12.46        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       37.87        26.27        58.42        50.01        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        22.78        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       39.16        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       24.95        29.23        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       26.17        17.13        32.78        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       49.58        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 
       24.79         5.13         5.95        35.41        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 
       17.16       129.21       108.95        76.24        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       54.74        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        9.70         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       140.78        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        8.42        28.34         2.50         4.14        64.83       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      111.16        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        1.84        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       47.97         2.10        49.71        18.41        57.47        35.54 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
      210.97        89.33         9.67         0.46        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
       25.94         0.07        34.09       100.57        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
      156.49         3.52        16.27        84.49        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 
      153.86        16.64         6.38        22.19        35.93        30.48 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        21.01       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
        1.05        45.96         6.51        88.87        48.20        60.43 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       67.86         0.76        56.61         7.07        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       35.34         6.38        29.79         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        51.12        13.25        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
        2.53        16.14        11.44        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-7848 
       33.86        18.02        20.45        37.58        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-7774 
       24.95         0.46        17.85        11.80        20.25        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       21.93        27.48        14.66        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65         6.90        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H8 TCGA-MT-A51W 
       13.68        13.84        19.04        15.48        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       18.97         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        27.39        21.07        19.73        12.89         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       16.96         6.87        15.91         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        3.12        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        2.83        49.51        49.45        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
             0.99              0.07 
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
            68.48            210.97 
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
            16.62             21.07 
[1] "1.0 - 68.5 (16.6)"  "0.1 - 211.0 (21.1)"
[1] "hr=" "1.4"
D61V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  SPTY2D1 MUTATED         0        1         0         3         0         0
  SPTY2D1 WILD-TYPE      25       74        80       250        11         1
D61V3, multiclass
           clus
vv          SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  STAGE I                 0                25
  STAGE II                1                74
  STAGE III               0                80
  STAGE IVA               3               250
  STAGE IVB               0                11
  STAGE IVC               0                 1
[1] 6 2
[1] 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
  SPTY2D1 MUTATED       1   2   1   1
  SPTY2D1 WILD-TYPE    46 135  98 171
D61V4, multiclass
       clus
vv      SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  T0+T1               1                46
  T2                  2               135
  T3                  1                98
  T4                  1               171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SPTY2D1 MUTATED     1   0   2   0
  SPTY2D1 WILD-TYPE 174  67 166   7
D61V5, multiclass
    clus
vv   SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  N0               1               174
  N1               0                67
  N2               2               166
  N3               0                 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"
D61V6, binary
                   cls
clus                  0   1
  SPTY2D1 MUTATED     2   0
  SPTY2D1 WILD-TYPE 189   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPTY2D1 MUTATED      2    0
  SPTY2D1 WILD-TYPE  189    1
   clus
vv  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  0               2               189
  1               0                 1
[1] 2 2
[1] FALSE
D61V7, binary
                   cls
clus                  0   1
  SPTY2D1 MUTATED     3   7
  SPTY2D1 WILD-TYPE 135 366
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPTY2D1 MUTATED      3    7
  SPTY2D1 WILD-TYPE  135  366
        clus
vv       SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  FEMALE               3               135
  MALE                 7               366
[1] 2 2
[1] FALSE
D61V8, binary
                   cls
clus                  0   1
  SPTY2D1 MUTATED     5   5
  SPTY2D1 WILD-TYPE 152 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPTY2D1 MUTATED      5    5
  SPTY2D1 WILD-TYPE  152  288
     clus
vv    SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  NO                5               152
  YES               5               288
[1] 2 2
[1] FALSE
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA
  SPTY2D1 MUTATED                                    10
  SPTY2D1 WILD-TYPE                                 490
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  SPTY2D1 MUTATED                                                   0
  SPTY2D1 WILD-TYPE                                                10
                   vv
clus                HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  SPTY2D1 MUTATED                                                           0
  SPTY2D1 WILD-TYPE                                                         1
D61V9, multiclass
                                                           clus
vv                                                          SPTY2D1 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    10
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT               0
                                                           clus
vv                                                          SPTY2D1 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                     490
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, continuous
D61V11, continuous
D61V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPTY2D1 MUTATED                                  0     0
  SPTY2D1 WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SPTY2D1 MUTATED                           0     9
  SPTY2D1 WILD-TYPE                        47   428
D61V13, multiclass
                                  clus
vv                                 SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                47
  WHITE                                          9               428
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V14, binary
                   cls
clus                  0   1
  SPTY2D1 MUTATED     1   9
  SPTY2D1 WILD-TYPE  24 440
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPTY2D1 MUTATED      1    9
  SPTY2D1 WILD-TYPE   24  440
                        clus
vv                       SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  HISPANIC OR LATINO                   1                24
  NOT HISPANIC OR LATINO               9               440
[1] 2 2
[1] FALSE

Clustering(62) Variable = PIWIL2 MUTATION ANALYSIS
D62V1, survival
                  sevent
clus2                0   1
  PIWIL2 MUTATED     5   2
  PIWIL2 WILD-TYPE 284 218
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
               7              502 
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
               2              218 
$`PIWIL2 MUTATED`
TCGA-CN-6992 TCGA-BB-8596 TCGA-CN-4729 TCGA-CR-7386 TCGA-CV-6961 TCGA-CV-7568 
       35.05        71.05        12.89        47.01         2.50        30.48 
TCGA-F7-A624 
       12.43 

$`PIWIL2 WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       11.08        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       34.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       23.84        65.59        15.52        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8601 TCGA-BB-A5HY 
        4.80         4.41        18.38        66.28        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 
       27.19        12.92         8.81         6.28        12.69        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       38.04         4.67        56.68        26.86        32.81        52.14 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       55.56        57.11        12.99        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        73.61        13.05        42.02        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       12.39        71.31        69.70         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.84        11.57        12.49         8.52        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
       19.07        34.13         6.74        10.45        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       17.29        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       70.45        62.37        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       41.19        15.75        32.38        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       11.34        11.64         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       29.95        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       76.24        19.20        17.95       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        4.14        64.83       172.67       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       89.65        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       95.34         4.96        11.87        47.97         2.10        49.71 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       18.41        57.47        35.54       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        0.46        22.85        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 
      100.57        14.89        56.48       156.49         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       84.49        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       22.19        35.93        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       48.20        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        37.25        33.86        18.02        20.45        37.58 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       31.13        18.94        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       20.25        13.38        15.16        15.06        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 
        0.36        13.84         4.27         3.65         6.90        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
       33.57         5.29        13.68        13.84        19.04        15.48 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.27        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         6.25        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        71.74        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        21.47         9.34        12.72        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       19.73        12.89         5.62        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       15.32         8.32        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ 
        7.10        32.45        13.71         3.12        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       20.35        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       18.05        13.94        20.75        22.36        32.65        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.55        14.56        13.35        18.15 

  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
            2.50             0.07 
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
           71.05           210.97 
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
           30.48            20.91 
[1] "2.5 - 71.0 (30.5)"  "0.1 - 211.0 (20.9)"
[1] "hr=" "1.5"
D62V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  PIWIL2 MUTATED         0        3         1         4         0         0
  PIWIL2 WILD-TYPE      25       72        79       249        11         1
D62V3, multiclass
           clus
vv          PIWIL2 MUTATED PIWIL2 WILD-TYPE
  STAGE I                0               25
  STAGE II               3               72
  STAGE III              1               79
  STAGE IVA              4              249
  STAGE IVB              0               11
  STAGE IVC              0                1
[1] 6 2
[1] 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
  PIWIL2 MUTATED       0   4   1   3
  PIWIL2 WILD-TYPE    47 133  98 169
D62V4, multiclass
       clus
vv      PIWIL2 MUTATED PIWIL2 WILD-TYPE
  T0+T1              0               47
  T2                 4              133
  T3                 1               98
  T4                 3              169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PIWIL2 MUTATED     2   1   2   0
  PIWIL2 WILD-TYPE 173  66 166   7
D62V5, multiclass
    clus
vv   PIWIL2 MUTATED PIWIL2 WILD-TYPE
  N0              2              173
  N1              1               66
  N2              2              166
  N3              0                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"
D62V6, binary
                  cls
clus                 0   1
  PIWIL2 MUTATED     3   0
  PIWIL2 WILD-TYPE 188   1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL2 MUTATED      3    0
  PIWIL2 WILD-TYPE  188    1
   clus
vv  PIWIL2 MUTATED PIWIL2 WILD-TYPE
  0              3              188
  1              0                1
[1] 2 2
[1] FALSE
D62V7, binary
                  cls
clus                 0   1
  PIWIL2 MUTATED     2   6
  PIWIL2 WILD-TYPE 136 367
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL2 MUTATED      2    6
  PIWIL2 WILD-TYPE  136  367
        clus
vv       PIWIL2 MUTATED PIWIL2 WILD-TYPE
  FEMALE              2              136
  MALE                6              367
[1] 2 2
[1] FALSE
D62V8, binary
                  cls
clus                 0   1
  PIWIL2 MUTATED     3   4
  PIWIL2 WILD-TYPE 154 289
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL2 MUTATED      3    4
  PIWIL2 WILD-TYPE  154  289
     clus
vv    PIWIL2 MUTATED PIWIL2 WILD-TYPE
  NO               3              154
  YES              4              289
[1] 2 2
[1] FALSE
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA
  PIWIL2 MUTATED                                     8
  PIWIL2 WILD-TYPE                                 492
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  PIWIL2 MUTATED                                                   0
  PIWIL2 WILD-TYPE                                                10
                  vv
clus               HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  PIWIL2 MUTATED                                                           0
  PIWIL2 WILD-TYPE                                                         1
D62V9, multiclass
                                                           clus
vv                                                          PIWIL2 MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    8
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          PIWIL2 WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                    492
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V10, continuous
D62V11, continuous
D62V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIWIL2 MUTATED                                  0     0
  PIWIL2 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIWIL2 MUTATED                           0     7
  PIWIL2 WILD-TYPE                        47   430
D62V13, multiclass
                                  clus
vv                                 PIWIL2 MUTATED PIWIL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               47
  WHITE                                         7              430
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V14, binary
                  cls
clus                 0   1
  PIWIL2 MUTATED     0   7
  PIWIL2 WILD-TYPE  25 442
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL2 MUTATED      0    7
  PIWIL2 WILD-TYPE   25  442
                        clus
vv                       PIWIL2 MUTATED PIWIL2 WILD-TYPE
  HISPANIC OR LATINO                  0               25
  NOT HISPANIC OR LATINO              7              442
[1] 2 2
[1] FALSE
