[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/19775211/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/20203267/transformed.cor.cli.txt"

nPatients in clinical file=528, in cluster file=510, common to both=510
[1]  49 510
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           359            151 
  TP53 MUTATED TP53 WILD-TYPE 
           359            151 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
             112              398 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
             112              398 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
             55             455 
  CASP8 MUTATED CASP8 WILD-TYPE 
             55             455 
[1] "NSD1 MUTATION ANALYSIS"
[1] 3
  NSD1 MUTATED NSD1 WILD-TYPE 
            63            447 
  NSD1 MUTATED NSD1 WILD-TYPE 
            63            447 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
             24             486 
  HLA-B MUTATED HLA-B WILD-TYPE 
             24             486 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            78            432 
  MLL2 MUTATED MLL2 WILD-TYPE 
            78            432 
[1] "TGFBR2 MUTATION ANALYSIS"
[1] 3
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              23              487 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              23              487 
[1] "FAT1 MUTATION ANALYSIS"
[1] 3
  FAT1 MUTATED FAT1 WILD-TYPE 
           114            396 
  FAT1 MUTATED FAT1 WILD-TYPE 
           114            396 
[1] "NOTCH1 MUTATION ANALYSIS"
[1] 3
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              87              423 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              87              423 
[1] "JUB MUTATION ANALYSIS"
[1] 3
  JUB MUTATED JUB WILD-TYPE 
           33           477 
  JUB MUTATED JUB WILD-TYPE 
           33           477 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              26              484 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              26              484 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             33             477 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             33             477 
[1] "ZNF750 MUTATION ANALYSIS"
[1] 3
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              19              491 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              19              491 
[1] "RAC1 MUTATION ANALYSIS"
[1] 3
  RAC1 MUTATED RAC1 WILD-TYPE 
            15            495 
  RAC1 MUTATED RAC1 WILD-TYPE 
            15            495 
[1] "EPHA2 MUTATION ANALYSIS"
[1] 3
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             24             486 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             24             486 
[1] "HLA-A MUTATION ANALYSIS"
[1] 3
  HLA-A MUTATED HLA-A WILD-TYPE 
             22             488 
  HLA-A MUTATED HLA-A WILD-TYPE 
             22             488 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            29            481 
  HRAS MUTATED HRAS WILD-TYPE 
            29            481 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              94              416 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              94              416 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
             39             471 
  EP300 MUTATED EP300 WILD-TYPE 
             39             471 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           18           492 
  RB1 MUTATED RB1 WILD-TYPE 
           18           492 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            14            496 
  PTEN MUTATED PTEN WILD-TYPE 
            14            496 
[1] "RASA1 MUTATION ANALYSIS"
[1] 3
  RASA1 MUTATED RASA1 WILD-TYPE 
             17             493 
  RASA1 MUTATED RASA1 WILD-TYPE 
             17             493 
[1] "MAPK1 MUTATION ANALYSIS"
[1] 3
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             501 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             501 
[1] "NAP1L2 MUTATION ANALYSIS"
[1] 3
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               7              503 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               7              503 
[1] "KEAP1 MUTATION ANALYSIS"
[1] 3
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             488 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             488 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
             17             493 
  KDM6A MUTATED KDM6A WILD-TYPE 
             17             493 
[1] "RHOA MUTATION ANALYSIS"
[1] 3
  RHOA MUTATED RHOA WILD-TYPE 
            10            500 
  RHOA MUTATED RHOA WILD-TYPE 
            10            500 
[1] "CREBBP MUTATION ANALYSIS"
[1] 3
  CREBBP MUTATED CREBBP WILD-TYPE 
              35              475 
  CREBBP MUTATED CREBBP WILD-TYPE 
              35              475 
[1] "NUDT11 MUTATION ANALYSIS"
[1] 3
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               8              502 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               8              502 
[1] "EMG1 MUTATION ANALYSIS"
[1] 3
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            506 
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            506 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             13             497 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             13             497 
[1] "CUL3 MUTATION ANALYSIS"
[1] 3
  CUL3 MUTATED CUL3 WILD-TYPE 
            14            496 
  CUL3 MUTATED CUL3 WILD-TYPE 
            14            496 
[1] "TIGD4 MUTATION ANALYSIS"
[1] 3
  TIGD4 MUTATED TIGD4 WILD-TYPE 
              7             503 
  TIGD4 MUTATED TIGD4 WILD-TYPE 
              7             503 
[1] "MYH9 MUTATION ANALYSIS"
[1] 3
  MYH9 MUTATED MYH9 WILD-TYPE 
            22            488 
  MYH9 MUTATED MYH9 WILD-TYPE 
            22            488 
[1] "C3ORF59 MUTATION ANALYSIS"
[1] 3
  C3ORF59 MUTATED C3ORF59 WILD-TYPE 
               11               499 
  C3ORF59 MUTATED C3ORF59 WILD-TYPE 
               11               499 
[1] "HUWE1 MUTATION ANALYSIS"
[1] 3
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             45             465 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             45             465 
[1] "SLC9A6 MUTATION ANALYSIS"
[1] 3
  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
               5              505 
  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
               5              505 
[1] "ZNF623 MUTATION ANALYSIS"
[1] 3
  ZNF623 MUTATED ZNF623 WILD-TYPE 
              11              499 
  ZNF623 MUTATED ZNF623 WILD-TYPE 
              11              499 
[1] "MLL4 MUTATION ANALYSIS"
[1] 3
  MLL4 MUTATED MLL4 WILD-TYPE 
            20            490 
  MLL4 MUTATED MLL4 WILD-TYPE 
            20            490 
[1] "CTCF MUTATION ANALYSIS"
[1] 3
  CTCF MUTATED CTCF WILD-TYPE 
            16            494 
  CTCF MUTATED CTCF WILD-TYPE 
            16            494 
[1] "NCOR1 MUTATION ANALYSIS"
[1] 3
  NCOR1 MUTATED NCOR1 WILD-TYPE 
             18             492 
  NCOR1 MUTATED NCOR1 WILD-TYPE 
             18             492 
[1] "PTPN14 MUTATION ANALYSIS"
[1] 3
  PTPN14 MUTATED PTPN14 WILD-TYPE 
              15              495 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
              15              495 
[1] "ITGB1 MUTATION ANALYSIS"
[1] 3
  ITGB1 MUTATED ITGB1 WILD-TYPE 
             13             497 
  ITGB1 MUTATED ITGB1 WILD-TYPE 
             13             497 
[1] "IRS4 MUTATION ANALYSIS"
[1] 3
  IRS4 MUTATED IRS4 WILD-TYPE 
            17            493 
  IRS4 MUTATED IRS4 WILD-TYPE 
            17            493 
[1] "SRPX MUTATION ANALYSIS"
[1] 3
  SRPX MUTATED SRPX WILD-TYPE 
             7            503 
  SRPX MUTATED SRPX WILD-TYPE 
             7            503 
[1] "KIAA1949 MUTATION ANALYSIS"
[1] 3
  KIAA1949 MUTATED KIAA1949 WILD-TYPE 
                 6                504 
  KIAA1949 MUTATED KIAA1949 WILD-TYPE 
                 6                504 
[1] "NOTCH2 MUTATION ANALYSIS"
[1] 3
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
              20              490 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
              20              490 
[1] "GAGE2A MUTATION ANALYSIS"
[1] 3
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               5              505 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               5              505 
[1] "LCP1 MUTATION ANALYSIS"
[1] 3
  LCP1 MUTATED LCP1 WILD-TYPE 
            15            495 
  LCP1 MUTATED LCP1 WILD-TYPE 
            15            495 
[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 510 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=200,	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=325,	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=5,	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=2,	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=22,	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=86,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=19,	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 510 columns, 1 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "GENDER"                        "RADIATION_THERAPY"            
 [7] "HISTOLOGICAL_TYPE"             "NUMBER_PACK_YEARS_SMOKED"     
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET" "NUMBER_OF_LYMPH_NODES"        
[11] "RACE"                          "ETHNICITY"                    
YEARS_TO_BIRTH, nv=60, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=5, 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  47 134  99 168 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   48   134    99   168 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  47 134  99 168 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   48   134    99   168 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
175  67 162   7 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
175  67 162   7 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
175  67 162   7 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
175  67 162   7 
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=86, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=58, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=19, 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   190 169
  TP53 WILD-TYPE 103  48
  TP53 MUTATED TP53 WILD-TYPE 
           359            151 
  TP53 MUTATED TP53 WILD-TYPE 
           169             48 
$`TP53 MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
       15.19         9.30        13.64         9.07        23.74        42.35 
TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        20.48        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6D8 
       12.62         4.01        41.85        29.42        30.18        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-A6DL TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-7871 
       20.48         9.14         4.41        36.72        66.28        24.66 
TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO 
       38.40        20.52        25.71        10.55        27.19         8.81 
TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
        6.28        55.86        38.04         4.67        51.29        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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       32.22        35.05        38.89         3.68        17.42        32.48 
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-CN-A6V3 TCGA-CQ-5326 
       31.69        12.39         4.41        12.07        24.39         2.93 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 
       70.45        62.37        45.99        10.42         4.24        41.19 
TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       15.75        32.38        32.88        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25        14.99        38.76        70.13        64.87        53.52 
TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       16.73        41.88        77.56        44.48        11.61        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CR-6474 TCGA-CR-6477 
       29.36        33.60        29.49        12.46        18.54        16.90 
TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
        6.02        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 
       29.82        32.65        44.25         7.10         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       126.15       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 
       47.47        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-7409 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 
       17.85         9.67         0.46        22.85        25.08        25.94 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
        0.07        34.09        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-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        18.84        34.36        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 
        9.60        23.05        16.14        11.44        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       17.72        12.36         7.63        24.95        13.94        12.10 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       11.11        58.45        30.94        33.86        18.02        14.04 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       46.32        37.58        39.12        37.18        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
        3.02        18.94        24.95         0.46        17.85        20.25 
TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
       12.43        15.16        13.61        21.11         0.07        28.47 
TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A633 
       21.93        27.48        14.66        12.66        22.85        13.84 
TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
        3.65        15.95        37.71        11.84        37.41        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66T 
        5.29        13.68        13.84        19.04        15.48        18.15 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA 
       10.75        14.37        15.42        17.98        15.78        71.74 
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-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH 
       16.01        13.15        21.07        21.21         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-T2-A6WZ 
        9.34        12.72        21.07        19.73        12.72        15.91 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       64.80        54.67         2.83        49.51        48.03        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       44.65        74.47        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7GZ 
       13.94        20.75        22.36        32.65        20.55 

$`TP53 WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6871 
       37.28        26.50        57.93        23.84        68.48         3.55 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6DF TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 
       28.11        20.45         7.82        13.38         6.15       105.90 
TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-8596 
        4.60        18.38        22.42        33.70        50.20        71.05 
TCGA-BB-A6UM TCGA-C9-A480 TCGA-CN-4730 TCGA-CN-4734 TCGA-CN-4741 TCGA-CN-5361 
       12.92        12.69        26.86        55.56        73.61        69.70 
TCGA-CN-5369 TCGA-CN-5374 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y 
       12.49        56.94        23.57        21.21        22.32        16.57 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
        2.70        23.44        19.82        20.88        19.53        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5333 TCGA-CQ-6227 TCGA-CQ-7068 
       52.37        21.50        54.58        11.21         4.24        43.04 
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-6472 
       37.87        26.27        58.42        50.01        39.52        34.52 
TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
       36.99        11.90        10.22        11.34         7.69        12.46 
TCGA-CR-6492 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7373 TCGA-CR-7382 TCGA-CR-7385 
       15.75        47.34        35.84        29.23        26.17        32.78 
TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7395 TCGA-CR-7404 TCGA-CV-5441 
       12.89        30.02        46.85        30.58        48.39        87.55 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6938 
       76.50        91.53        23.05        21.07         9.60         4.73 
TCGA-CV-6939 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6961 TCGA-CV-7100 TCGA-CV-7183 
       21.90        65.82        10.98         2.50         9.01       130.88 
TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7423 
       95.34        36.13        57.47       210.97        89.33       100.57 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45T 
       56.48       156.49         3.52        22.19        27.98       159.65 
TCGA-CV-A45V TCGA-CV-A6JO TCGA-CV-A6K0 TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-6827 
        1.05         6.48        19.92        10.55         2.53        18.67 
TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7591 
       28.77        22.59        12.79        37.25        46.45        20.45 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-A50J TCGA-F7-A622 TCGA-H7-7774 
       40.24        40.04        41.59        31.13        11.80        13.38 
TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 
       20.94        25.74        27.48        22.03         0.36         4.27 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61I TCGA-KU-A66S 
        6.90        34.75        38.53        14.50         0.07        13.35 
TCGA-KU-A6H7 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       19.27         7.96        30.05         1.84        12.62         6.25 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T6 
        7.13        16.08        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        18.64        16.96         6.87         7.10        32.45 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A7JC TCGA-UF-A7JV TCGA-UP-A6WW 
       13.55        13.25        20.35        17.95         2.96        17.03 
TCGA-WA-A7H4 
       14.56 

  TP53 MUTATED TP53 WILD-TYPE 
          0.07           0.07 
  TP53 MUTATED TP53 WILD-TYPE 
        180.16         210.97 
  TP53 MUTATED TP53 WILD-TYPE 
         20.55          22.32 
[1] "0.1 - 180.2 (20.6)" "0.1 - 211.0 (22.3)"
[1] "hr=" "1.7"
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  TP53 MUTATED        17       50        58       189         9
  TP53 WILD-TYPE       8       25        24        59         2
D1V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I             17              8
  STAGE II            50             25
  STAGE III           58             24
  STAGE IVA          189             59
  STAGE IVB            9              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  TP53 MUTATED      30  89  78 131
  TP53 WILD-TYPE    18  45  21  37
D1V4, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T0+T1           30             18
  T2              89             45
  T3              78             21
  T4             131             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  49 125   5
  TP53 WILD-TYPE  50  18  37   2
D1V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0          125             50
  N1           49             18
  N2          125             37
  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   100 259
  TP53 WILD-TYPE  40 111
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    100  259
  TP53 WILD-TYPE   40  111
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE          100             40
  MALE            259            111
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus               0   1
  TP53 MUTATED    99 195
  TP53 WILD-TYPE  47  79
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     99  195
  TP53 WILD-TYPE   47   79
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            99             47
  YES          195             79
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  TP53 MUTATED                                     357
  TP53 WILD-TYPE                                   145
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  TP53 MUTATED                                                             1
  TP53 WILD-TYPE                                                           0
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  TP53 MUTATED                                                     1
  TP53 WILD-TYPE                                                   6
D1V8, multiclass
                                                             clus
vv                                                            TP53 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                357
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    1
                                                             clus
vv                                                            TP53 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  145
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, continuous
D1V10, continuous
D1V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  2     8
  TP53 WILD-TYPE                                0     3
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                          29   306
  TP53 WILD-TYPE                         8   140
D1V12, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            2              0
  ASIAN                                       8              3
  BLACK OR AFRICAN AMERICAN                  29              8
  WHITE                                     306            140
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, binary
                cls
clus               0   1
  TP53 MUTATED    22 309
  TP53 WILD-TYPE   4 139
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     22  309
  TP53 WILD-TYPE    4  139
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO               22              4
  NOT HISPANIC OR LATINO          309            139
[1] 2 2
[1] FALSE

Clustering(2) Variable = CDKN2A MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2                0   1
  CDKN2A MUTATED    61  51
  CDKN2A WILD-TYPE 232 166
  CDKN2A MUTATED CDKN2A WILD-TYPE 
             112              398 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              51              166 
$`CDKN2A MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6872 
        9.30         9.07        42.35        20.48        65.59        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DG 
        4.01        41.85        29.42        11.54         5.69         2.27 
TCGA-BB-7862 TCGA-BB-A5HY TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4731 TCGA-CN-4736 
       36.72        10.55        12.69        55.86        32.81        12.99 
TCGA-CN-4738 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 
       14.33        12.39        71.31         8.52        52.08        48.00 
TCGA-CN-6013 TCGA-CN-6021 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A640 
       23.90         9.07        17.42        32.48        11.74         4.41 
TCGA-CN-A6V3 TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-6220 TCGA-CQ-6224 
       24.39         2.93        62.37        45.99        32.38        56.58 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-A4C6 TCGA-CQ-A4CD TCGA-CR-5247 TCGA-CR-6491 
       38.76        70.13        44.48        33.60        11.77        22.78 
TCGA-CR-6492 TCGA-CR-7370 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7386 TCGA-CR-7394 
       15.75         3.45        34.06        19.92        47.01        44.25 
TCGA-CV-5432 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
      129.21       107.51        80.12        86.83        48.59        60.49 
TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6951 
       54.74        62.43        11.24       140.78        19.79        30.08 
TCGA-CV-6953 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7101 TCGA-CV-7178 
       53.95         8.42         4.14       126.15         5.26        71.21 
TCGA-CV-7180 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7413 
       10.75        31.36        26.20        47.97         2.10         9.67 
TCGA-CV-7414 TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45P 
        0.46        14.89        84.49        30.48        27.98        21.01 
TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A45Z TCGA-CV-A465 TCGA-CV-A6JD TCGA-CV-A6JE 
      180.16        45.96        48.20         7.07         5.98        35.34 
TCGA-CV-A6JM TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6825 TCGA-D6-A6EM TCGA-D6-A6EN 
        6.38        13.25        25.41        16.14         7.63        22.59 
TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7595 TCGA-F7-A50I TCGA-F7-A61S TCGA-H7-8501 
       11.11        30.94        39.12         3.02        18.94        15.16 
TCGA-H7-A6C4 TCGA-HD-8224 TCGA-HD-A633 TCGA-IQ-A6SH TCGA-MT-A67A TCGA-P3-A5QA 
       13.61        14.66        13.84        15.48        30.05        71.74 
TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6II 
       47.01        18.97        21.07        21.21         7.30         9.34 
TCGA-QK-A6IJ TCGA-RS-A6TO TCGA-UF-A7J9 TCGA-UF-A7JO 
       12.72        12.72        44.65        20.75 

$`CDKN2A WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 
       15.19        13.64        37.28        26.50        23.74        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        68.48        15.52        21.17        14.83 
TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB 
        3.55        28.11        20.45        30.18        27.95         7.10 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 
       14.47         7.82        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       33.70        50.20        66.28        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        25.71        27.19        12.92         8.81         6.28 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       38.04         4.67        51.29        56.68        12.89        26.86 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 
       52.14        55.56        57.11        20.55        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5361 
       73.61        13.05        42.02        46.32         8.58        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-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       56.94        50.07        30.67        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
       34.13         6.74         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A498 
       32.22        35.05        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-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       19.82        20.88        19.53        48.20        52.37        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       54.58        70.45        10.42        11.21         4.24        41.19 
TCGA-CQ-6219 TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 
       15.75        32.88        66.28        46.95        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
       14.99        64.87        53.52        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE 
       43.10        77.56        11.61        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-6472 TCGA-CR-6473 
       26.27        58.42        50.01        39.52        34.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       18.54        16.90         6.02        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       11.64         7.69        12.46         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-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        0.99        31.96         9.17        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        29.82        30.02        46.85        32.65 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58         7.10         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
       48.39       139.43        17.16       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 
       17.95        87.55        76.50        91.53        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6933 
       23.05         7.07        43.23        21.07         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-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6954 
       26.43        12.03        42.38        15.09         6.08        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7091 
       10.98         7.13        28.34         2.50        64.83       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 
       18.81        12.66         7.99         9.01         1.84        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       12.92        21.80       130.88        77.16         4.73        47.47 
TCGA-CV-7242 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       36.00        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
       36.13        18.41        57.47        35.54        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
       89.33        22.85        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 
      100.57        56.48       156.49         3.52        16.27        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-A45Q TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y 
      169.38       159.65        35.47         1.05         6.51        88.87 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JN 
       60.43        67.86         0.76        56.61        15.25        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-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
       22.52        10.42        10.42        10.55        18.84        34.36 
TCGA-CX-A4AQ TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 
       51.12         9.60        23.05         2.53        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO 
       24.95        25.32        17.72        12.36        28.77        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-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       18.02        14.04        46.32        46.45        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       40.24        40.04        41.59        37.18        21.63        20.25 
TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       31.13        24.95         0.46        17.85        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       12.43        13.38        21.11        20.94         0.07        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 
       25.74        21.93        27.48        27.48        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
       22.85         0.36         4.27         3.65         6.90        34.75 
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-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        19.27        10.75        14.37         7.96 
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-A5Q6 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 
       17.98        15.78        51.25        10.85        36.82        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       75.55         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TP 
       23.15        21.47        18.64        21.07        19.73        16.96 
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-A71D 
       20.35        64.80        54.67         2.83        49.51        48.03 
TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       49.45        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       18.05        13.94        22.36        32.65         2.96        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            0.46             0.07 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
          180.16           210.97 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           21.90            21.09 
[1] "0.5 - 180.2 (21.9)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1"  
D2V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  CDKN2A MUTATED         7       12        25        51         1
  CDKN2A WILD-TYPE      18       63        57       197        10
D2V3, multiclass
           clus
vv          CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE I                7               18
  STAGE II              12               63
  STAGE III             25               57
  STAGE IVA             51              197
  STAGE IVB              1               10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CDKN2A MUTATED      11  26  24  37
  CDKN2A WILD-TYPE    37 108  75 131
D2V4, multiclass
       clus
vv      CDKN2A MUTATED CDKN2A WILD-TYPE
  T0+T1             11               37
  T2                26              108
  T3                24               75
  T4                37              131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CDKN2A MUTATED    36  17  32   0
  CDKN2A WILD-TYPE 139  50 130   7
D2V5, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  N0             36              139
  N1             17               50
  N2             32              130
  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    31  81
  CDKN2A WILD-TYPE 109 289
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     31   81
  CDKN2A WILD-TYPE  109  289
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE             31              109
  MALE               81              289
[1] 2 2
[1] FALSE
D2V7, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    29  62
  CDKN2A WILD-TYPE 117 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     29   62
  CDKN2A WILD-TYPE  117  212
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO              29              117
  YES             62              212
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  CDKN2A MUTATED                                     112
  CDKN2A WILD-TYPE                                   390
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  CDKN2A MUTATED                                                             0
  CDKN2A WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  CDKN2A MUTATED                                                     0
  CDKN2A WILD-TYPE                                                   7
D2V8, multiclass
                                                             clus
vv                                                            CDKN2A MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  112
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
                                                             clus
vv                                                            CDKN2A WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    390
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, continuous
D2V10, continuous
D2V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDKN2A MUTATED                                  0     3
  CDKN2A WILD-TYPE                                2     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED                           6   101
  CDKN2A WILD-TYPE                        31   345
D2V12, multiclass
                                  clus
vv                                 CDKN2A MUTATED CDKN2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     6               31
  WHITE                                       101              345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     7 101
  CDKN2A WILD-TYPE  19 347
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      7  101
  CDKN2A WILD-TYPE   19  347
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  7               19
  NOT HISPANIC OR LATINO            101              347
[1] 2 2
[1] FALSE

Clustering(3) Variable = CASP8 MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED    29  26
  CASP8 WILD-TYPE 264 191
  CASP8 MUTATED CASP8 WILD-TYPE 
             55             455 
  CASP8 MUTATED CASP8 WILD-TYPE 
             26             191 
$`CASP8 MUTATED`
TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-6873 TCGA-CN-4734 TCGA-CN-5369 TCGA-CN-A642 
       23.74        23.84         4.01        55.56        12.49         2.70 
TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6220 
       52.37        54.58        45.99        11.21         4.24        32.38 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7394 TCGA-CR-7395 
       43.04        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-H7-7774 TCGA-H7-8501 TCGA-HD-A4C1 TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A6T2 
       13.38        15.16         0.36         1.84        12.62        75.55 
TCGA-QK-A64Z TCGA-QK-A6IG TCGA-QK-A6VB TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6X2 
       21.07         7.30        21.07        12.72         6.87        32.45 
TCGA-UF-A7JO 
       20.75 

$`CASP8 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       42.35        57.93        17.10        20.48        65.59        68.48 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 
       15.52        21.17        14.83         3.55        12.62        41.85 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
       29.42        28.11        20.45        30.18        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-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       13.38        20.48         6.15       105.90         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.41        18.38        22.42        36.72        33.70        50.20 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU 
       66.28        24.66        38.40        71.05        20.52        25.71 
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-4727 TCGA-CN-4728 TCGA-CN-4729 
       55.86        38.04         4.67        51.29        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       26.86        32.81        52.14        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-5370 TCGA-CN-5373 
       16.21        11.54        11.84        11.57         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-6021 TCGA-CN-6022 
       28.04        19.07        34.13         6.74         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
       52.08        11.08        10.45        32.22        35.05        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        3.68        17.42        32.48        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-A6UY 
       22.32        12.39        16.57         4.41        12.07        23.44 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5325 
       19.82        24.39        20.88        19.53        48.20        21.50 
TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6219 
        2.93        70.45        62.37        10.42        41.19        15.75 
TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.88        66.28        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
       14.99        38.76        70.13        64.87        53.52        16.73 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
       39.52        34.52        36.99        18.54        16.90         6.02 
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-7380 TCGA-CR-7383 TCGA-CR-7385 
        0.99        31.96         9.17        19.92        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        29.82        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 
       32.65         7.10         5.13         5.95        35.41        48.39 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
      139.43        17.16       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       17.95       107.51        87.55        76.50        91.53        80.12 
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-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-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-7100 
        4.14        64.83       126.15       111.16        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        47.47        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        36.13        18.41        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
       17.85       210.97        89.33         0.46        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7427 
       25.94         0.07        34.09       100.57        14.89       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-A45Q 
       16.64         6.38        22.19        35.93        30.48       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-A464 TCGA-CV-A465 TCGA-CV-A6JE 
       48.20        60.43        67.86        56.61         7.07        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-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        18.84        34.36        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-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        13.94        12.10        12.79        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       37.25        30.94        33.86        18.02        14.04        46.32 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       46.45        20.45        37.58        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       41.59        37.18        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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.61        21.11        20.94         0.07        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
       21.93        27.48        27.48        14.66        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
       22.85        13.84         4.27         3.65         6.90        34.75 
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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       15.48        13.35        18.15        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
        7.96        30.05         6.25        15.42         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       17.98        15.78        71.74        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       47.01        19.00        18.97         2.04        29.00        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
       16.01        13.15        21.21        23.15        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 
       12.72        18.64        19.73        16.96        15.91         7.10 
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-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       49.51        48.03        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-A7JS 
       24.30        55.43        29.46        18.05        13.94        22.36 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       32.65         2.96        17.03        20.55        14.56 

  CASP8 MUTATED CASP8 WILD-TYPE 
           0.36            0.07 
  CASP8 MUTATED CASP8 WILD-TYPE 
          75.55          210.97 
  CASP8 MUTATED CASP8 WILD-TYPE 
          18.81           21.50 
[1] "0.4 - 75.5 (18.8)"  "0.1 - 211.0 (21.5)"
[1] "hr=" "1.5"
D3V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  CASP8 MUTATED         2       11        10        25         1
  CASP8 WILD-TYPE      23       64        72       223        10
D3V3, multiclass
           clus
vv          CASP8 MUTATED CASP8 WILD-TYPE
  STAGE I               2              23
  STAGE II             11              64
  STAGE III            10              72
  STAGE IVA            25             223
  STAGE IVB             1              10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CASP8 MUTATED       2  17  10  21
  CASP8 WILD-TYPE    46 117  89 147
D3V4, multiclass
       clus
vv      CASP8 MUTATED CASP8 WILD-TYPE
  T0+T1             2              46
  T2               17             117
  T3               10              89
  T4               21             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
  CASP8 MUTATED    25   6  10   1
  CASP8 WILD-TYPE 150  61 152   6
D3V5, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  N0            25             150
  N1             6              61
  N2            10             152
  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"
D3V6, binary
                 cls
clus                0   1
  CASP8 MUTATED    27  28
  CASP8 WILD-TYPE 113 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     27   28
  CASP8 WILD-TYPE  113  342
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  FEMALE            27             113
  MALE              28             342
[1] 2 2
[1] FALSE
D3V7, binary
                 cls
clus                0   1
  CASP8 MUTATED    20  27
  CASP8 WILD-TYPE 126 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     20   27
  CASP8 WILD-TYPE  126  247
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO             20             126
  YES            27             247
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  CASP8 MUTATED                                      55
  CASP8 WILD-TYPE                                   447
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  CASP8 MUTATED                                                             0
  CASP8 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  CASP8 MUTATED                                                     0
  CASP8 WILD-TYPE                                                   7
D3V8, multiclass
                                                             clus
vv                                                            CASP8 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  55
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
                                                             clus
vv                                                            CASP8 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   447
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, continuous
D3V10, continuous
D3V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASP8 MUTATED                                  0     1
  CASP8 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CASP8 MUTATED                           2    50
  CASP8 WILD-TYPE                        35   396
D3V12, multiclass
                                  clus
vv                                 CASP8 MUTATED CASP8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              35
  WHITE                                       50             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"
D3V13, binary
                 cls
clus                0   1
  CASP8 MUTATED     4  49
  CASP8 WILD-TYPE  22 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      4   49
  CASP8 WILD-TYPE   22  399
                        clus
vv                       CASP8 MUTATED CASP8 WILD-TYPE
  HISPANIC OR LATINO                 4              22
  NOT HISPANIC OR LATINO            49             399
[1] 2 2
[1] FALSE

Clustering(4) Variable = NSD1 MUTATION ANALYSIS
D4V1, survival
                sevent
clus2              0   1
  NSD1 MUTATED    43  20
  NSD1 WILD-TYPE 250 197
  NSD1 MUTATED NSD1 WILD-TYPE 
            63            447 
  NSD1 MUTATED NSD1 WILD-TYPE 
            20            197 
$`NSD1 MUTATED`
TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BB-7870 
       17.10        21.17        29.42        14.47        20.48        66.28 
TCGA-BB-A5HZ TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-5360 
       27.19        51.29        26.86        45.83        46.32        71.31 
TCGA-CN-A497 TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V3 
       35.01         7.40        31.69        12.39        12.07        24.39 
TCGA-CQ-7072 TCGA-CR-5247 TCGA-CR-6481 TCGA-CR-7364 TCGA-CR-7385 TCGA-CR-7395 
       77.56        11.77        10.22        47.18        32.78        30.58 
TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5441 TCGA-CV-6441 TCGA-CV-6941 TCGA-CV-6942 
        5.13        29.95        87.55         9.60        11.24       140.78 
TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7250 
        7.13        28.34         2.50        36.00        26.20        95.34 
TCGA-CV-7253 TCGA-CV-7409 TCGA-CV-7427 TCGA-CV-7440 TCGA-CV-7568 TCGA-CV-A45Z 
       11.87        17.85       156.49        22.19        30.48        48.20 
TCGA-CV-A461 TCGA-CV-A468 TCGA-CV-A6JU TCGA-D6-8569 TCGA-D6-A6EO TCGA-D6-A74Q 
       67.86        15.25         3.62        25.32        24.95        11.11 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A623 TCGA-H7-A6C5 TCGA-HD-7917 TCGA-KU-A66S 
       39.12        37.18        20.25        21.11        27.48        13.35 
TCGA-P3-A5QF TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A6VB TCGA-TN-A7HL TCGA-UF-A719 
       10.85        12.99        13.15        21.07        20.35        54.67 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JF 
       49.51        48.03        55.43 

$`NSD1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       23.74        42.35        57.93        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
       68.48        15.52        14.83         3.55        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
       41.85        28.11        20.45        30.18        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-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15       105.90         9.14         4.60         4.41        18.38 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-7872 
       22.42        36.72        33.70        50.20        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A6UM TCGA-BB-A6UO 
       71.05        20.52        25.71        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-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        34.13         6.74         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       11.08        10.45        32.22        35.05        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       17.42        32.48        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-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       23.44        19.82        20.88        19.53        48.20        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-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.88        66.28        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
       14.99        38.76        70.13        64.87        53.52        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       43.04        41.88        43.10        44.48        11.61        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-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       84.23        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
       39.52        34.52        36.99        18.54        16.90         6.02 
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-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       15.75         9.27        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-7386 
        9.17        34.06        19.92        26.17        17.13        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        29.82        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 
       44.25         7.10         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-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
      107.51        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-6933 TCGA-CV-6934 TCGA-CV-6935 
       54.74        21.07        62.43        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6943 
        5.46        20.52         4.73        21.90        26.43        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-6959 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
       65.82        10.98         8.42         4.14        64.83       126.15 
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-7243 TCGA-CV-7247 
      130.88        77.16         4.73        47.47        31.36        18.97 
TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 
       17.13         4.96        47.97         2.10        36.13        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-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       14.89        56.48         3.52        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7446 TCGA-CV-A45O 
        7.17       153.86        16.64         6.38        35.93        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-A463 TCGA-CV-A464 
       45.96         6.51        88.87        60.43         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-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
       28.01        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 
       10.42        10.55        18.84        34.36        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-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       18.67        24.95        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 
       22.59        13.94        12.10        12.79        58.45        37.25 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       30.94        33.86        18.02        14.04        46.32        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8489 
       20.45        37.58        40.24        40.04        41.59        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-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 
       17.85        11.80        12.43        13.38        15.16        13.61 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       20.94         0.07        28.47        25.74        21.93        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
        4.27         3.65         6.90        34.75        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-A66T 
        5.29        13.68        13.84        19.04        15.48        18.15 
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-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-A6T7 TCGA-QK-A64Z 
       75.55        18.97         2.04        29.00        16.01        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-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       18.64        19.73        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A71A 
        7.10        32.45        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-UF-A7JV 
       18.05        13.94        20.75        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

  NSD1 MUTATED NSD1 WILD-TYPE 
          2.50           0.07 
  NSD1 MUTATED NSD1 WILD-TYPE 
        156.49         210.97 
  NSD1 MUTATED NSD1 WILD-TYPE 
         26.20          20.75 
[1] "2.5 - 156.5 (26.2)" "0.1 - 211.0 (20.8)"
[1] "hr=" "1.6"
D4V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  NSD1 MUTATED         0       14         9        30         2
  NSD1 WILD-TYPE      25       61        73       218         9
D4V3, multiclass
           clus
vv          NSD1 MUTATED NSD1 WILD-TYPE
  STAGE I              0             25
  STAGE II            14             61
  STAGE III            9             73
  STAGE IVA           30            218
  STAGE IVB            2              9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  NSD1 MUTATED       6  13  12  26
  NSD1 WILD-TYPE    42 121  87 142
D4V4, multiclass
       clus
vv      NSD1 MUTATED NSD1 WILD-TYPE
  T0+T1            6             42
  T2              13            121
  T3              12             87
  T4              26            142
[1] 4 2
[1] TRUE
[1] "dimension of 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   6  13   1
  NSD1 WILD-TYPE 144  61 149   6
D4V5, multiclass
    clus
vv   NSD1 MUTATED NSD1 WILD-TYPE
  N0           31            144
  N1            6             61
  N2           13            149
  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
  NSD1 MUTATED    11  52
  NSD1 WILD-TYPE 129 318
[1] "tbl2"
                cls
clus             [,1] [,2]
  NSD1 MUTATED     11   52
  NSD1 WILD-TYPE  129  318
        clus
vv       NSD1 MUTATED NSD1 WILD-TYPE
  FEMALE           11            129
  MALE             52            318
[1] 2 2
[1] FALSE
D4V7, binary
                cls
clus               0   1
  NSD1 MUTATED    20  35
  NSD1 WILD-TYPE 126 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  NSD1 MUTATED     20   35
  NSD1 WILD-TYPE  126  239
     clus
vv    NSD1 MUTATED NSD1 WILD-TYPE
  NO            20            126
  YES           35            239
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  NSD1 MUTATED                                      62
  NSD1 WILD-TYPE                                   440
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  NSD1 MUTATED                                                             0
  NSD1 WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  NSD1 MUTATED                                                     1
  NSD1 WILD-TYPE                                                   6
D4V8, multiclass
                                                             clus
vv                                                            NSD1 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                 62
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    1
                                                             clus
vv                                                            NSD1 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  440
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, continuous
D4V10, continuous
D4V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NSD1 MUTATED                                  0     0
  NSD1 WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NSD1 MUTATED                           5    55
  NSD1 WILD-TYPE                        32   391
D4V12, multiclass
                                  clus
vv                                 NSD1 MUTATED NSD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   5             32
  WHITE                                      55            391
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, binary
                cls
clus               0   1
  NSD1 MUTATED     5  53
  NSD1 WILD-TYPE  21 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  NSD1 MUTATED      5   53
  NSD1 WILD-TYPE   21  395
                        clus
vv                       NSD1 MUTATED NSD1 WILD-TYPE
  HISPANIC OR LATINO                5             21
  NOT HISPANIC OR LATINO           53            395
[1] 2 2
[1] FALSE

Clustering(5) Variable = HLA-B MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  HLA-B MUTATED    14  10
  HLA-B WILD-TYPE 279 207
  HLA-B MUTATED HLA-B WILD-TYPE 
             24             486 
  HLA-B MUTATED HLA-B WILD-TYPE 
             10             207 
$`HLA-B MUTATED`
TCGA-BA-5559 TCGA-BA-A6D8 TCGA-BA-A6DJ TCGA-CN-4723 TCGA-CN-A63Y TCGA-CN-A642 
       68.48        27.95        13.38        55.86        16.57         2.70 
TCGA-CQ-5324 TCGA-CQ-7071 TCGA-CR-6481 TCGA-CR-7395 TCGA-CV-5973 TCGA-CV-7099 
       52.37        43.10        10.22        30.58        86.83         7.99 
TCGA-CV-7255 TCGA-CV-A6JD TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-D6-6516 TCGA-F7-A620 
        2.10         5.98        22.52        10.42        25.41        17.85 
TCGA-HD-A4C1 TCGA-T2-A6X2 TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JO TCGA-UF-A7JT 
        0.36        32.45        48.03        49.45        20.75        32.65 

$`HLA-B WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       65.59        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        4.01        41.85        29.42        28.11        20.45        30.18 
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-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       11.05        20.48         6.15       105.90         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.41        18.38        22.42        36.72        33.70        50.20 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU 
       66.28        24.66        38.40        71.05        20.52        25.71 
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-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       38.04         4.67        51.29        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-6021 
       47.44        28.04        19.07        34.13         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        9.24        52.08        11.08        10.45        32.22        35.05 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 
       38.89         3.68        17.42        32.48        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-A6UY 
       31.69        22.32        12.39         4.41        12.07        23.44 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5325 
       19.82        24.39        20.88        19.53        48.20        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-6221 
       11.21         4.24        41.19        15.75        32.38        32.88 
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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       38.76        70.13        64.87        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
       39.52        34.52        36.99        18.54        16.90         6.02 
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        29.82        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       46.85        32.65        44.25         7.10         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        87.55 
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-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       126.15       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 
       47.47        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 
       95.34         4.96        11.87        47.97        36.13        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       57.47        35.54        17.85       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-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
        7.07        15.25        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CX-7082 
       28.01         3.62        21.24        23.47        19.92        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 
       10.55        18.84        34.36        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        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       37.25        30.94        33.86        18.02        14.04        46.32 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       46.45        20.45        37.58        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       41.59        37.18        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       18.94        24.95         0.46        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       13.38        15.16        13.61        21.11        20.94         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       28.47        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       22.03        12.66        22.85        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 
       13.84        19.04        15.48        13.35        18.15        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-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-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-RS-A6TO 
        9.34        12.72        18.64        21.07        19.73        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-TN-A7HJ 
       16.96         6.87        15.91         7.10        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7J9 
       20.35        64.80        54.67         2.83        49.51        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-A7JS TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       13.94        22.36         2.96        17.03        20.55        14.56 

  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          21.090 
[1] "0.4 - 86.8 (24.0)"  "0.1 - 211.0 (21.1)"
[1] "hr=" "1"  
D5V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  HLA-B MUTATED         1        3         5        11         1
  HLA-B WILD-TYPE      24       72        77       237        10
D5V3, multiclass
           clus
vv          HLA-B MUTATED HLA-B WILD-TYPE
  STAGE I               1              24
  STAGE II              3              72
  STAGE III             5              77
  STAGE IVA            11             237
  STAGE IVB             1              10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HLA-B MUTATED       1   4   4  12
  HLA-B WILD-TYPE    47 130  95 156
D5V4, multiclass
       clus
vv      HLA-B MUTATED HLA-B WILD-TYPE
  T0+T1             1              47
  T2                4             130
  T3                4              95
  T4               12             156
[1] 4 2
[1] TRUE
[1] "dimension of 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  64 159   6
D5V5, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  N0            13             162
  N1             3              64
  N2             3             159
  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"
D5V6, binary
                 cls
clus                0   1
  HLA-B MUTATED    10  14
  HLA-B WILD-TYPE 130 356
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED     10   14
  HLA-B WILD-TYPE  130  356
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  FEMALE            10             130
  MALE              14             356
[1] 2 2
[1] FALSE
D5V7, binary
                 cls
clus                0   1
  HLA-B MUTATED    11  11
  HLA-B WILD-TYPE 135 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED     11   11
  HLA-B WILD-TYPE  135  263
     clus
vv    HLA-B MUTATED HLA-B WILD-TYPE
  NO             11             135
  YES            11             263
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  HLA-B MUTATED                                      23
  HLA-B WILD-TYPE                                   479
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  HLA-B MUTATED                                                             0
  HLA-B WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  HLA-B MUTATED                                                     1
  HLA-B WILD-TYPE                                                   6
D5V8, multiclass
                                                             clus
vv                                                            HLA-B MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  23
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     1
                                                             clus
vv                                                            HLA-B WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   479
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, continuous
D5V10, continuous
D5V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HLA-B MUTATED                                  0     1
  HLA-B WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HLA-B MUTATED                           2    21
  HLA-B WILD-TYPE                        35   425
D5V12, multiclass
                                  clus
vv                                 HLA-B MUTATED HLA-B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              35
  WHITE                                       21             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"
D5V13, binary
                 cls
clus                0   1
  HLA-B MUTATED     0  18
  HLA-B WILD-TYPE  26 430
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      0   18
  HLA-B WILD-TYPE   26  430
                        clus
vv                       HLA-B MUTATED HLA-B WILD-TYPE
  HISPANIC OR LATINO                 0              26
  NOT HISPANIC OR LATINO            18             430
[1] 2 2
[1] FALSE

Clustering(6) Variable = MLL2 MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  MLL2 MUTATED    36  42
  MLL2 WILD-TYPE 257 175
  MLL2 MUTATED MLL2 WILD-TYPE 
            78            432 
  MLL2 MUTATED MLL2 WILD-TYPE 
            42            175 
$`MLL2 MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5558 
       15.19         9.30        13.64        37.28        26.50        65.59 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A6DF TCGA-BA-A6DI TCGA-BB-7862 TCGA-BB-7870 
       14.83         3.55         7.82        11.05        36.72        66.28 
TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4741 TCGA-CN-5370 TCGA-CN-6011 
       32.81        57.11        20.55        73.61         8.52        30.67 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A6V6 
        9.07         9.24        52.08        17.42        32.48        20.88 
TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-6225 TCGA-CR-5243 TCGA-CR-6473 TCGA-CR-6478 
       48.20        32.88        13.25        84.23        36.99         6.02 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-7379 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7402 
       11.64         7.69        34.06        27.06        12.89        29.95 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-6441 TCGA-CV-6950 TCGA-CV-7178 
      108.95        19.20        87.55         9.60        15.09        71.21 
TCGA-CV-7183 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7409 
      130.88        17.13         4.96        47.97        36.13        17.85 
TCGA-CV-7422 TCGA-CV-7430 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7568 
       34.09        16.27         7.17       153.86        16.64        30.48 
TCGA-CV-A45V TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A6JM TCGA-CV-A6K1 TCGA-CX-7086 
        1.05        48.20        67.86         6.38        22.52        18.84 
TCGA-D6-8568 TCGA-D6-A6ES TCGA-DQ-7593 TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A624 
       24.95        12.79        40.24         0.46        11.80        12.43 
TCGA-H7-8501 TCGA-H7-A6C5 TCGA-HD-8635 TCGA-IQ-7632 TCGA-MT-A67A TCGA-MT-A67D 
       15.16        21.11        22.85        14.50        30.05         1.84 
TCGA-P3-A5QF TCGA-P3-A6T4 TCGA-RS-A6TO TCGA-RS-A6TP TCGA-UF-A7JH TCGA-UF-A7JT 
       10.85         2.04        12.72        16.96        29.46        32.65 

$`MLL2 WILD-TYPE`
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-5557 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 
       20.48        68.48        15.52        21.17        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
       41.85        29.42        28.11        20.45        30.18        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-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       20.48         6.15       105.90         9.14         4.60         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-7872 
       18.38        22.42        33.70        50.20        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       71.05        20.52        25.71        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-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4734 
       51.29        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-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-5373 
       16.21        11.54        11.84        11.57        12.49        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       56.94        50.07        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
       19.07        34.13         6.74        11.08        10.45        32.22 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       35.05        38.89         3.68        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-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
       23.44        19.82        24.39        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-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       46.95        56.58         4.24        14.99        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
       64.87        53.52        16.73        43.04        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       77.56        44.48        11.61        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 
       29.49        14.14        12.46        31.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
       37.87        26.27        58.42        50.01        39.52        34.52 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6488 
       18.54        16.90        11.90        10.22        11.34        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-7380 TCGA-CR-7382 TCGA-CR-7383 
        0.99        31.96         9.17        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       32.78        47.01        29.82        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         7.10         5.13         5.95        35.41 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5439 
       48.39       139.43        17.16       129.21        76.24        17.95 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
      107.51        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-6933 TCGA-CV-6934 TCGA-CV-6935 
       54.74        21.07        62.43        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-6951 TCGA-CV-6952 
      140.78        19.79        12.03        42.38        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       126.15       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-7180 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       12.92        21.80        10.75        77.16         4.73        47.47 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7253 
       36.00        31.36        26.20        18.97        95.34        11.87 
TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 
        2.10        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-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7432 
      100.57        14.89        56.48       156.49         3.52        84.49 
TCGA-CV-7433 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A45O TCGA-CV-A45P 
       19.76         6.38        22.19        35.93        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X 
      169.38       180.16       159.65        35.47        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       88.87        60.43         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        5.98        35.34        29.79         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
       21.24        23.47        19.92        10.42        10.42        10.55 
TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       34.36        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-5629 TCGA-DQ-5630 
       12.10        11.11        58.45        37.25        30.94        33.86 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       18.02        14.04        46.32        46.45        20.45        37.58 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       40.04        39.12        41.59        37.18        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A623 
        3.02        31.13        18.94        24.95        17.85        20.25 
TCGA-H7-7774 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.38        13.61        20.94         0.07        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
       21.93        27.48        27.48        14.66        22.03        12.66 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
        0.36        13.84         4.27         3.65         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       15.95        38.53        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        19.27        10.75        14.37         7.96 
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-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-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       75.55        18.97        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-T2-A6WX TCGA-T2-A6WZ 
       12.72        18.64        21.07        19.73         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
        7.10        32.45        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        49.51        48.03        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK 
       74.47        17.95        24.30        55.43        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36         2.96        17.03        20.55        14.56 

  MLL2 MUTATED MLL2 WILD-TYPE 
          0.46           0.07 
  MLL2 MUTATED MLL2 WILD-TYPE 
        153.86         210.97 
  MLL2 MUTATED MLL2 WILD-TYPE 
        19.875         21.225 
[1] "0.5 - 153.9 (19.9)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.4"
D6V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  MLL2 MUTATED         3        9         7        42         1
  MLL2 WILD-TYPE      22       66        75       206        10
D6V3, multiclass
           clus
vv          MLL2 MUTATED MLL2 WILD-TYPE
  STAGE I              3             22
  STAGE II             9             66
  STAGE III            7             75
  STAGE IVA           42            206
  STAGE IVB            1             10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MLL2 MUTATED       5  13  15  30
  MLL2 WILD-TYPE    43 121  84 138
D6V4, multiclass
       clus
vv      MLL2 MUTATED MLL2 WILD-TYPE
  T0+T1            5             43
  T2              13            121
  T3              15             84
  T4              30            138
[1] 4 2
[1] TRUE
[1] "dimension of 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    26   8  22   1
  MLL2 WILD-TYPE 149  59 140   6
D6V5, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  N0           26            149
  N1            8             59
  N2           22            140
  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"
D6V6, binary
                cls
clus               0   1
  MLL2 MUTATED    22  56
  MLL2 WILD-TYPE 118 314
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     22   56
  MLL2 WILD-TYPE  118  314
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  FEMALE           22            118
  MALE             56            314
[1] 2 2
[1] FALSE
D6V7, binary
                cls
clus               0   1
  MLL2 MUTATED    23  41
  MLL2 WILD-TYPE 123 233
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     23   41
  MLL2 WILD-TYPE  123  233
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO            23            123
  YES           41            233
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  MLL2 MUTATED                                      78
  MLL2 WILD-TYPE                                   424
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  MLL2 MUTATED                                                             0
  MLL2 WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  MLL2 MUTATED                                                     0
  MLL2 WILD-TYPE                                                   7
D6V8, multiclass
                                                             clus
vv                                                            MLL2 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                 78
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
                                                             clus
vv                                                            MLL2 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  424
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, continuous
D6V10, continuous
D6V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL2 MUTATED                                  0     2
  MLL2 WILD-TYPE                                2     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MLL2 MUTATED                          10    64
  MLL2 WILD-TYPE                        27   382
D6V12, multiclass
                                  clus
vv                                 MLL2 MUTATED MLL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                  10             27
  WHITE                                      64            382
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, binary
                cls
clus               0   1
  MLL2 MUTATED     2  71
  MLL2 WILD-TYPE  24 377
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      2   71
  MLL2 WILD-TYPE   24  377
                        clus
vv                       MLL2 MUTATED MLL2 WILD-TYPE
  HISPANIC OR LATINO                2             24
  NOT HISPANIC OR LATINO           71            377
[1] 2 2
[1] FALSE

Clustering(7) Variable = TGFBR2 MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2                0   1
  TGFBR2 MUTATED    12  11
  TGFBR2 WILD-TYPE 281 206
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              23              487 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              11              206 
$`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-IQ-A61H 
       21.01        10.42        41.59        21.63        11.80        37.41 
TCGA-IQ-A61J TCGA-P3-A5QF TCGA-QK-A6II TCGA-QK-A6VB TCGA-T2-A6X2 
       33.57        10.85         9.34        21.07        32.45 

$`TGFBR2 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        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-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       36.72        33.70        50.20        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       71.05        20.52        25.71        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-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4734 
       51.29        56.68        12.89        26.86        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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       34.13         6.74         9.07         9.24        52.08        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        32.22        35.05        38.89         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       32.48        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-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       24.39        20.88        19.53        48.20        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-6221 
       11.21         4.24        41.19        15.75        32.38        32.88 
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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       38.76        70.13        64.87        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
       39.52        34.52        36.99        18.54        16.90         6.02 
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-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
        0.99         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        29.82        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         7.10         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-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        87.55 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       76.50        91.53        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-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-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       126.15 
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        47.47        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-7409 
        2.10        36.13        18.41        57.47        35.54        17.85 
TCGA-CV-7410 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 
      210.97         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-A45Q 
       16.64         6.38        22.19        35.93        30.48       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-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ 
       22.52        10.42        10.55        18.84        34.36        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-5629 TCGA-DQ-5630 
       12.79        11.11        58.45        37.25        30.94        33.86 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       18.02        14.04        46.32        46.45        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A50I 
       40.24        40.04        39.12        37.18        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
       31.13        18.94        24.95         0.46        17.85        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       12.43        13.38        15.16        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
        4.27         3.65         6.90        34.75        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L 
       14.50        37.71        11.84         0.07         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
       13.84        19.04        15.48        13.35        18.15        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-A5Q6 
        6.25        15.42         7.13        16.08        17.98        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-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-A6IJ 
       21.07        21.21        23.15         7.30        21.47        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       18.64        19.73        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        7.10        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        49.51        48.03        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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
            2.50             0.07 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
           89.33           210.97 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
           27.98            21.07 
[1] "2.5 - 89.3 (28.0)"  "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D7V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  TGFBR2 MUTATED         1        4         5        10         0
  TGFBR2 WILD-TYPE      24       71        77       238        11
D7V3, multiclass
           clus
vv          TGFBR2 MUTATED TGFBR2 WILD-TYPE
  STAGE I                1               24
  STAGE II               4               71
  STAGE III              5               77
  STAGE IVA             10              238
  STAGE IVB              0               11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  TGFBR2 MUTATED       1   7   3   9
  TGFBR2 WILD-TYPE    47 127  96 159
D7V4, multiclass
       clus
vv      TGFBR2 MUTATED TGFBR2 WILD-TYPE
  T0+T1              1               47
  T2                 7              127
  T3                 3               96
  T4                 9              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
  TGFBR2 MUTATED     9   3   4   0
  TGFBR2 WILD-TYPE 166  64 158   7
D7V5, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  N0              9              166
  N1              3               64
  N2              4              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"
D7V6, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     6  17
  TGFBR2 WILD-TYPE 134 353
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      6   17
  TGFBR2 WILD-TYPE  134  353
        clus
vv       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  FEMALE              6              134
  MALE               17              353
[1] 2 2
[1] FALSE
D7V7, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     9  11
  TGFBR2 WILD-TYPE 137 263
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      9   11
  TGFBR2 WILD-TYPE  137  263
     clus
vv    TGFBR2 MUTATED TGFBR2 WILD-TYPE
  NO               9              137
  YES             11              263
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  TGFBR2 MUTATED                                      23
  TGFBR2 WILD-TYPE                                   479
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  TGFBR2 MUTATED                                                             0
  TGFBR2 WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  TGFBR2 MUTATED                                                     0
  TGFBR2 WILD-TYPE                                                   7
D7V8, multiclass
                                                             clus
vv                                                            TGFBR2 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   23
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
                                                             clus
vv                                                            TGFBR2 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    479
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, continuous
D7V10, continuous
D7V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TGFBR2 MUTATED                                  0     0
  TGFBR2 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TGFBR2 MUTATED                           3    20
  TGFBR2 WILD-TYPE                        34   426
D7V12, multiclass
                                  clus
vv                                 TGFBR2 MUTATED TGFBR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     3               34
  WHITE                                        20              426
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     1  21
  TGFBR2 WILD-TYPE  25 427
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      1   21
  TGFBR2 WILD-TYPE   25  427
                        clus
vv                       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  HISPANIC OR LATINO                  1               25
  NOT HISPANIC OR LATINO             21              427
[1] 2 2
[1] FALSE

Clustering(8) Variable = FAT1 MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  FAT1 MUTATED    60  54
  FAT1 WILD-TYPE 233 163
  FAT1 MUTATED FAT1 WILD-TYPE 
           114            396 
  FAT1 MUTATED FAT1 WILD-TYPE 
            54            163 
$`FAT1 MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DI 
        9.30         9.07         3.55        41.85        29.42        11.05 
TCGA-BA-A6DJ TCGA-BB-7872 TCGA-CN-4731 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 
       13.38        38.40        32.81        11.84        12.49         8.52 
TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-A49A 
       48.00        47.44        19.07        11.08        32.22        17.29 
TCGA-CN-A640 TCGA-CQ-5327 TCGA-CQ-6218 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-7064 
        4.41        54.58        41.19        66.28        46.95        64.87 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-6477 TCGA-CR-6492 
       33.60        29.49        14.14        31.23        16.90        15.75 
TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7386 TCGA-CR-7390 
        3.45         0.99        34.06        26.17        47.01        29.82 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5966 
       44.25        30.58         5.13       139.43       108.95        17.92 
TCGA-CV-5976 TCGA-CV-6441 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6942 TCGA-CV-6943 
       48.59         9.60         5.46         4.73       140.78        19.79 
TCGA-CV-6952 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-7089 TCGA-CV-7091 
        6.08        10.98         7.13         8.42        64.83       111.16 
TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7103 TCGA-CV-7183 TCGA-CV-7242 TCGA-CV-7250 
       18.81         7.99        52.31       130.88        36.00        95.34 
TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7263 TCGA-CV-7409 TCGA-CV-7413 TCGA-CV-7414 
        4.96        47.97        18.41        17.85         9.67         0.46 
TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45O TCGA-CV-A45Q 
       34.09       156.49       153.86        16.64        27.98       169.38 
TCGA-CV-A45R TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A463 TCGA-CV-A6JD TCGA-CV-A6JE 
      180.16         1.05        45.96         0.76         5.98        35.34 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
        3.62        23.47        22.52        10.42        10.42        10.55 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN TCGA-DQ-5629 TCGA-DQ-5631 
       17.72        12.36        28.77        22.59        30.94        18.02 
TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A622 
       37.58        39.12        21.63         3.02        18.94        11.80 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 
       12.43        13.38        15.16         0.36        13.84         6.90 
TCGA-HL-7533 TCGA-IQ-A61E TCGA-MT-A67A TCGA-P3-A6T0 TCGA-QK-A64Z TCGA-QK-A6II 
       34.75        37.71        30.05        19.00        21.07         9.34 
TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JT TCGA-WA-A7GZ 
       48.03        44.65        18.05        20.75        32.65        20.55 

$`FAT1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
       15.19        13.64        37.28        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       57.93        17.10        23.84        20.48        65.59        68.48 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IG 
       15.52        21.17        14.83        12.62         4.01        28.11 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       20.45        30.18        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 
       14.47         7.82         2.27        20.48         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 
       33.70        50.20        66.28        24.66        71.05        20.52 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       25.71        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
       12.69        55.86        38.04         4.67        51.29        56.68 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
       12.89        26.86        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-5367 TCGA-CN-5373 TCGA-CN-5374 
        8.32        16.21        11.54        11.57        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 
       50.07        30.67        23.90        28.04        34.13         6.74 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 
        9.07         9.24        52.08        10.45        35.05        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        3.68        17.42        32.48        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-A6V1 
       12.39        16.57        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       24.39        20.88        19.53        48.20        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-5334 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6225 
        4.24        15.75        32.38        32.88        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 
        4.24        14.99        38.76        70.13        53.52        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       43.04        41.88        43.10        77.56        44.48        11.61 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       23.24        29.36        12.46        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
       37.87        26.27        58.42        50.01        39.52        34.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54         6.02        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-7371 TCGA-CR-7372 
       39.16        47.34        40.93        35.84         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7385 
       29.23        31.96         9.17        19.92        17.13        32.78 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7397 
       27.06        12.89        30.02        46.85        32.65         7.10 
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-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       76.24        19.20        17.95       107.51        87.55        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 
       91.53        80.12        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-6933 
        7.07        43.23        54.74        21.07        62.43        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        2.14         9.70        20.52        21.90        26.43        11.24 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6954 
       12.03        42.38        15.09        30.08        53.95        65.82 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7100 
       28.34         2.50         4.14       126.15        12.66         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        5.26         1.84        12.92        21.80        71.21        10.75 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
       77.16         4.73        47.47        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 
       17.13        11.87         2.10        36.13        57.47        35.54 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
      210.97        89.33        22.85        25.08        25.94         0.07 
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-7433 TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 
       19.76         7.17         6.38        22.19        35.93        30.48 
TCGA-CV-A45P TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
       21.01       159.65        35.47         6.51        88.87        48.20 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JM 
       60.43        67.86        56.61         7.07        15.25         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CX-7086 
       29.79         6.48        28.01        21.24        19.92        18.84 
TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       34.36        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-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        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       58.45        37.25        33.86        14.04        46.32        46.45 
TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-A50G 
       20.45        40.24        40.04        41.59        37.18        20.25 
TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-A6C4 
       31.13        24.95         0.46        17.85        20.25        13.61 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       21.11        20.94         0.07        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       27.48        27.48        14.66        22.03        12.66        22.85 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G 
        4.27         3.65        15.95        38.53        14.50        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       19.04        15.48        13.35        18.15        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-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-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       10.85        36.82        47.01        75.55        18.97         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IF 
       29.00        12.99        16.01        13.15        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
        7.30        21.47        12.72        18.64        21.07        19.73 
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-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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
       29.46        13.94        22.36         2.96        17.03        14.56 

  FAT1 MUTATED FAT1 WILD-TYPE 
          0.36           0.07 
  FAT1 MUTATED FAT1 WILD-TYPE 
        180.16         210.97 
  FAT1 MUTATED FAT1 WILD-TYPE 
        20.170         21.225 
[1] "0.4 - 180.2 (20.2)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.1"
D8V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  FAT1 MUTATED         4       20        18        52         3
  FAT1 WILD-TYPE      21       55        64       196         8
D8V3, multiclass
           clus
vv          FAT1 MUTATED FAT1 WILD-TYPE
  STAGE I              4             21
  STAGE II            20             55
  STAGE III           18             64
  STAGE IVA           52            196
  STAGE IVB            3              8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  FAT1 MUTATED       4  33  18  43
  FAT1 WILD-TYPE    44 101  81 125
D8V4, multiclass
       clus
vv      FAT1 MUTATED FAT1 WILD-TYPE
  T0+T1            4             44
  T2              33            101
  T3              18             81
  T4              43            125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  FAT1 MUTATED    43  14  27   1
  FAT1 WILD-TYPE 132  53 135   6
D8V5, multiclass
    clus
vv   FAT1 MUTATED FAT1 WILD-TYPE
  N0           43            132
  N1           14             53
  N2           27            135
  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
  FAT1 MUTATED    42  72
  FAT1 WILD-TYPE  98 298
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED     42   72
  FAT1 WILD-TYPE   98  298
        clus
vv       FAT1 MUTATED FAT1 WILD-TYPE
  FEMALE           42             98
  MALE             72            298
[1] 2 2
[1] FALSE
D8V7, binary
                cls
clus               0   1
  FAT1 MUTATED    32  60
  FAT1 WILD-TYPE 114 214
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED     32   60
  FAT1 WILD-TYPE  114  214
     clus
vv    FAT1 MUTATED FAT1 WILD-TYPE
  NO            32            114
  YES           60            214
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  FAT1 MUTATED                                     113
  FAT1 WILD-TYPE                                   389
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  FAT1 MUTATED                                                             0
  FAT1 WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  FAT1 MUTATED                                                     1
  FAT1 WILD-TYPE                                                   6
D8V8, multiclass
                                                             clus
vv                                                            FAT1 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                113
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    1
                                                             clus
vv                                                            FAT1 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  389
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, continuous
D8V10, continuous
D8V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAT1 MUTATED                                  1     3
  FAT1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FAT1 MUTATED                           7    99
  FAT1 WILD-TYPE                        30   347
D8V12, multiclass
                                  clus
vv                                 FAT1 MUTATED FAT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   7             30
  WHITE                                      99            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, binary
                cls
clus               0   1
  FAT1 MUTATED     7  96
  FAT1 WILD-TYPE  19 352
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED      7   96
  FAT1 WILD-TYPE   19  352
                        clus
vv                       FAT1 MUTATED FAT1 WILD-TYPE
  HISPANIC OR LATINO                7             19
  NOT HISPANIC OR LATINO           96            352
[1] 2 2
[1] FALSE

Clustering(9) Variable = NOTCH1 MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2                0   1
  NOTCH1 MUTATED    46  41
  NOTCH1 WILD-TYPE 247 176
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              87              423 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              41              176 
$`NOTCH1 MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-6868 TCGA-BA-6873 TCGA-BA-A4IF 
        9.30        13.64        26.50        15.52         4.01        29.42 
TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BB-4225 TCGA-BB-7863 TCGA-BB-7864 
       27.95        14.47         7.82         4.60        33.70        50.20 
TCGA-BB-7872 TCGA-BB-8596 TCGA-CN-4723 TCGA-CN-4729 TCGA-CN-4736 TCGA-CN-4742 
       38.40        71.05        55.86        12.89        12.99        13.05 
TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-5369 TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6021 
       42.02         8.32        12.49        30.67        47.44         9.07 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-A63W TCGA-CQ-5329 TCGA-CQ-5333 TCGA-CQ-5334 
       32.22        38.89        12.39        70.45        11.21         4.24 
TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CR-5243 TCGA-CR-6492 
       15.75        32.38        43.10        44.48        84.23        15.75 
TCGA-CR-7365 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7390 
       39.16        31.96         9.17        34.06        19.92        29.82 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5966 
       44.25        30.58        19.20        17.95        87.55        17.92 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-6938 TCGA-CV-6942 TCGA-CV-6955 TCGA-CV-6959 
       23.05        86.83         4.73       140.78        10.98         8.42 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7236 TCGA-CV-7238 
        4.14        64.83         7.99         5.26         4.73        47.47 
TCGA-CV-7411 TCGA-CV-7427 TCGA-CV-7433 TCGA-CV-7568 TCGA-CV-A45V TCGA-CV-A463 
       89.33       156.49        19.76        30.48         1.05         0.76 
TCGA-CV-A465 TCGA-CV-A6JM TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CX-7085 TCGA-D6-A6EK 
        7.07         6.38        21.24        22.52        10.55        28.77 
TCGA-D6-A6EN TCGA-DQ-5625 TCGA-DQ-5631 TCGA-F7-A50I TCGA-F7-A622 TCGA-HD-8635 
       22.59        37.25        18.02         3.02        11.80        22.85 
TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-MT-A67A TCGA-MT-A67D TCGA-P3-A6T8 TCGA-QK-A652 
        6.90        37.71        30.05         1.84        13.15        21.21 
TCGA-QK-A6II TCGA-T2-A6X2 TCGA-TN-A7HL 
        9.34        32.45        20.35 

$`NOTCH1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       15.19        37.28         9.07        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 
       17.10        23.84        20.48        65.59        68.48        21.17 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH 
       14.83         3.55        12.62        41.85        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DG TCGA-BA-A6DI 
       30.18        11.54         7.10         5.69         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 
       13.38        20.48         6.15       105.90         9.14         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8601 
       18.38        22.42        36.72        66.28        24.66        20.52 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       25.71        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 
       12.69        38.04         4.67        51.29        56.68        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-5356 TCGA-CN-5358 TCGA-CN-5359 
       45.83        27.58        73.61        46.32         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       71.31        69.70        16.21        11.54        11.84        11.57 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 
        8.52        52.08        56.94        50.07        48.00        23.90 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 
       28.04        19.07        34.13         6.74         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       11.08        10.45        35.05         3.68        17.42        32.48 
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-A63Y TCGA-CN-A640 
       21.21         7.40        31.69        22.32        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        23.44        19.82        24.39        20.88 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       19.53        48.20        52.37        21.50         2.93        54.58 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6222 
       62.37        45.99        10.42        41.19        32.88        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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
       70.13        64.87        53.52        16.73        43.04        41.88 
TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       77.56        11.61        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       14.14        12.46        31.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
       26.27        58.42        50.01        39.52        34.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       18.54        16.90         6.02        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-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-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       29.23         0.99        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-7397 
       27.06        12.89        30.02        46.85        32.65         7.10 
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-5440 TCGA-CV-5442 
       17.16       129.21       108.95        76.24       107.51        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       91.53        80.12        13.35        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-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
       11.24        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 
        6.08        53.95        65.82         7.13        28.34         2.50 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7102 
      126.15       111.16        18.81        12.66         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-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       77.16        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        36.13 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7413 
       18.41        57.47        35.54        17.85       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-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO 
       56.61        15.25         5.98        35.34        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7082 
       28.01         3.62        23.47        19.92        10.42        10.42 
TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       18.84        34.36        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-A6EO TCGA-D6-A6EP 
       25.32        17.72        12.36         7.63        24.95        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 
       12.10        12.79        11.11        58.45        30.94        33.86 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       14.04        46.32        46.45        20.45        37.58        40.24 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       40.04        39.12        41.59        37.18        21.63        20.25 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
       31.13        18.94        24.95         0.46        17.85        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       12.43        13.38        15.16        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       14.66        22.03        12.66         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G 
        3.65        34.75        15.95        38.53        14.50        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       19.04        15.48        13.35        18.15        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-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       16.08        17.98        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-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG 
       29.00        12.99        16.01        21.07        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO 
       21.47        12.72        18.64        21.07        19.73        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-TN-A7HJ 
       16.96         6.87        15.91         7.10        13.55        13.25 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       64.80        54.67         2.83        49.51        48.03        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-UF-A7JV 
       18.05        13.94        20.75        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
            0.76             0.07 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
          156.49           210.97 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
           20.35            21.17 
[1] "0.8 - 156.5 (20.4)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.2"
D9V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  NOTCH1 MUTATED         3       13        17        42         2
  NOTCH1 WILD-TYPE      22       62        65       206         9
D9V3, multiclass
           clus
vv          NOTCH1 MUTATED NOTCH1 WILD-TYPE
  STAGE I                3               22
  STAGE II              13               62
  STAGE III             17               65
  STAGE IVA             42              206
  STAGE IVB              2                9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  NOTCH1 MUTATED       6  20  17  35
  NOTCH1 WILD-TYPE    42 114  82 133
D9V4, multiclass
       clus
vv      NOTCH1 MUTATED NOTCH1 WILD-TYPE
  T0+T1              6               42
  T2                20              114
  T3                17               82
  T4                35              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
  NOTCH1 MUTATED    33  12  21   1
  NOTCH1 WILD-TYPE 142  55 141   6
D9V5, multiclass
    clus
vv   NOTCH1 MUTATED NOTCH1 WILD-TYPE
  N0             33              142
  N1             12               55
  N2             21              141
  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    31  56
  NOTCH1 WILD-TYPE 109 314
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED     31   56
  NOTCH1 WILD-TYPE  109  314
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  FEMALE             31              109
  MALE               56              314
[1] 2 2
[1] FALSE
D9V7, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED    31  36
  NOTCH1 WILD-TYPE 115 238
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED     31   36
  NOTCH1 WILD-TYPE  115  238
     clus
vv    NOTCH1 MUTATED NOTCH1 WILD-TYPE
  NO              31              115
  YES             36              238
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  NOTCH1 MUTATED                                      87
  NOTCH1 WILD-TYPE                                   415
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  NOTCH1 MUTATED                                                             0
  NOTCH1 WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  NOTCH1 MUTATED                                                     0
  NOTCH1 WILD-TYPE                                                   7
D9V8, multiclass
                                                             clus
vv                                                            NOTCH1 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   87
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
                                                             clus
vv                                                            NOTCH1 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    415
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, continuous
D9V10, continuous
D9V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOTCH1 MUTATED                                  0     2
  NOTCH1 WILD-TYPE                                2     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NOTCH1 MUTATED                           5    79
  NOTCH1 WILD-TYPE                        32   367
D9V12, multiclass
                                  clus
vv                                 NOTCH1 MUTATED NOTCH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     5               32
  WHITE                                        79              367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED     7  77
  NOTCH1 WILD-TYPE  19 371
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      7   77
  NOTCH1 WILD-TYPE   19  371
                        clus
vv                       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  HISPANIC OR LATINO                  7               19
  NOT HISPANIC OR LATINO             77              371
[1] 2 2
[1] FALSE

Clustering(10) Variable = JUB MUTATION ANALYSIS
D10V1, survival
               sevent
clus2             0   1
  JUB MUTATED    12  21
  JUB WILD-TYPE 281 196
  JUB MUTATED JUB WILD-TYPE 
           33           477 
  JUB MUTATED JUB WILD-TYPE 
           21           196 
$`JUB MUTATED`
TCGA-BA-5556 TCGA-BB-A5HY TCGA-BB-A6UO TCGA-CN-4738 TCGA-CN-6997 TCGA-CN-6998 
       23.84        10.55         8.81        14.33        32.48        11.74 
TCGA-CN-A63V TCGA-CQ-5327 TCGA-CR-6491 TCGA-CR-6493 TCGA-CV-5431 TCGA-CV-5435 
       22.32        54.58        22.78         9.27        17.16        76.24 
TCGA-CV-6003 TCGA-CV-6950 TCGA-CV-7099 TCGA-CV-7177 TCGA-CV-7418 TCGA-CV-7424 
       54.74        15.09         7.99        21.80        25.94        14.89 
TCGA-CV-7432 TCGA-CV-A45Q TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A6JM TCGA-CV-A6K2 
       84.49       169.38        60.43         0.76         6.38        10.42 
TCGA-CX-7082 TCGA-D6-A6EN TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-7588 TCGA-HD-7753 
       10.42        22.59        13.94        11.11        14.04        28.47 
TCGA-P3-A5QF TCGA-UF-A71D TCGA-UF-A7JF 
       10.85        48.03        55.43 

$`JUB WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 
       23.74        42.35        57.93        17.10        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       68.48        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        4.01        41.85        29.42        28.11        20.45        30.18 
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-BB-4217 TCGA-BB-4223 
        2.27        11.05        13.38        20.48         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       33.70        50.20        66.28        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-C9-A47Z TCGA-C9-A480 
       20.52        25.71        27.19        12.92         6.28        12.69 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       55.86        38.04         4.67        51.29        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-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       20.55        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-6021 
       47.44        28.04        19.07        34.13         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        9.24        52.08        11.08        10.45        32.22        35.05 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       38.89         3.68        17.42        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W 
       17.29        29.72        21.21         7.40        31.69        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       24.39        20.88        19.53        48.20        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-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6222 
        4.24        41.19        15.75        32.38        32.88        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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
       70.13        64.87        53.52        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       43.10        77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
       39.52        34.52        36.99        18.54        16.90         6.02 
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-6492 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       15.75        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        29.82        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         7.10         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
       35.41        29.95        48.39       139.43       129.21       108.95 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        87.55        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-6433 TCGA-CV-6436 TCGA-CV-6441 
       60.49         7.07        43.23        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-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       42.38        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-7100 TCGA-CV-7101 
      126.15       111.16        18.81        12.66         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
        1.84        52.31        12.92        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        47.47        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-7409 
        2.10        36.13        18.41        57.47        35.54        17.85 
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-7219 
       23.47        19.92        22.52        10.55        18.84        34.36 
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-A6EQ TCGA-D6-A6ES 
       12.36        28.77         7.63        24.95        12.10        12.79 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 
       58.45        37.25        30.94        33.86        18.02        46.32 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       46.45        20.45        37.58        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       41.59        37.18        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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       12.43        13.38        15.16        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
        0.07        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       22.03        12.66        22.85         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        3.65         6.90        34.75        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-A66S TCGA-KU-A66T 
       13.68        13.84        19.04        15.48        13.35        18.15 
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-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-RS-A6TO 
        9.34        12.72        18.64        21.07        19.73        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI 
       16.96         6.87        15.91         7.10        32.45        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-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-UF-A7JV 
       18.05        13.94        20.75        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

  JUB MUTATED JUB WILD-TYPE 
         0.76          0.07 
  JUB MUTATED JUB WILD-TYPE 
       169.38        210.97 
  JUB MUTATED JUB WILD-TYPE 
        17.16         21.17 
[1] "0.8 - 169.4 (17.2)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.6"
D10V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  JUB MUTATED         1        5         3        21         0
  JUB WILD-TYPE      24       70        79       227        11
D10V3, multiclass
           clus
vv          JUB MUTATED JUB WILD-TYPE
  STAGE I             1            24
  STAGE II            5            70
  STAGE III           3            79
  STAGE IVA          21           227
  STAGE IVB           0            11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  JUB MUTATED       2   7   9  12
  JUB WILD-TYPE    46 127  90 156
D10V4, multiclass
       clus
vv      JUB MUTATED JUB WILD-TYPE
  T0+T1           2            46
  T2              7           127
  T3              9            90
  T4             12           156
[1] 4 2
[1] TRUE
[1] "dimension of 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  16   0
  JUB WILD-TYPE 165  65 146   7
D10V5, multiclass
    clus
vv   JUB MUTATED JUB WILD-TYPE
  N0          10           165
  N1           2            65
  N2          16           146
  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
  JUB MUTATED     9  24
  JUB WILD-TYPE 131 346
[1] "tbl2"
               cls
clus            [,1] [,2]
  JUB MUTATED      9   24
  JUB WILD-TYPE  131  346
        clus
vv       JUB MUTATED JUB WILD-TYPE
  FEMALE           9           131
  MALE            24           346
[1] 2 2
[1] FALSE
D10V7, binary
               cls
clus              0   1
  JUB MUTATED     8  20
  JUB WILD-TYPE 138 254
[1] "tbl2"
               cls
clus            [,1] [,2]
  JUB MUTATED      8   20
  JUB WILD-TYPE  138  254
     clus
vv    JUB MUTATED JUB WILD-TYPE
  NO            8           138
  YES          20           254
[1] 2 2
[1] FALSE
               vv
clus            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  JUB MUTATED                                      33
  JUB WILD-TYPE                                   469
               vv
clus            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  JUB MUTATED                                                             0
  JUB WILD-TYPE                                                           1
               vv
clus            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  JUB MUTATED                                                     0
  JUB WILD-TYPE                                                   7
D10V8, multiclass
                                                             clus
vv                                                            JUB MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                33
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                   0
                                                             clus
vv                                                            JUB WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                 469
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, continuous
D10V10, continuous
D10V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  JUB MUTATED                                  0     2
  JUB WILD-TYPE                                2     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  JUB MUTATED                           4    27
  JUB WILD-TYPE                        33   419
D10V12, multiclass
                                  clus
vv                                 JUB MUTATED JUB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      2             9
  BLACK OR AFRICAN AMERICAN                  4            33
  WHITE                                     27           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"
D10V13, binary
               cls
clus              0   1
  JUB MUTATED     2  28
  JUB WILD-TYPE  24 420
[1] "tbl2"
               cls
clus            [,1] [,2]
  JUB MUTATED      2   28
  JUB WILD-TYPE   24  420
                        clus
vv                       JUB MUTATED JUB WILD-TYPE
  HISPANIC OR LATINO               2            24
  NOT HISPANIC OR LATINO          28           420
[1] 2 2
[1] FALSE

Clustering(11) Variable = NFE2L2 MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2                0   1
  NFE2L2 MUTATED    13  13
  NFE2L2 WILD-TYPE 280 204
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              26              484 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              13              204 
$`NFE2L2 MUTATED`
TCGA-BA-7269 TCGA-CN-4723 TCGA-CN-6019 TCGA-CQ-5324 TCGA-CQ-A4CG TCGA-CR-7383 
       41.85        55.86        34.13        52.37        14.14        17.13 
TCGA-CV-6935 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6951 TCGA-CV-6955 TCGA-CV-7099 
        9.70        26.43       140.78        30.08        10.98         7.99 
TCGA-CV-7177 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7437 TCGA-D6-A6EK TCGA-H7-7774 
       21.80        14.89         3.52        16.64        28.77        13.38 
TCGA-HD-A6HZ TCGA-IQ-A61H TCGA-MT-A67A TCGA-P3-A5QF TCGA-P3-A6T4 TCGA-TN-A7HL 
        3.65        37.41        30.05        10.85         2.04        20.35 
TCGA-UF-A71B TCGA-UF-A71D 
       49.51        48.03 

$`NFE2L2 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
       12.62         4.01        29.42        28.11        20.45        30.18 
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-BB-4217 TCGA-BB-4223 
        2.27        11.05        13.38        20.48         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       33.70        50.20        66.28        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       20.52        25.71        10.55        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
        6.28        12.69        38.04         4.67        51.29        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-6020 
       48.00        23.90        47.44        28.04        19.07         6.74 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        9.07         9.24        52.08        11.08        10.45        32.22 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       35.05        38.89         3.68        17.42        32.48        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-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        23.44        19.82        24.39        20.88 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       19.53        48.20        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-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       15.75        32.38        32.88        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       13.25         4.24        14.99        38.76        70.13        64.87 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       53.52        16.73        43.04        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        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-6472 TCGA-CR-6473 
       26.27        58.42        50.01        39.52        34.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       18.54        16.90         6.02        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-7385 TCGA-CR-7386 TCGA-CR-7388 
       34.06        19.92        26.17        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        29.82        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         7.10         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        87.55        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-6936 TCGA-CV-6937 TCGA-CV-6938 
        9.60        90.12         2.14         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       21.90        11.24        19.79        12.03        42.38        15.09 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
        6.08        53.95        65.82         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       126.15       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-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        47.47 
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        36.13        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       57.47        35.54        17.85       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-7425 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
      100.57        56.48       156.49        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-7568 
        7.17       153.86         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-7082 
       21.24        23.47        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.55        18.84        34.36        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-A6EM TCGA-D6-A6EN 
       24.95        25.32        17.72        12.36         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        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       37.25        30.94        33.86        18.02        14.04        46.32 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       46.45        20.45        37.58        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       41.59        37.18        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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       12.43        15.16        13.61        21.11        20.94         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       28.47        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       22.03        12.66        22.85         0.36        13.84         4.27 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       11.84         0.07        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       19.04        15.48        13.35        18.15        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-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
        7.13        16.08        17.98        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        18.64        21.07 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       19.73        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       32.45        13.55        13.25        64.80        54.67         2.83 
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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        17.03        20.55        14.56 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            2.04             0.07 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
          140.78           210.97 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
          21.075           21.140 
[1] "2.0 - 140.8 (21.1)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.3"
D11V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  NFE2L2 MUTATED         2        6         6        12         0
  NFE2L2 WILD-TYPE      23       69        76       236        11
D11V3, multiclass
           clus
vv          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE I                2               23
  STAGE II               6               69
  STAGE III              6               76
  STAGE IVA             12              236
  STAGE IVB              0               11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  NFE2L2 MUTATED       2  10   5   9
  NFE2L2 WILD-TYPE    46 124  94 159
D11V4, multiclass
       clus
vv      NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T0+T1              2               46
  T2                10              124
  T3                 5               94
  T4                 9              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
  NFE2L2 MUTATED    10   5   6   0
  NFE2L2 WILD-TYPE 165  62 156   7
D11V5, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0             10              165
  N1              5               62
  N2              6              156
  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
  NFE2L2 MUTATED    11  15
  NFE2L2 WILD-TYPE 129 355
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     11   15
  NFE2L2 WILD-TYPE  129  355
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE             11              129
  MALE               15              355
[1] 2 2
[1] FALSE
D11V7, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED    10   8
  NFE2L2 WILD-TYPE 136 266
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     10    8
  NFE2L2 WILD-TYPE  136  266
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  NO              10              136
  YES              8              266
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  NFE2L2 MUTATED                                      26
  NFE2L2 WILD-TYPE                                   476
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  NFE2L2 MUTATED                                                             0
  NFE2L2 WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  NFE2L2 MUTATED                                                     0
  NFE2L2 WILD-TYPE                                                   7
D11V8, multiclass
                                                             clus
vv                                                            NFE2L2 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   26
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
                                                             clus
vv                                                            NFE2L2 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    476
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, continuous
D11V10, continuous
D11V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFE2L2 MUTATED                                  0     1
  NFE2L2 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NFE2L2 MUTATED                           0    24
  NFE2L2 WILD-TYPE                        37   422
D11V12, multiclass
                                  clus
vv                                 NFE2L2 MUTATED NFE2L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               37
  WHITE                                        24              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"
D11V13, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     2  20
  NFE2L2 WILD-TYPE  24 428
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      2   20
  NFE2L2 WILD-TYPE   24  428
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  2               24
  NOT HISPANIC OR LATINO             20              428
[1] 2 2
[1] FALSE

Clustering(12) Variable = FBXW7 MUTATION ANALYSIS
D12V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED    15  18
  FBXW7 WILD-TYPE 278 199
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             33             477 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             18             199 
$`FBXW7 MUTATED`
TCGA-BA-6868 TCGA-BA-A6DF TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8601 TCGA-BB-A6UO 
       15.52         7.82        18.38        66.28        20.52         8.81 
TCGA-CN-4730 TCGA-CN-5366 TCGA-CN-6992 TCGA-CN-A498 TCGA-CN-A6V7 TCGA-CQ-5332 
       26.86        11.84        35.05        25.41        19.53        10.42 
TCGA-CQ-6221 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-7379 TCGA-CR-7398 TCGA-CV-6436 
       32.88        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-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       65.59        68.48        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        4.01        41.85        29.42        28.11        20.45        30.18 
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-4223 TCGA-BB-4224 
       11.05        13.38        20.48         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.60         4.41        22.42        36.72        33.70        50.20 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ 
       24.66        38.40        71.05        25.71        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-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       51.29        56.68        12.89        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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       32.22        38.89         3.68        17.42        32.48        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-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5323 
        2.70        23.44        19.82        24.39        20.88        48.20 
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-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 
       45.99        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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       38.76        70.13        64.87        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.36        33.60        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       34.52        36.99        18.54        16.90         6.02        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-7382 TCGA-CR-7383 TCGA-CR-7385 
       31.96         9.17        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        29.82        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 
       32.65        44.25        30.58         7.10         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        87.55        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-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-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       12.03        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-7097 TCGA-CV-7099 TCGA-CV-7100 
       64.83       126.15       111.16        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        47.47        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-7406 TCGA-CV-7407 
       11.87        47.97         2.10        36.13        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       17.85       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-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-A45T TCGA-CV-A45U TCGA-CV-A45X 
       27.98        21.01       169.38       159.65        35.47         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-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
        6.48        28.01         3.62        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ 
       10.42        10.42        10.55        18.84        34.36        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-5629 TCGA-DQ-5630 
       12.79        11.11        58.45        37.25        30.94        33.86 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       18.02        14.04        46.32        46.45        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
       40.24        40.04        39.12        41.59        37.18        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-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 
       17.85        20.25        12.43        13.38        15.16        13.61 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       21.11        20.94         0.07        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       27.48        27.48        14.66        22.03        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
        0.36        13.84         4.27         3.65         6.90        34.75 
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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       15.48        13.35        18.15        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
        7.96         1.84        12.62         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
       16.08        17.98        15.78        71.74        51.25        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-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       12.99        13.15        21.07        21.21        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO 
       21.47        12.72        18.64        21.07        19.73        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI 
       16.96         6.87        15.91         7.10        32.45        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-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       48.03        49.45        74.47        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       29.46        18.05        13.94        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

  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           21.21 
[1] "1.1 - 180.2 (20.5)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.3"
D12V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  FBXW7 MUTATED         1        5         8        16         1
  FBXW7 WILD-TYPE      24       70        74       232        10
D12V3, multiclass
           clus
vv          FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I               1              24
  STAGE II              5              70
  STAGE III             8              74
  STAGE IVA            16             232
  STAGE IVB             1              10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  FBXW7 MUTATED       1   8   9  14
  FBXW7 WILD-TYPE    47 126  90 154
D12V4, multiclass
       clus
vv      FBXW7 MUTATED FBXW7 WILD-TYPE
  T0+T1             1              47
  T2                8             126
  T3                9              90
  T4               14             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
  FBXW7 MUTATED    14   3   8   1
  FBXW7 WILD-TYPE 161  64 154   6
D12V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0            14             161
  N1             3              64
  N2             8             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"
D12V6, binary
                 cls
clus                0   1
  FBXW7 MUTATED    13  20
  FBXW7 WILD-TYPE 127 350
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     13   20
  FBXW7 WILD-TYPE  127  350
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE            13             127
  MALE              20             350
[1] 2 2
[1] FALSE
D12V7, binary
                 cls
clus                0   1
  FBXW7 MUTATED    12  17
  FBXW7 WILD-TYPE 134 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     12   17
  FBXW7 WILD-TYPE  134  257
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO             12             134
  YES            17             257
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  FBXW7 MUTATED                                      33
  FBXW7 WILD-TYPE                                   469
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  FBXW7 MUTATED                                                             0
  FBXW7 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  FBXW7 MUTATED                                                     0
  FBXW7 WILD-TYPE                                                   7
D12V8, multiclass
                                                             clus
vv                                                            FBXW7 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  33
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
                                                             clus
vv                                                            FBXW7 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   469
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, continuous
D12V10, continuous
D12V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXW7 MUTATED                                  0     0
  FBXW7 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FBXW7 MUTATED                           3    28
  FBXW7 WILD-TYPE                        34   418
D12V12, multiclass
                                  clus
vv                                 FBXW7 MUTATED FBXW7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    3              34
  WHITE                                       28             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"
D12V13, binary
                 cls
clus                0   1
  FBXW7 MUTATED     2  27
  FBXW7 WILD-TYPE  24 421
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      2   27
  FBXW7 WILD-TYPE   24  421
                        clus
vv                       FBXW7 MUTATED FBXW7 WILD-TYPE
  HISPANIC OR LATINO                 2              24
  NOT HISPANIC OR LATINO            27             421
[1] 2 2
[1] FALSE

Clustering(13) Variable = ZNF750 MUTATION ANALYSIS
D13V1, survival
                  sevent
clus2                0   1
  ZNF750 MUTATED    11   8
  ZNF750 WILD-TYPE 282 209
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              19              491 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               8              209 
$`ZNF750 MUTATED`
TCGA-BB-7870 TCGA-CN-A63Y TCGA-CR-6481 TCGA-CR-7368 TCGA-CR-7404 TCGA-CV-5434 
       66.28        16.57        10.22        40.93        48.39       108.95 
TCGA-CV-5444 TCGA-CV-6961 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-A45Z TCGA-DQ-5629 
       80.12         2.50         0.46        25.94        48.20        30.94 
TCGA-HL-7533 TCGA-KU-A6H7 TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5QF TCGA-T2-A6WX 
       34.75        19.27         6.25        17.98        10.85         6.87 
TCGA-TN-A7HL 
       20.35 

$`ZNF750 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        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-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       36.72        33.70        50.20        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       20.52        25.71        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-4727 
        6.28        12.69        55.86        38.04         4.67        51.29 
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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       34.13         6.74         9.07         9.24        52.08        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        32.22        35.05        38.89         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       32.48        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-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        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-6221 TCGA-CQ-6222 
        4.24        41.19        15.75        32.38        32.88        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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
       70.13        64.87        53.52        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       43.10        77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
       39.52        34.52        36.99        18.54        16.90         6.02 
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-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        29.82        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         7.10         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 
       35.41        29.95       139.43        17.16       129.21        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        87.55        76.50        91.53 
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-7089 
       10.98         7.13         8.42        28.34         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      126.15       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        47.47        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        36.13        18.41        57.47 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 
       35.54        17.85       210.97        89.33         9.67        22.85 
TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
       25.08         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-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-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-7082 TCGA-CX-7085 
       23.47        19.92        22.52        10.42        10.42        10.55 
TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       18.84        34.36        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        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       37.25        33.86        18.02        14.04        46.32        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45        37.58        40.24        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       37.18        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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       13.38        15.16        13.61        21.11        20.94         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       28.47        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       22.03        12.66        22.85         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-A66S TCGA-KU-A66T TCGA-KU-A6H8 
       13.84        19.04        15.48        13.35        18.15        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-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
        7.13        16.08        15.78        71.74        51.25        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        18.64        21.07 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       19.73        12.72        16.96        15.91         7.10        32.45 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.55        13.25        64.80        54.67         2.83        49.51 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       48.03        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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       32.65         2.96        17.03        20.55        14.56 

  ZNF750 MUTATED ZNF750 WILD-TYPE 
            0.46             0.07 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
          108.95           210.97 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
           20.35            21.17 
[1] "0.5 - 109.0 (20.4)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1"  
D13V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  ZNF750 MUTATED         0        3         0        11         0
  ZNF750 WILD-TYPE      25       72        82       237        11
D13V3, multiclass
           clus
vv          ZNF750 MUTATED ZNF750 WILD-TYPE
  STAGE I                0               25
  STAGE II               3               72
  STAGE III              0               82
  STAGE IVA             11              237
  STAGE IVB              0               11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF750 MUTATED       2   3   2   7
  ZNF750 WILD-TYPE    46 131  97 161
D13V4, multiclass
       clus
vv      ZNF750 MUTATED ZNF750 WILD-TYPE
  T0+T1              2               46
  T2                 3              131
  T3                 2               97
  T4                 7              161
[1] 4 2
[1] TRUE
[1] "dimension of 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   8   0
  ZNF750 WILD-TYPE 171  65 154   7
D13V5, multiclass
    clus
vv   ZNF750 MUTATED ZNF750 WILD-TYPE
  N0              4              171
  N1              2               65
  N2              8              154
  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
  ZNF750 MUTATED     3  16
  ZNF750 WILD-TYPE 137 354
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      3   16
  ZNF750 WILD-TYPE  137  354
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  FEMALE              3              137
  MALE               16              354
[1] 2 2
[1] FALSE
D13V7, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     6  12
  ZNF750 WILD-TYPE 140 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      6   12
  ZNF750 WILD-TYPE  140  262
     clus
vv    ZNF750 MUTATED ZNF750 WILD-TYPE
  NO               6              140
  YES             12              262
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  ZNF750 MUTATED                                      19
  ZNF750 WILD-TYPE                                   483
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  ZNF750 MUTATED                                                             0
  ZNF750 WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  ZNF750 MUTATED                                                     0
  ZNF750 WILD-TYPE                                                   7
D13V8, multiclass
                                                             clus
vv                                                            ZNF750 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   19
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
                                                             clus
vv                                                            ZNF750 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    483
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V9, continuous
D13V10, continuous
D13V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF750 MUTATED                                  0     0
  ZNF750 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF750 MUTATED                           3    16
  ZNF750 WILD-TYPE                        34   430
D13V12, multiclass
                                  clus
vv                                 ZNF750 MUTATED ZNF750 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     3               34
  WHITE                                        16              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"
D13V13, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     0  19
  ZNF750 WILD-TYPE  26 429
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      0   19
  ZNF750 WILD-TYPE   26  429
                        clus
vv                       ZNF750 MUTATED ZNF750 WILD-TYPE
  HISPANIC OR LATINO                  0               26
  NOT HISPANIC OR LATINO             19              429
[1] 2 2
[1] FALSE

Clustering(14) Variable = RAC1 MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  RAC1 MUTATED     7   8
  RAC1 WILD-TYPE 286 209
  RAC1 MUTATED RAC1 WILD-TYPE 
            15            495 
  RAC1 MUTATED RAC1 WILD-TYPE 
             8            209 
$`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-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
       15.19         9.30        13.64        37.28        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       42.35        57.93        17.10        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       68.48        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        4.01        41.85        29.42        28.11        20.45        30.18 
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-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
        2.27        11.05        20.48         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       50.20        66.28        24.66        38.40        71.05        20.52 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       25.71        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
       12.69        55.86        38.04         4.67        51.29        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-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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        9.07         9.24        52.08        11.08        10.45        32.22 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       35.05        38.89         3.68        17.42        32.48        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-A641 
        7.40        31.69        22.32        12.39        16.57        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
        2.70        23.44        19.82        24.39        20.88        19.53 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        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-6221 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6225 
       15.75        32.38        32.88        66.28        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        4.24        14.99        38.76        70.13        64.87        53.52 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       16.73        43.04        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       11.61        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-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
       58.42        50.01        39.52        34.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       16.90         6.02        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-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
       39.16        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-7389 TCGA-CR-7390 
       26.17        17.13        32.78        47.01        12.89        29.82 
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         7.10 
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        87.55        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 
      126.15       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        47.47        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        36.13        18.41        57.47 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       35.54        17.85       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-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       14.89        56.48         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-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       30.48        27.98       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-CV-A6K2 TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 
       23.47        19.92        10.42        10.42        18.84        34.36 
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-5629 
       12.10        12.79        11.11        58.45        37.25        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
       33.86        18.02        14.04        46.32        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       37.58        40.24        40.04        39.12        41.59        37.18 
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-H7-8501 
        0.46        17.85        11.80        20.25        12.43        15.16 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.61        21.11        20.94         0.07        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
       21.93        27.48        27.48        14.66        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.85         0.36        13.84         4.27         3.65         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
       34.75        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       19.04        15.48        13.35        18.15        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-A5Q6 TCGA-P3-A5QA 
       15.42         7.13        16.08        17.98        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-RS-A6TO TCGA-RS-A6TP 
       12.72        18.64        21.07        19.73        12.72        16.96 
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-A71D 
       20.35        64.80        54.67         2.83        49.51        48.03 
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-A7JV 
       29.46        18.05        13.94        20.75        22.36         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

  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          21.17 
[1] "4.4 - 156.5 (21.0)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.3"
D14V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  RAC1 MUTATED         2        2         0         7         0
  RAC1 WILD-TYPE      23       73        82       241        11
D14V3, multiclass
           clus
vv          RAC1 MUTATED RAC1 WILD-TYPE
  STAGE I              2             23
  STAGE II             2             73
  STAGE III            0             82
  STAGE IVA            7            241
  STAGE IVB            0             11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  RAC1 MUTATED       2   3   0   6
  RAC1 WILD-TYPE    46 131  99 162
D14V4, multiclass
       clus
vv      RAC1 MUTATED RAC1 WILD-TYPE
  T0+T1            2             46
  T2               3            131
  T3               0             99
  T4               6            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
  RAC1 MUTATED     7   1   2   0
  RAC1 WILD-TYPE 168  66 160   7
D14V5, multiclass
    clus
vv   RAC1 MUTATED RAC1 WILD-TYPE
  N0            7            168
  N1            1             66
  N2            2            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"
D14V6, binary
                cls
clus               0   1
  RAC1 MUTATED     9   6
  RAC1 WILD-TYPE 131 364
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      9    6
  RAC1 WILD-TYPE  131  364
        clus
vv       RAC1 MUTATED RAC1 WILD-TYPE
  FEMALE            9            131
  MALE              6            364
[1] 2 2
[1] FALSE
D14V7, binary
                cls
clus               0   1
  RAC1 MUTATED     4   9
  RAC1 WILD-TYPE 142 265
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      4    9
  RAC1 WILD-TYPE  142  265
     clus
vv    RAC1 MUTATED RAC1 WILD-TYPE
  NO             4            142
  YES            9            265
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  RAC1 MUTATED                                      15
  RAC1 WILD-TYPE                                   487
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  RAC1 MUTATED                                                             0
  RAC1 WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  RAC1 MUTATED                                                     0
  RAC1 WILD-TYPE                                                   7
D14V8, multiclass
                                                             clus
vv                                                            RAC1 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                 15
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
                                                             clus
vv                                                            RAC1 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  487
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V9, continuous
D14V10, continuous
D14V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAC1 MUTATED                                  0     1
  RAC1 WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RAC1 MUTATED                           0    14
  RAC1 WILD-TYPE                        37   432
D14V12, multiclass
                                  clus
vv                                 RAC1 MUTATED RAC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             37
  WHITE                                      14            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"
D14V13, binary
                cls
clus               0   1
  RAC1 MUTATED     0  14
  RAC1 WILD-TYPE  26 434
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      0   14
  RAC1 WILD-TYPE   26  434
                        clus
vv                       RAC1 MUTATED RAC1 WILD-TYPE
  HISPANIC OR LATINO                0             26
  NOT HISPANIC OR LATINO           14            434
[1] 2 2
[1] FALSE

Clustering(15) Variable = EPHA2 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  EPHA2 MUTATED    12  12
  EPHA2 WILD-TYPE 281 205
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             24             486 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             12             205 
$`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-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
       15.19         9.30        13.64         9.07        26.50        23.74 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       57.93        17.10        23.84        20.48        65.59        68.48 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 
       15.52        21.17        14.83         3.55        12.62        41.85 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
       29.42        28.11        20.45        30.18        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-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       13.38        20.48         6.15       105.90         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.41        18.38        22.42        36.72        33.70        50.20 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU 
       66.28        24.66        38.40        71.05        20.52        25.71 
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-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       55.86        38.04        51.29        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       32.81        52.14        57.11        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 
       45.83        27.58        73.61        13.05        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-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        34.13         6.74         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       11.08        10.45        32.22        35.05        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        32.48        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       17.29        29.72        21.21        31.69        22.32        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       24.39        20.88        19.53        48.20        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-6221 TCGA-CQ-6222 TCGA-CQ-6223 
       41.19        15.75        32.38        32.88        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       56.58        13.25         4.24        14.99        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 
       64.87        53.52        16.73        43.04        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        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-6472 
       37.87        26.27        58.42        50.01        39.52        34.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
       36.99        18.54        16.90         6.02        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        29.82        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         7.10         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        87.55 
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       126.15       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-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
       52.31        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        47.47        36.00        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       17.13        95.34        11.87        47.97         2.10        36.13 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       18.41        57.47        35.54        17.85       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-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-7446 
       84.49        19.76         7.17       153.86        16.64        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-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
       35.47         1.05         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-7082 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       18.84        34.36        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-A6EO 
       25.32        17.72        12.36        28.77         7.63        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        11.11        58.45        37.25 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       30.94        33.86        18.02        14.04        46.32        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45        37.58        40.24        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       37.18        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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       15.16        13.61        21.11        20.94         0.07        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       25.74        21.93        27.48        27.48        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G 
        6.90        34.75        15.95        38.53        14.50        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       19.04        15.48        13.35        18.15        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-A5Q6 TCGA-P3-A5QA 
       15.42         7.13        16.08        17.98        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-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6WZ 
       18.64        21.07        19.73        12.72         6.87        15.91 
TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        7.10        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        49.51        48.03        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       17.95        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36        32.65         2.96        17.03        20.55        14.56 

  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           21.09 
[1] "4.0 - 56.5 (22.4)"  "0.1 - 211.0 (21.1)"
[1] "hr=" "1.4"
D15V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  EPHA2 MUTATED         1        6         4        13         0
  EPHA2 WILD-TYPE      24       69        78       235        11
D15V3, multiclass
           clus
vv          EPHA2 MUTATED EPHA2 WILD-TYPE
  STAGE I               1              24
  STAGE II              6              69
  STAGE III             4              78
  STAGE IVA            13             235
  STAGE IVB             0              11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EPHA2 MUTATED       1   8   7   8
  EPHA2 WILD-TYPE    47 126  92 160
D15V4, multiclass
       clus
vv      EPHA2 MUTATED EPHA2 WILD-TYPE
  T0+T1             1              47
  T2                8             126
  T3                7              92
  T4                8             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
  EPHA2 MUTATED    11   1   8   0
  EPHA2 WILD-TYPE 164  66 154   7
D15V5, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  N0            11             164
  N1             1              66
  N2             8             154
  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     8  16
  EPHA2 WILD-TYPE 132 354
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      8   16
  EPHA2 WILD-TYPE  132  354
        clus
vv       EPHA2 MUTATED EPHA2 WILD-TYPE
  FEMALE             8             132
  MALE              16             354
[1] 2 2
[1] FALSE
D15V7, binary
                 cls
clus                0   1
  EPHA2 MUTATED     9  11
  EPHA2 WILD-TYPE 137 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      9   11
  EPHA2 WILD-TYPE  137  263
     clus
vv    EPHA2 MUTATED EPHA2 WILD-TYPE
  NO              9             137
  YES            11             263
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  EPHA2 MUTATED                                      24
  EPHA2 WILD-TYPE                                   478
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  EPHA2 MUTATED                                                             0
  EPHA2 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  EPHA2 MUTATED                                                     0
  EPHA2 WILD-TYPE                                                   7
D15V8, multiclass
                                                             clus
vv                                                            EPHA2 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  24
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
                                                             clus
vv                                                            EPHA2 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   478
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V9, continuous
D15V10, continuous
D15V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPHA2 MUTATED                                  0     1
  EPHA2 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EPHA2 MUTATED                           2    20
  EPHA2 WILD-TYPE                        35   426
D15V12, multiclass
                                  clus
vv                                 EPHA2 MUTATED EPHA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              35
  WHITE                                       20             426
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, binary
                 cls
clus                0   1
  EPHA2 MUTATED     1  22
  EPHA2 WILD-TYPE  25 426
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      1   22
  EPHA2 WILD-TYPE   25  426
                        clus
vv                       EPHA2 MUTATED EPHA2 WILD-TYPE
  HISPANIC OR LATINO                 1              25
  NOT HISPANIC OR LATINO            22             426
[1] 2 2
[1] FALSE

Clustering(16) Variable = HLA-A MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  HLA-A MUTATED    14   8
  HLA-A WILD-TYPE 279 209
  HLA-A MUTATED HLA-A WILD-TYPE 
             22             488 
  HLA-A MUTATED HLA-A WILD-TYPE 
              8             209 
$`HLA-A MUTATED`
TCGA-BA-5152 TCGA-BA-6868 TCGA-CN-A6V1 TCGA-CQ-7071 TCGA-CR-6467 TCGA-CR-7373 
       42.35        15.52        19.82        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-DQ-7594 TCGA-F7-A624 TCGA-H7-8501 TCGA-HD-A4C1 
       10.42        28.77        40.04        12.43        15.16         0.36 
TCGA-QK-A6IF TCGA-RS-A6TO TCGA-UF-A7JJ TCGA-UF-A7JT 
       23.15        12.72        18.05        32.65 

$`HLA-A WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       23.74        57.93        17.10        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
       68.48        21.17        14.83         3.55        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
       41.85        29.42        28.11        20.45        30.18        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-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       11.05        13.38        20.48         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       50.20        66.28        24.66        38.40        71.05        20.52 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       25.71        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
       12.69        55.86        38.04         4.67        51.29        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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       32.22        35.05        38.89         3.68        17.42        32.48 
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-A6V3 TCGA-CN-A6V6 
        4.41        12.07         2.70        23.44        24.39        20.88 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       19.53        48.20        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-6221 TCGA-CQ-6222 TCGA-CQ-6223 
       41.19        15.75        32.38        32.88        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       56.58        13.25         4.24        14.99        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7072 
       64.87        53.52        16.73        43.04        41.88        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        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-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
       37.87        26.27        50.01        39.52        34.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       18.54        16.90         6.02        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-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        3.09        24.95         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        29.82        30.02        46.85        32.65        44.25 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         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-5436 
      139.43        17.16       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       17.95       107.51        87.55        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 
       17.92        13.35        23.05        86.83        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-6938 TCGA-CV-6939 TCGA-CV-6940 
        2.14         9.70         5.46         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
       11.24       140.78        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       126.15       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        47.47        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-7409 TCGA-CV-7410 
       36.13        18.41        57.47        35.54        17.85       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-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-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-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
       19.92        22.52        10.42        10.55        18.84        34.36 
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-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       12.36         7.63        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
       12.79        11.11        58.45        37.25        30.94        33.86 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       18.02        14.04        46.32        46.45        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       40.24        39.12        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-H7-7774 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       11.80        20.25        13.38        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A634 
       14.66        22.03        12.66        22.85        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        3.65         6.90        34.75        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-A66S TCGA-KU-A66T 
       13.68        13.84        19.04        15.48        13.35        18.15 
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-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-A6IG TCGA-QK-A6IH 
       16.01        13.15        21.07        21.21         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TP 
        9.34        12.72        18.64        21.07        19.73        16.96 
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-A71D 
       20.35        64.80        54.67         2.83        49.51        48.03 
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-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JV TCGA-UP-A6WW 
       29.46        13.94        20.75        22.36         2.96        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  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 
         21.835          21.140 
[1] "0.4 - 67.9 (21.8)"  "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D16V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  HLA-A MUTATED         0        4         4        10         0
  HLA-A WILD-TYPE      25       71        78       238        11
D16V3, multiclass
           clus
vv          HLA-A MUTATED HLA-A WILD-TYPE
  STAGE I               0              25
  STAGE II              4              71
  STAGE III             4              78
  STAGE IVA            10             238
  STAGE IVB             0              11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HLA-A MUTATED       0   8   1   9
  HLA-A WILD-TYPE    48 126  98 159
D16V4, multiclass
       clus
vv      HLA-A MUTATED HLA-A WILD-TYPE
  T0+T1             0              48
  T2                8             126
  T3                1              98
  T4                9             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
  HLA-A MUTATED     6   5   4   0
  HLA-A WILD-TYPE 169  62 158   7
D16V5, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  N0             6             169
  N1             5              62
  N2             4             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"
D16V6, binary
                 cls
clus                0   1
  HLA-A MUTATED     6  16
  HLA-A WILD-TYPE 134 354
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      6   16
  HLA-A WILD-TYPE  134  354
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  FEMALE             6             134
  MALE              16             354
[1] 2 2
[1] FALSE
D16V7, binary
                 cls
clus                0   1
  HLA-A MUTATED     3  15
  HLA-A WILD-TYPE 143 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      3   15
  HLA-A WILD-TYPE  143  259
     clus
vv    HLA-A MUTATED HLA-A WILD-TYPE
  NO              3             143
  YES            15             259
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  HLA-A MUTATED                                      22
  HLA-A WILD-TYPE                                   480
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  HLA-A MUTATED                                                             0
  HLA-A WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  HLA-A MUTATED                                                     0
  HLA-A WILD-TYPE                                                   7
D16V8, multiclass
                                                             clus
vv                                                            HLA-A MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  22
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
                                                             clus
vv                                                            HLA-A WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   480
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V9, continuous
D16V10, continuous
D16V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HLA-A MUTATED                                  0     0
  HLA-A WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HLA-A MUTATED                           2    19
  HLA-A WILD-TYPE                        35   427
D16V12, multiclass
                                  clus
vv                                 HLA-A MUTATED HLA-A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              35
  WHITE                                       19             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"
D16V13, binary
                 cls
clus                0   1
  HLA-A MUTATED     0  18
  HLA-A WILD-TYPE  26 430
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      0   18
  HLA-A WILD-TYPE   26  430
                        clus
vv                       HLA-A MUTATED HLA-A WILD-TYPE
  HISPANIC OR LATINO                 0              26
  NOT HISPANIC OR LATINO            18             430
[1] 2 2
[1] FALSE

Clustering(17) Variable = HRAS MUTATION ANALYSIS
D17V1, survival
                sevent
clus2              0   1
  HRAS MUTATED    19  10
  HRAS WILD-TYPE 274 207
  HRAS MUTATED HRAS WILD-TYPE 
            29            481 
  HRAS MUTATED HRAS WILD-TYPE 
            10            207 
$`HRAS MUTATED`
TCGA-BA-5556 TCGA-BA-A6DJ TCGA-CN-A63V TCGA-CN-A642 TCGA-CQ-5324 TCGA-CQ-5333 
       23.84        13.38        22.32         2.70        52.37        11.21 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CG TCGA-CR-7382 TCGA-CR-7394 
       70.13        43.04        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-A61E TCGA-P3-A6T2 TCGA-T2-A6WX 
        0.36         6.90        37.71        75.55         6.87 

$`HRAS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 
       23.74        42.35        57.93        17.10        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       68.48        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        4.01        41.85        29.42        28.11        20.45        30.18 
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-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
        2.27        11.05        20.48         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       50.20        66.28        24.66        38.40        71.05        20.52 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       25.71        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
       12.69        55.86        38.04         4.67        51.29        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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       32.22        35.05        38.89         3.68        17.42        32.48 
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-A63W TCGA-CN-A63Y TCGA-CN-A640 
       21.21         7.40        31.69        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
       12.07        23.44        19.82        24.39        20.88        19.53 
TCGA-CQ-5323 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       48.20        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 
       45.99        10.42         4.24        41.19        15.75        32.38 
TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.88        66.28        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 
       14.99        38.76        64.87        53.52        16.73        41.88 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       77.56        44.48        11.61        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       29.49        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-6472 
       37.87        26.27        58.42        50.01        39.52        34.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
       36.99        18.54        16.90         6.02        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-7383 TCGA-CR-7385 TCGA-CR-7386 
        9.17        34.06        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        29.82        30.02        46.85        32.65 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         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-5436 
      139.43        17.16       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       17.95       107.51        87.55        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-6441 TCGA-CV-6933 
        7.07        43.23        54.74        21.07         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       126.15 
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-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       77.16         4.73        47.47        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       18.97        17.13         4.96        11.87        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
       36.13        18.41        57.47        35.54        17.85       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-A45O TCGA-CV-A45Q 
       16.64         6.38        22.19        35.93        27.98       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-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JT 
        7.07        15.25        35.34         6.38        29.79        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-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 
       10.42        10.55        18.84        34.36        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-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       18.67        24.95        17.72        12.36        28.77         7.63 
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        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       37.25        30.94        33.86        18.02        14.04        46.32 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       46.45        20.45        37.58        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       41.59        37.18        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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       12.43        13.38        13.61        21.11        20.94         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       28.47        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       22.03        12.66        22.85        13.84         4.27         3.65 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H 
       34.75        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       15.48        13.35        18.15        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        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 
       21.07        19.73        12.72        16.96        15.91         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       32.45        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        49.51        48.03        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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  HRAS MUTATED HRAS WILD-TYPE 
          0.36           0.07 
  HRAS MUTATED HRAS WILD-TYPE 
        130.88         210.97 
  HRAS MUTATED HRAS WILD-TYPE 
         23.84          21.07 
[1] "0.4 - 130.9 (23.8)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.3"
D17V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  HRAS MUTATED         2        7         5        12         1
  HRAS WILD-TYPE      23       68        77       236        10
D17V3, multiclass
           clus
vv          HRAS MUTATED HRAS WILD-TYPE
  STAGE I              2             23
  STAGE II             7             68
  STAGE III            5             77
  STAGE IVA           12            236
  STAGE IVB            1             10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  HRAS MUTATED       2  10   5  10
  HRAS WILD-TYPE    46 124  94 158
D17V4, multiclass
       clus
vv      HRAS MUTATED HRAS WILD-TYPE
  T0+T1            2             46
  T2              10            124
  T3               5             94
  T4              10            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
  HRAS MUTATED    14   4   5   1
  HRAS WILD-TYPE 161  63 157   6
D17V5, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  N0           14            161
  N1            4             63
  N2            5            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"
D17V6, binary
                cls
clus               0   1
  HRAS MUTATED    12  17
  HRAS WILD-TYPE 128 353
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED     12   17
  HRAS WILD-TYPE  128  353
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  FEMALE           12            128
  MALE             17            353
[1] 2 2
[1] FALSE
D17V7, binary
                cls
clus               0   1
  HRAS MUTATED    11  13
  HRAS WILD-TYPE 135 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED     11   13
  HRAS WILD-TYPE  135  261
     clus
vv    HRAS MUTATED HRAS WILD-TYPE
  NO            11            135
  YES           13            261
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  HRAS MUTATED                                      29
  HRAS WILD-TYPE                                   473
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  HRAS MUTATED                                                             0
  HRAS WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  HRAS MUTATED                                                     0
  HRAS WILD-TYPE                                                   7
D17V8, multiclass
                                                             clus
vv                                                            HRAS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                 29
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
                                                             clus
vv                                                            HRAS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  473
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V9, continuous
D17V10, continuous
D17V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HRAS MUTATED                                  0     1
  HRAS WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HRAS MUTATED                           1    27
  HRAS WILD-TYPE                        36   419
D17V12, multiclass
                                  clus
vv                                 HRAS MUTATED HRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             36
  WHITE                                      27            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"
D17V13, binary
                cls
clus               0   1
  HRAS MUTATED     0  29
  HRAS WILD-TYPE  26 419
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0   29
  HRAS WILD-TYPE   26  419
                        clus
vv                       HRAS MUTATED HRAS WILD-TYPE
  HISPANIC OR LATINO                0             26
  NOT HISPANIC OR LATINO           29            419
[1] 2 2
[1] FALSE

Clustering(18) Variable = PIK3CA MUTATION ANALYSIS
D18V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    50  44
  PIK3CA WILD-TYPE 243 173
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              94              416 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              44              173 
$`PIK3CA MUTATED`
TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5557 TCGA-BA-A4IF TCGA-BA-A6DF TCGA-BB-4223 
       37.28        26.50        20.48        29.42         7.82       105.90 
TCGA-BB-7863 TCGA-CN-4723 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5360 TCGA-CN-5365 
       33.70        55.86        45.83        73.61        71.31        11.54 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6994 
       52.08        50.07        23.90         9.07        11.08        38.89 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A6V1 TCGA-CQ-5331 TCGA-CQ-6218 
       11.74        25.41        17.29        19.82        45.99        41.19 
TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-A4C6 TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5249 
       15.75        66.28        44.48        14.14        84.23        37.87 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6487 TCGA-CR-7367 TCGA-CR-7371 TCGA-CR-7374 
       39.52        34.52         7.69        47.34         3.09         0.99 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5435 
       44.25        30.58         5.95        35.41        48.39        76.24 
TCGA-CV-5442 TCGA-CV-6436 TCGA-CV-6935 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6952 
       76.50        62.43         9.70        12.03        42.38         6.08 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-7177 TCGA-CV-7250 TCGA-CV-7261 
       10.98         7.13        28.34        21.80        95.34        36.13 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7438 
       57.47       210.97        89.33        34.09        14.89         6.38 
TCGA-CV-7568 TCGA-CV-A45O TCGA-CV-A45R TCGA-CV-A45V TCGA-CV-A460 TCGA-CV-A461 
       30.48        27.98       180.16         1.05        60.43        67.86 
TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CX-7082 TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6824 
        6.38         6.48        10.42        13.25         9.60         2.53 
TCGA-DQ-5630 TCGA-DQ-7589 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-H7-7774 
       33.86        46.32        21.63        31.13        18.94        13.38 
TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8634 TCGA-HL-7533 TCGA-IQ-A61E TCGA-MZ-A6I9 
       25.74        27.48        12.66        34.75        37.71        16.08 
TCGA-P3-A5QF TCGA-P3-A6T0 TCGA-T2-A6WZ TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A71B 
       10.85        19.00        15.91        13.55        20.35        49.51 
TCGA-UF-A7J9 TCGA-UF-A7JF TCGA-UF-A7JO TCGA-UF-A7JV 
       44.65        55.43        20.75         2.96 

$`PIK3CA WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
       15.19         9.30        13.64         9.07        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
       57.93        17.10        23.84        65.59        68.48        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       21.17        14.83         3.55        12.62         4.01        41.85 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       28.11        20.45        30.18        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
        5.69        14.47         2.27        11.05        13.38        20.48 
TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
        6.15         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       36.72        50.20        66.28        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       20.52        25.71        10.55        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
        6.28        12.69        38.04         4.67        51.29        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-4740 TCGA-CN-4742 TCGA-CN-5355 
       12.99        20.55        14.33        27.58        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 
       46.32         8.58        12.39        69.70         8.32        16.21 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6011 
       11.84        11.57        12.49         8.52        56.94        30.67 
TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       48.00        47.44        28.04        19.07        34.13         6.74 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 
        9.24        52.08        10.45        32.22        35.05         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C 
       17.42        32.48        35.01        23.57        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-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
       12.07         2.70        23.44        24.39        20.88        19.53 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-6221 
       62.37        10.42        11.21         4.24        32.38        32.88 
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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
       70.13        64.87        53.52        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        77.56        11.61        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5250 
       29.49        12.46        31.23        11.77        54.67        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
       58.42        50.01        36.99        18.54        16.90         6.02 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 
       11.90        10.22        11.34        11.64        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 
       15.75         9.27        47.18        39.16        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        3.45        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-7397 
       12.89        29.82        30.02        46.85        32.65         7.10 
TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
        5.13        29.95       139.43        17.16       129.21       108.95 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 
       19.20        17.95       107.51        87.55        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-6441 TCGA-CV-6933 
        7.07        43.23        54.74        21.07         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        2.14         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6953 
       11.24       140.78        19.79        15.09        30.08        53.95 
TCGA-CV-6954 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
       65.82         8.42         2.50         4.14        64.83       126.15 
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-7178 TCGA-CV-7180 TCGA-CV-7183 
        1.84        52.31        12.92        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        47.47        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       18.97        17.13         4.96        11.87        47.97         2.10 
TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       18.41        35.54        17.85         9.67         0.46        22.85 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 
       25.08        25.94         0.07       100.57        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-7440 TCGA-CV-7446 TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T 
       16.64        22.19        35.93        21.01       169.38       159.65 
TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A463 
       35.47        45.96         6.51        88.87        48.20         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
       56.61         7.07        15.25         5.98        35.34        29.79 
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-7219 TCGA-CX-A4AQ TCGA-D6-6516 
       10.42        10.55        18.84        34.36        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        11.11        58.45        37.25 
TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       30.94        18.02        14.04        46.45        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-A50G 
       40.24        40.04        39.12        41.59        37.18        20.25 
TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
        3.02        24.95         0.46        17.85        11.80        20.25 
TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       12.43        15.16        13.61        21.11        20.94         0.07 
TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 
       28.47        21.93        27.48        14.66        22.03        22.85 
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-A66S 
        5.29        13.68        13.84        19.04        15.48        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        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-A7D7 
        1.84        12.62         6.25        15.42         7.13        17.98 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
       15.78        71.74        51.25        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-RS-A6TO TCGA-RS-A6TP 
       12.72        18.64        21.07        19.73        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 
        6.87         7.10        32.45        13.25        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
        2.83        48.03        49.45        74.47        17.95        24.30 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       29.46        18.05        13.94        22.36        32.65        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.99             0.07 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          210.97           169.38 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           28.16            20.55 
[1] "1.0 - 211.0 (28.2)" "0.1 - 169.4 (20.6)"
[1] "hr=" "1.1"
D18V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  PIK3CA MUTATED         5        9        13        49         3
  PIK3CA WILD-TYPE      20       66        69       199         8
D18V3, multiclass
           clus
vv          PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                5               20
  STAGE II               9               66
  STAGE III             13               69
  STAGE IVA             49              199
  STAGE IVB              3                8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PIK3CA MUTATED       7  18  21  35
  PIK3CA WILD-TYPE    41 116  78 133
D18V4, multiclass
       clus
vv      PIK3CA MUTATED PIK3CA WILD-TYPE
  T0+T1              7               41
  T2                18              116
  T3                21               78
  T4                35              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
  PIK3CA MUTATED    39   8  27   2
  PIK3CA WILD-TYPE 136  59 135   5
D18V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             39              136
  N1              8               59
  N2             27              135
  N3              2                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    34  60
  PIK3CA WILD-TYPE 106 310
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     34   60
  PIK3CA WILD-TYPE  106  310
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             34              106
  MALE               60              310
[1] 2 2
[1] FALSE
D18V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    26  50
  PIK3CA WILD-TYPE 120 224
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     26   50
  PIK3CA WILD-TYPE  120  224
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              26              120
  YES             50              224
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  PIK3CA MUTATED                                      94
  PIK3CA WILD-TYPE                                   408
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  PIK3CA MUTATED                                                             0
  PIK3CA WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  PIK3CA MUTATED                                                     0
  PIK3CA WILD-TYPE                                                   7
D18V8, multiclass
                                                             clus
vv                                                            PIK3CA MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   94
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
                                                             clus
vv                                                            PIK3CA WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    408
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V9, continuous
D18V10, continuous
D18V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3CA MUTATED                                  0     2
  PIK3CA WILD-TYPE                                2     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED                           1    90
  PIK3CA WILD-TYPE                        36   356
D18V12, multiclass
                                  clus
vv                                 PIK3CA MUTATED PIK3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               36
  WHITE                                        90              356
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     4  83
  PIK3CA WILD-TYPE  22 365
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      4   83
  PIK3CA WILD-TYPE   22  365
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  4               22
  NOT HISPANIC OR LATINO             83              365
[1] 2 2
[1] FALSE

Clustering(19) Variable = EP300 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  EP300 MUTATED    19  20
  EP300 WILD-TYPE 274 197
  EP300 MUTATED EP300 WILD-TYPE 
             39             471 
  EP300 MUTATED EP300 WILD-TYPE 
             20             197 
$`EP300 MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5559 TCGA-BA-A6DA TCGA-BB-7863 TCGA-BB-7870 
        9.30        13.64        68.48        11.54        33.70        66.28 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-A63W TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CQ-5326 
       12.92         8.81        12.39         2.70        20.88         2.93 
TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6487 TCGA-CR-7394 
       54.58        45.99        50.01        39.52         7.69        44.25 
TCGA-CR-7395 TCGA-CV-5434 TCGA-CV-6938 TCGA-CV-6943 TCGA-CV-7095 TCGA-CV-7100 
       30.58       108.95         4.73        19.79        18.81         9.01 
TCGA-CV-7178 TCGA-CV-7427 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6K2 TCGA-CX-7219 
       71.21       156.49        15.25         5.98        10.42        34.36 
TCGA-D6-6516 TCGA-DQ-7593 TCGA-DQ-7595 TCGA-F7-A623 TCGA-H7-7774 TCGA-HD-A6HZ 
       25.41        40.24        39.12        20.25        13.38         3.65 
TCGA-MZ-A7D7 TCGA-P3-A6T4 TCGA-QK-A6IG 
       17.98         2.04         7.30 

$`EP300 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
       15.19        37.28         9.07        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 
       57.93        17.10        23.84        20.48        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       21.17        14.83         3.55        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB 
       29.42        28.11        20.45        30.18        27.95         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-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       20.48         6.15       105.90         9.14         4.60         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-7872 
       18.38        22.42        36.72        50.20        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-C9-A47Z 
       71.05        20.52        25.71        10.55        27.19         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
       12.69        55.86        38.04         4.67        51.29        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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       32.22        35.05        38.89         3.68        17.42        32.48 
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-A63Y TCGA-CN-A640 
       21.21         7.40        31.69        22.32        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 
       12.07        23.44        19.82        24.39        19.53        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 
       52.37        21.50        70.45        62.37        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6222 
        4.24        41.19        15.75        32.38        32.88        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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
       70.13        64.87        53.52        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       43.10        77.56        44.48        11.61        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-6472 
       11.77        54.67        37.87        26.27        58.42        34.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
       36.99        18.54        16.90         6.02        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.34        11.64        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        29.82        30.02        46.85        32.65 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         5.13         5.95        35.41        29.95        48.39 
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-5444 TCGA-CV-5966 
      107.51        87.55        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-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
       11.24       140.78        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       126.15       111.16 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
       12.66         7.99         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       21.80        10.75       130.88        77.16         4.73        47.47 
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        36.13        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       57.47        35.54        17.85       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-7429 TCGA-CV-7430 TCGA-CV-7432 
      100.57        14.89        56.48         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-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-7082 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-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       18.84        51.12        13.25         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-5629 
       12.10        12.79        11.11        58.45        37.25        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
       33.86        18.02        14.04        46.32        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       37.58        40.04        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-A624 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       11.80        12.43        15.16        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         6.90        34.75        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-A66S TCGA-KU-A66T 
       13.68        13.84        19.04        15.48        13.35        18.15 
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-P3-A5Q6 
       12.62         6.25        15.42         7.13        16.08        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-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       75.55        18.97        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.07        21.21        23.15        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       18.64        21.07        19.73        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       15.91         7.10        32.45        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       64.80        54.67         2.83        49.51        48.03        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-UF-A7JV 
       18.05        13.94        20.75        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

  EP300 MUTATED EP300 WILD-TYPE 
           2.04            0.07 
  EP300 MUTATED EP300 WILD-TYPE 
         156.49          210.97 
  EP300 MUTATED EP300 WILD-TYPE 
          18.81           21.24 
[1] "2.0 - 156.5 (18.8)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.3"
D19V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  EP300 MUTATED         2        5         7        18         1
  EP300 WILD-TYPE      23       70        75       230        10
D19V3, multiclass
           clus
vv          EP300 MUTATED EP300 WILD-TYPE
  STAGE I               2              23
  STAGE II              5              70
  STAGE III             7              75
  STAGE IVA            18             230
  STAGE IVB             1              10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EP300 MUTATED       4  10   5  15
  EP300 WILD-TYPE    44 124  94 153
D19V4, multiclass
       clus
vv      EP300 MUTATED EP300 WILD-TYPE
  T0+T1             4              44
  T2               10             124
  T3                5              94
  T4               15             153
[1] 4 2
[1] TRUE
[1] "dimension of 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    10   5  13   1
  EP300 WILD-TYPE 165  62 149   6
D19V5, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  N0            10             165
  N1             5              62
  N2            13             149
  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"
D19V6, binary
                 cls
clus                0   1
  EP300 MUTATED    13  26
  EP300 WILD-TYPE 127 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     13   26
  EP300 WILD-TYPE  127  344
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  FEMALE            13             127
  MALE              26             344
[1] 2 2
[1] FALSE
D19V7, binary
                 cls
clus                0   1
  EP300 MUTATED    11  22
  EP300 WILD-TYPE 135 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     11   22
  EP300 WILD-TYPE  135  252
     clus
vv    EP300 MUTATED EP300 WILD-TYPE
  NO             11             135
  YES            22             252
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  EP300 MUTATED                                      39
  EP300 WILD-TYPE                                   463
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  EP300 MUTATED                                                             0
  EP300 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  EP300 MUTATED                                                     0
  EP300 WILD-TYPE                                                   7
D19V8, multiclass
                                                             clus
vv                                                            EP300 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  39
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
                                                             clus
vv                                                            EP300 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   463
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V9, continuous
D19V10, continuous
D19V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EP300 MUTATED                                  0     1
  EP300 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EP300 MUTATED                           3    33
  EP300 WILD-TYPE                        34   413
D19V12, multiclass
                                  clus
vv                                 EP300 MUTATED EP300 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    3              34
  WHITE                                       33             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"
D19V13, binary
                 cls
clus                0   1
  EP300 MUTATED     3  34
  EP300 WILD-TYPE  23 414
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      3   34
  EP300 WILD-TYPE   23  414
                        clus
vv                       EP300 MUTATED EP300 WILD-TYPE
  HISPANIC OR LATINO                 3              23
  NOT HISPANIC OR LATINO            34             414
[1] 2 2
[1] FALSE

Clustering(20) Variable = RB1 MUTATION ANALYSIS
D20V1, survival
               sevent
clus2             0   1
  RB1 MUTATED    16   2
  RB1 WILD-TYPE 277 215
  RB1 MUTATED RB1 WILD-TYPE 
           18           492 
  RB1 MUTATED RB1 WILD-TYPE 
            2           215 
$`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-DQ-7594 TCGA-F7-A50J TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-QK-A6V9 TCGA-T2-A6WZ 
       40.04        31.13        19.04        19.27        18.64        15.91 

$`RB1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        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-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       36.72        33.70        50.20        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       71.05        20.52        25.71        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-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       51.29        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-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       12.39        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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       34.13         6.74         9.07         9.24        52.08        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        32.22        35.05        38.89         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B 
       32.48        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-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        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-6221 TCGA-CQ-6222 TCGA-CQ-6223 
       41.19        15.75        32.38        32.88        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       56.58        13.25         4.24        14.99        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        16.73        43.04        77.56        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       11.61        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-6472 TCGA-CR-6473 
       26.27        58.42        50.01        39.52        34.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       18.54        16.90         6.02        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
       11.64        12.46        22.78        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 
       39.16        47.34        40.93        35.84         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        29.82 
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         7.10 
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-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        87.55 
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-6940 TCGA-CV-6941 TCGA-CV-6942 
        5.46        20.52         4.73        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       126.15       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        47.47        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-7409 TCGA-CV-7410 
       36.13        18.41        57.47        35.54        17.85       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-7082 TCGA-CX-7086 
       23.47        19.92        22.52        10.42        10.42        18.84 
TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       34.36        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        11.11        58.45        37.25 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       30.94        33.86        18.02        14.04        46.32        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       20.45        37.58        40.24        39.12        41.59        37.18 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       21.63        20.25         3.02        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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.61        21.11        20.94         0.07        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
       21.93        27.48        27.48        14.66        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.85         0.36        13.84         4.27         3.65         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
       34.75        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-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       15.48        13.35        18.15        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-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       16.08        17.98        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-A6VB 
       23.15         7.30        21.47         9.34        12.72        21.07 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
       19.73        12.72        16.96         6.87         7.10        32.45 
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-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       49.51        48.03        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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36        32.65         2.96        17.03        20.55        14.56 

  RB1 MUTATED RB1 WILD-TYPE 
         0.99          0.07 
  RB1 MUTATED RB1 WILD-TYPE 
        71.31        210.97 
  RB1 MUTATED RB1 WILD-TYPE 
       20.585        21.140 
[1] "1.0 - 71.3 (20.6)"  "0.1 - 211.0 (21.1)"
[1] "hr=" "3.5"
D20V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  RB1 MUTATED         2        4         3         4         0
  RB1 WILD-TYPE      23       71        79       244        11
D20V3, multiclass
           clus
vv          RB1 MUTATED RB1 WILD-TYPE
  STAGE I             2            23
  STAGE II            4            71
  STAGE III           3            79
  STAGE IVA           4           244
  STAGE IVB           0            11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  RB1 MUTATED       2   6   4   2
  RB1 WILD-TYPE    46 128  95 166
D20V4, multiclass
       clus
vv      RB1 MUTATED RB1 WILD-TYPE
  T0+T1           2            46
  T2              6           128
  T3              4            95
  T4              2           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
  RB1 MUTATED     8   1   4   0
  RB1 WILD-TYPE 167  66 158   7
D20V5, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  N0           8           167
  N1           1            66
  N2           4           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"
D20V6, binary
               cls
clus              0   1
  RB1 MUTATED    11   7
  RB1 WILD-TYPE 129 363
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     11    7
  RB1 WILD-TYPE  129  363
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE          11           129
  MALE             7           363
[1] 2 2
[1] FALSE
D20V7, binary
               cls
clus              0   1
  RB1 MUTATED     5  11
  RB1 WILD-TYPE 141 263
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      5   11
  RB1 WILD-TYPE  141  263
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO            5           141
  YES          11           263
[1] 2 2
[1] FALSE
               vv
clus            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  RB1 MUTATED                                      18
  RB1 WILD-TYPE                                   484
               vv
clus            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  RB1 MUTATED                                                             0
  RB1 WILD-TYPE                                                           1
               vv
clus            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  RB1 MUTATED                                                     0
  RB1 WILD-TYPE                                                   7
D20V8, multiclass
                                                             clus
vv                                                            RB1 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                18
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                   0
                                                             clus
vv                                                            RB1 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                 484
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V9, continuous
D20V10, continuous
D20V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RB1 MUTATED                                  0     1
  RB1 WILD-TYPE                                2    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED                           0    17
  RB1 WILD-TYPE                        37   429
D20V12, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  0            37
  WHITE                                     17           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"
D20V13, binary
               cls
clus              0   1
  RB1 MUTATED     1  16
  RB1 WILD-TYPE  25 432
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      1   16
  RB1 WILD-TYPE   25  432
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               1            25
  NOT HISPANIC OR LATINO          16           432
[1] 2 2
[1] FALSE

Clustering(21) Variable = PTEN MUTATION ANALYSIS
D21V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    11   3
  PTEN WILD-TYPE 282 214
  PTEN MUTATED PTEN WILD-TYPE 
            14            496 
  PTEN MUTATED PTEN WILD-TYPE 
             3            214 
$`PTEN MUTATED`
TCGA-BA-4074 TCGA-BA-5559 TCGA-BB-A6UM TCGA-CN-4723 TCGA-CN-A499 TCGA-CR-7369 
       15.19        68.48        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        47.47        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-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
        9.30        13.64        37.28         9.07        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       42.35        57.93        17.10        23.84        20.48        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
       15.52        21.17        14.83         3.55        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
       41.85        29.42        28.11        20.45        30.18        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-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       11.05        13.38        20.48         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       50.20        66.28        24.66        38.40        71.05        20.52 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       25.71        10.55        27.19         8.81         6.28        12.69 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       38.04         4.67        51.29        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-6021 
       47.44        28.04        19.07        34.13         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        9.24        52.08        11.08        10.45        32.22        35.05 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 
       38.89         3.68        17.42        32.48        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-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       23.44        19.82        24.39        20.88        19.53        48.20 
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-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       32.38        32.88        66.28        46.95        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        4.24        14.99        38.76        70.13        64.87        53.52 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       16.73        43.04        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       11.61        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-6472 TCGA-CR-6473 
       26.27        58.42        50.01        39.52        34.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       18.54        16.90         6.02        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-7370 TCGA-CR-7371 
       47.18        39.16        47.34        40.93         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 
       29.82        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         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-5436 
      139.43        17.16       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       17.95       107.51        87.55        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-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       126.15       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-7242 
       71.21        10.75       130.88        77.16         4.73        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        36.13        18.41        57.47 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       35.54        17.85       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-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ 
       10.42        10.42        10.55        18.84        34.36        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-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
       11.11        58.45        37.25        30.94        33.86        18.02 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       14.04        46.32        46.45        20.45        37.58        40.24 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       40.04        39.12        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-A6C4 
       11.80        20.25        12.43        13.38        15.16        13.61 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       21.11        20.94         0.07        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       27.48        27.48        14.66        22.03        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
        0.36        13.84         4.27         3.65         6.90        34.75 
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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       15.48        13.35        18.15        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 
        7.96        30.05         1.84         6.25         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       17.98        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        18.64        19.73 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-TN-A7HI 
       12.72        16.96         6.87        15.91        32.45        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-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       48.03        49.45        44.65        74.47        17.95        24.30 
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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        17.03        20.55        14.56 

  PTEN MUTATED PTEN WILD-TYPE 
          0.99           0.07 
  PTEN MUTATED PTEN WILD-TYPE 
         68.48         210.97 
  PTEN MUTATED PTEN WILD-TYPE 
        18.245         21.190 
[1] "1.0 - 68.5 (18.2)"  "0.1 - 211.0 (21.2)"
[1] "hr=" "1.8"
D21V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  PTEN MUTATED         0        2         1         8         0
  PTEN WILD-TYPE      25       73        81       240        11
D21V3, multiclass
           clus
vv          PTEN MUTATED PTEN WILD-TYPE
  STAGE I              0             25
  STAGE II             2             73
  STAGE III            1             81
  STAGE IVA            8            240
  STAGE IVB            0             11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PTEN MUTATED       1   3   0   6
  PTEN WILD-TYPE    47 131  99 162
D21V4, multiclass
       clus
vv      PTEN MUTATED PTEN WILD-TYPE
  T0+T1            1             47
  T2               3            131
  T3               0             99
  T4               6            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
  PTEN MUTATED     6   0   4   0
  PTEN WILD-TYPE 169  67 158   7
D21V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0            6            169
  N1            0             67
  N2            4            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"
D21V6, binary
                cls
clus               0   1
  PTEN MUTATED     4  10
  PTEN WILD-TYPE 136 360
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4   10
  PTEN WILD-TYPE  136  360
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            4            136
  MALE             10            360
[1] 2 2
[1] FALSE
D21V7, binary
                cls
clus               0   1
  PTEN MUTATED     4   8
  PTEN WILD-TYPE 142 266
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4    8
  PTEN WILD-TYPE  142  266
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             4            142
  YES            8            266
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  PTEN MUTATED                                      14
  PTEN WILD-TYPE                                   488
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  PTEN MUTATED                                                             0
  PTEN WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  PTEN MUTATED                                                     0
  PTEN WILD-TYPE                                                   7
D21V8, multiclass
                                                             clus
vv                                                            PTEN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                 14
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
                                                             clus
vv                                                            PTEN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  488
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V9, continuous
D21V10, continuous
D21V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTEN MUTATED                                  0     0
  PTEN WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED                           0    14
  PTEN WILD-TYPE                        37   432
D21V12, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             37
  WHITE                                      14            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"
D21V13, binary
                cls
clus               0   1
  PTEN MUTATED     0  12
  PTEN WILD-TYPE  26 436
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0   12
  PTEN WILD-TYPE   26  436
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0             26
  NOT HISPANIC OR LATINO           12            436
[1] 2 2
[1] FALSE

Clustering(22) Variable = RASA1 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2               0   1
  RASA1 MUTATED    11   6
  RASA1 WILD-TYPE 282 211
  RASA1 MUTATED RASA1 WILD-TYPE 
             17             493 
  RASA1 MUTATED RASA1 WILD-TYPE 
              6             211 
$`RASA1 MUTATED`
TCGA-BB-7863 TCGA-BB-8601 TCGA-CN-4723 TCGA-CN-5366 TCGA-CN-6023 TCGA-CQ-6219 
       33.70        20.52        55.86        11.84        52.08        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-DQ-5629 TCGA-HD-7831 TCGA-IQ-7630 
        0.46        22.52        30.94        21.93        15.95 

$`RASA1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        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-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       36.72        50.20        66.28        24.66        38.40        71.05 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       25.71        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       12.69        38.04         4.67        51.29        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-5367 TCGA-CN-5369 TCGA-CN-5370 
        8.32        16.21        11.54        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-6021 
       47.44        28.04        19.07        34.13         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
        9.24        11.08        10.45        32.22        35.05        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        3.68        17.42        32.48        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-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       23.44        19.82        24.39        20.88        19.53        48.20 
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-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       32.88        66.28        46.95        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       38.76        70.13        64.87        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       50.01        39.52        34.52        36.99        18.54        16.90 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        6.02        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
       12.46        22.78         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        29.82        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         7.10         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 
       87.55        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-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
       28.34         2.50         4.14        64.83       126.15       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-7245 TCGA-CV-7247 
       77.16         4.73        47.47        36.00        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-7409 TCGA-CV-7410 
       36.13        18.41        57.47        35.54        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
       89.33        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-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ 
       10.42        10.42        10.55        18.84        34.36        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        11.11        58.45        37.25        33.86        18.02 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       14.04        46.32        46.45        20.45        37.58        40.24 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       40.04        39.12        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-A6C4 
       11.80        20.25        12.43        13.38        15.16        13.61 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 
       21.11        20.94         0.07        28.47        25.74        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
       27.48        14.66        22.03        12.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
       13.84         4.27         3.65         6.90        34.75        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-A66S 
        5.29        13.68        13.84        19.04        15.48        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        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-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       17.98        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        18.64        21.07 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       19.73        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       32.45        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        49.51        48.03        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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  RASA1 MUTATED RASA1 WILD-TYPE 
           0.46            0.07 
  RASA1 MUTATED RASA1 WILD-TYPE 
          56.58          210.97 
  RASA1 MUTATED RASA1 WILD-TYPE 
          21.93           21.11 
[1] "0.5 - 56.6 (21.9)"  "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D22V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  RASA1 MUTATED         0        2         5         9         0
  RASA1 WILD-TYPE      25       73        77       239        11
D22V3, multiclass
           clus
vv          RASA1 MUTATED RASA1 WILD-TYPE
  STAGE I               0              25
  STAGE II              2              73
  STAGE III             5              77
  STAGE IVA             9             239
  STAGE IVB             0              11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RASA1 MUTATED       0   6   5   5
  RASA1 WILD-TYPE    48 128  94 163
D22V4, multiclass
       clus
vv      RASA1 MUTATED RASA1 WILD-TYPE
  T0+T1             0              48
  T2                6             128
  T3                5              94
  T4                5             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
  RASA1 MUTATED     7   3   6   0
  RASA1 WILD-TYPE 168  64 156   7
D22V5, multiclass
    clus
vv   RASA1 MUTATED RASA1 WILD-TYPE
  N0             7             168
  N1             3              64
  N2             6             156
  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     3  14
  RASA1 WILD-TYPE 137 356
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      3   14
  RASA1 WILD-TYPE  137  356
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  FEMALE             3             137
  MALE              14             356
[1] 2 2
[1] FALSE
D22V7, binary
                 cls
clus                0   1
  RASA1 MUTATED     6   9
  RASA1 WILD-TYPE 140 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      6    9
  RASA1 WILD-TYPE  140  265
     clus
vv    RASA1 MUTATED RASA1 WILD-TYPE
  NO              6             140
  YES             9             265
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  RASA1 MUTATED                                      17
  RASA1 WILD-TYPE                                   485
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  RASA1 MUTATED                                                             0
  RASA1 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  RASA1 MUTATED                                                     0
  RASA1 WILD-TYPE                                                   7
D22V8, multiclass
                                                             clus
vv                                                            RASA1 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  17
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
                                                             clus
vv                                                            RASA1 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   485
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V9, continuous
D22V10, continuous
D22V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RASA1 MUTATED                                  0     0
  RASA1 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RASA1 MUTATED                           1    16
  RASA1 WILD-TYPE                        36   430
D22V12, multiclass
                                  clus
vv                                 RASA1 MUTATED RASA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              36
  WHITE                                       16             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"
D22V13, binary
                 cls
clus                0   1
  RASA1 MUTATED     2  15
  RASA1 WILD-TYPE  24 433
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      2   15
  RASA1 WILD-TYPE   24  433
                        clus
vv                       RASA1 MUTATED RASA1 WILD-TYPE
  HISPANIC OR LATINO                 2              24
  NOT HISPANIC OR LATINO            15             433
[1] 2 2
[1] FALSE

Clustering(23) Variable = MAPK1 MUTATION ANALYSIS
D23V1, survival
                 sevent
clus2               0   1
  MAPK1 MUTATED     8   1
  MAPK1 WILD-TYPE 285 216
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             501 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              1             216 
$`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        36.13 
TCGA-D6-A74Q TCGA-MT-A67F TCGA-TN-A7HL 
       11.11        12.62        20.35 

$`MAPK1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        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-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       36.72        33.70        50.20        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       71.05        20.52        25.71        10.55        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
        8.81         6.28        55.86        38.04         4.67        51.29 
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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       34.13         6.74         9.07         9.24        52.08        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        32.22        35.05        38.89         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       32.48        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-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        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-6221 TCGA-CQ-6222 TCGA-CQ-6223 
       41.19        15.75        32.38        32.88        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       56.58        13.25         4.24        14.99        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
       64.87        53.52        16.73        43.04        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       34.52        36.99        18.54        16.90         6.02        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        29.82        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         7.10         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-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 
       87.55        91.53        80.12        17.92        13.35        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       126.15       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        47.47        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-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       18.41        57.47        35.54        17.85       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-7082 TCGA-CX-7085 TCGA-CX-7086 
       19.92        22.52        10.42        10.42        10.55        18.84 
TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       34.36        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-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
       13.94        12.10        12.79        58.45        37.25        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
       33.86        18.02        14.04        46.32        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       37.58        40.24        40.04        39.12        41.59        37.18 
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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       15.16        13.61        21.11        20.94         0.07        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       25.74        21.93        27.48        27.48        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 
       13.84        19.04        15.48        13.35        18.15        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-A5Q6 TCGA-P3-A5QA 
       15.42         7.13        16.08        17.98        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-RS-A6TO TCGA-RS-A6TP 
       12.72        18.64        21.07        19.73        12.72        16.96 
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-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       64.80        54.67         2.83        49.51        48.03        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-UF-A7JV 
       18.05        13.94        20.75        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

  MAPK1 MUTATED MAPK1 WILD-TYPE 
           4.24            0.07 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
          76.50          210.97 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
          16.57           21.21 
[1] "4.2 - 76.5 (16.6)"  "0.1 - 211.0 (21.2)"
[1] "hr=" "3.3"
D23V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  MAPK1 MUTATED         0        1         1         7         0
  MAPK1 WILD-TYPE      25       74        81       241        11
D23V3, multiclass
           clus
vv          MAPK1 MUTATED MAPK1 WILD-TYPE
  STAGE I               0              25
  STAGE II              1              74
  STAGE III             1              81
  STAGE IVA             7             241
  STAGE IVB             0              11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MAPK1 MUTATED       0   1   3   5
  MAPK1 WILD-TYPE    48 133  96 163
D23V4, multiclass
       clus
vv      MAPK1 MUTATED MAPK1 WILD-TYPE
  T0+T1             0              48
  T2                1             133
  T3                3              96
  T4                5             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
  MAPK1 MUTATED     5   0   4   0
  MAPK1 WILD-TYPE 170  67 158   7
D23V5, multiclass
    clus
vv   MAPK1 MUTATED MAPK1 WILD-TYPE
  N0             5             170
  N1             0              67
  N2             4             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"
D23V6, binary
                 cls
clus                0   1
  MAPK1 MUTATED     3   6
  MAPK1 WILD-TYPE 137 364
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      3    6
  MAPK1 WILD-TYPE  137  364
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  FEMALE             3             137
  MALE               6             364
[1] 2 2
[1] FALSE
D23V7, binary
                 cls
clus                0   1
  MAPK1 MUTATED     2   4
  MAPK1 WILD-TYPE 144 270
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      2    4
  MAPK1 WILD-TYPE  144  270
     clus
vv    MAPK1 MUTATED MAPK1 WILD-TYPE
  NO              2             144
  YES             4             270
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  MAPK1 MUTATED                                       9
  MAPK1 WILD-TYPE                                   493
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  MAPK1 MUTATED                                                             0
  MAPK1 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  MAPK1 MUTATED                                                     0
  MAPK1 WILD-TYPE                                                   7
D23V8, multiclass
                                                             clus
vv                                                            MAPK1 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   9
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
                                                             clus
vv                                                            MAPK1 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   493
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V9, continuous
[1] "Remove cluster labels:" "MAPK1 MUTATED"         
clus
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              2             284 
     TCGA-BA-4074      TCGA-BA-4075      TCGA-BA-4076      TCGA-BA-4077 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-BA-4078      TCGA-BA-5149      TCGA-BA-5151      TCGA-BA-5555 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-BA-5556      TCGA-BA-6868      TCGA-BA-6869      TCGA-BA-6870 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-BA-6871      TCGA-BA-6872      TCGA-BA-6873      TCGA-BA-7269 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-BA-A4IF      TCGA-BA-A4IH      TCGA-BA-A4II      TCGA-BA-A6D8 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-BA-A6DA      TCGA-BA-A6DD      TCGA-BA-A6DE      TCGA-BA-A6DG 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-BA-A6DI      TCGA-BA-A6DJ      TCGA-BA-A6DL      TCGA-BB-4217 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-BB-4225      TCGA-BB-4227      TCGA-BB-4228      TCGA-BB-7862 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-BB-7864      TCGA-BB-7870      TCGA-BB-7871      TCGA-BB-8596 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-BB-A5HY      TCGA-BB-A6UM      TCGA-BB-A6UO      TCGA-CN-4726 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-4727      TCGA-CN-4728      TCGA-CN-4729      TCGA-CN-4730 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-4731      TCGA-CN-4735      TCGA-CN-4736      TCGA-CN-4738 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-4739      TCGA-CN-4740      TCGA-CN-4741      TCGA-CN-4742 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-5355      TCGA-CN-5358      TCGA-CN-5359      TCGA-CN-5360 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-5361      TCGA-CN-5363      TCGA-CN-5365      TCGA-CN-5366 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-5367      TCGA-CN-5373      TCGA-CN-5374      TCGA-CN-6010 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-6011      TCGA-CN-6012      TCGA-CN-6016      TCGA-CN-6017 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-6019      TCGA-CN-6021      TCGA-CN-6023      TCGA-CN-6024 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-6988      TCGA-CN-6989      TCGA-CN-6992      TCGA-CN-6994 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-6997      TCGA-CN-6998      TCGA-CN-A498      TCGA-CN-A49B 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-A49C      TCGA-CN-A63T      TCGA-CN-A63U      TCGA-CN-A63V 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-A641      TCGA-CN-A642      TCGA-CN-A6UY      TCGA-CN-A6V3 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CN-A6V6      TCGA-CQ-5323      TCGA-CQ-5324      TCGA-CQ-5325 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CQ-5326      TCGA-CQ-5330      TCGA-CQ-5331      TCGA-CQ-5332 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CQ-5333      TCGA-CQ-6218      TCGA-CQ-6219      TCGA-CQ-6221 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CQ-6222      TCGA-CQ-6223      TCGA-CQ-6224      TCGA-CQ-6227 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CQ-6228      TCGA-CQ-7063      TCGA-CQ-7072      TCGA-CQ-A4C6 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CQ-A4C7      TCGA-CQ-A4C9      TCGA-CQ-A4CB      TCGA-CQ-A4CG 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CQ-A4CI      TCGA-CR-5247      TCGA-CR-5248      TCGA-CR-5250 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-6467      TCGA-CR-6471      TCGA-CR-6473      TCGA-CR-6474 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-6482      TCGA-CR-6487      TCGA-CR-6491      TCGA-CR-6492 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-6493      TCGA-CR-7364      TCGA-CR-7367      TCGA-CR-7368 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-7369      TCGA-CR-7370      TCGA-CR-7371      TCGA-CR-7373 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-7374      TCGA-CR-7376      TCGA-CR-7377      TCGA-CR-7379 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-7383      TCGA-CR-7385      TCGA-CR-7386      TCGA-CR-7388 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-7389      TCGA-CR-7390      TCGA-CR-7392      TCGA-CR-7394 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-7395      TCGA-CR-7398      TCGA-CR-7399      TCGA-CR-7401 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-7402      TCGA-CV-6436      TCGA-CV-6441      TCGA-CV-6933 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-6934      TCGA-CV-6940      TCGA-CV-6941      TCGA-CV-6945 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-6952      TCGA-CV-6961      TCGA-CV-7095      TCGA-CV-7097 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-7235      TCGA-CV-7242      TCGA-CV-7245      TCGA-CV-7248 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-7250      TCGA-CV-7254      TCGA-CV-7263      TCGA-CV-7406 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-7410      TCGA-CV-7418      TCGA-CV-7422      TCGA-CV-7424 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-7427      TCGA-CV-7430      TCGA-CV-7432      TCGA-CV-7433 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-7434      TCGA-CV-7440      TCGA-CV-7446      TCGA-CV-7568 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-A45Y      TCGA-CV-A45Z      TCGA-CV-A460      TCGA-CV-A464 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-A468      TCGA-CV-A6JD      TCGA-CV-A6JN      TCGA-CV-A6JO 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-A6JU      TCGA-CV-A6JZ      TCGA-CV-A6K1      TCGA-CV-A6K2 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CX-7082      TCGA-CX-7085      TCGA-CX-7086      TCGA-CX-7219 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CX-A4AQ      TCGA-D6-6516      TCGA-D6-6517      TCGA-D6-6823 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-D6-6824      TCGA-D6-6825      TCGA-D6-6827      TCGA-D6-8568 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-D6-8569      TCGA-D6-A4Z9      TCGA-D6-A4ZB      TCGA-D6-A6EK 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-D6-A6EP      TCGA-DQ-5625      TCGA-DQ-5629      TCGA-DQ-5630 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-DQ-5631      TCGA-DQ-7588      TCGA-DQ-7589      TCGA-DQ-7590 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-DQ-7591      TCGA-DQ-7592      TCGA-DQ-7593      TCGA-DQ-7595 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-F7-7848      TCGA-F7-8489      TCGA-F7-A50G      TCGA-F7-A50I 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-F7-A50J      TCGA-F7-A61S      TCGA-F7-A61V      TCGA-F7-A61W 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-F7-A620      TCGA-F7-A623      TCGA-H7-7774      TCGA-H7-A6C4 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-H7-A6C5      TCGA-HD-7753      TCGA-HD-7754      TCGA-HD-7832 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-HD-8634      TCGA-HD-8635      TCGA-HD-A634      TCGA-HD-A6I0 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-HL-7533      TCGA-IQ-7631      TCGA-IQ-7632      TCGA-IQ-A61E 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-IQ-A61G      TCGA-IQ-A61H      TCGA-IQ-A61K      TCGA-IQ-A6SH 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-KU-A66S      TCGA-KU-A6H7      TCGA-KU-A6H8      TCGA-MT-A51W 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-MT-A51X      TCGA-MT-A67D      TCGA-MZ-A6I9      TCGA-MZ-A7D7 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-P3-A5Q6      TCGA-P3-A6SW      TCGA-P3-A6SX      TCGA-P3-A6T0 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-P3-A6T4      TCGA-P3-A6T5      TCGA-P3-A6T7      TCGA-P3-A6T8 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-QK-A6IG      TCGA-QK-A6II      TCGA-QK-A6IJ      TCGA-RS-A6TP 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-T2-A6WZ      TCGA-T2-A6X0      TCGA-T2-A6X2      TCGA-TN-A7HI 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-UF-A718      TCGA-UF-A71B      TCGA-UF-A71D      TCGA-UF-A7J9 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-UF-A7JC      TCGA-UF-A7JD      TCGA-UF-A7JF      TCGA-UF-A7JH 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-UF-A7JJ      TCGA-UF-A7JS      TCGA-WA-A7GZ      TCGA-WA-A7H4 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
D23V10, continuous
D23V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAPK1 MUTATED                                  0     1
  MAPK1 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MAPK1 MUTATED                           0     8
  MAPK1 WILD-TYPE                        37   438
D23V12, multiclass
                                  clus
vv                                 MAPK1 MUTATED MAPK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              37
  WHITE                                        8             438
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, binary
                 cls
clus                0   1
  MAPK1 MUTATED     0   9
  MAPK1 WILD-TYPE  26 439
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      0    9
  MAPK1 WILD-TYPE   26  439
                        clus
vv                       MAPK1 MUTATED MAPK1 WILD-TYPE
  HISPANIC OR LATINO                 0              26
  NOT HISPANIC OR LATINO             9             439
[1] 2 2
[1] FALSE

Clustering(24) Variable = NAP1L2 MUTATION ANALYSIS
D24V1, survival
                  sevent
clus2                0   1
  NAP1L2 MUTATED     3   4
  NAP1L2 WILD-TYPE 290 213
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               7              503 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               4              213 
$`NAP1L2 MUTATED`
TCGA-CQ-6218 TCGA-CV-5436 TCGA-CV-7409 TCGA-CV-A6K2 TCGA-IQ-A61G TCGA-IQ-A61L 
       41.19        19.20        17.85        10.42        11.84        13.68 
TCGA-UF-A71E 
       49.45 

$`NAP1L2 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        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-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       36.72        33.70        50.20        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       71.05        20.52        25.71        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-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       51.29        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-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        34.13         6.74         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       11.08        10.45        32.22        35.05        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        32.48        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-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       19.82        24.39        20.88        19.53        48.20        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-6219 TCGA-CQ-6220 TCGA-CQ-6221 
       10.42        11.21         4.24        15.75        32.38        32.88 
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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       38.76        70.13        64.87        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       50.01        39.52        34.52        36.99        18.54        16.90 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        6.02        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-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 
       29.82        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         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-5439 
      139.43        17.16       129.21       108.95        76.24        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        87.55        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 
      126.15       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        47.47        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        36.13        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-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7082 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.55        18.84        34.36        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        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       58.45        37.25        30.94        33.86        18.02        14.04 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       46.32        46.45        20.45        37.58        40.24        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       39.12        41.59        37.18        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-A6C4 TCGA-H7-A6C5 
       20.25        12.43        13.38        15.16        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       20.94         0.07        28.47        25.74        21.93        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
       27.48        14.66        22.03        12.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
       13.84         4.27         3.65         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       38.53        14.50        37.71        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T 
        5.29        13.84        19.04        15.48        13.35        18.15 
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-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        18.64        21.07        19.73 
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-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-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        48.03        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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       32.65         2.96        17.03        20.55        14.56 

  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
           10.42             0.07 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
           49.45           210.97 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
           17.85            21.21 
[1] "10.4 - 49.5 (17.9)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.6"
D24V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  NAP1L2 MUTATED         0        1         0         5         1
  NAP1L2 WILD-TYPE      25       74        82       243        10
D24V3, multiclass
           clus
vv          NAP1L2 MUTATED NAP1L2 WILD-TYPE
  STAGE I                0               25
  STAGE II               1               74
  STAGE III              0               82
  STAGE IVA              5              243
  STAGE IVB              1               10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  NAP1L2 MUTATED       0   1   2   4
  NAP1L2 WILD-TYPE    48 133  97 164
D24V4, multiclass
       clus
vv      NAP1L2 MUTATED NAP1L2 WILD-TYPE
  T0+T1              0               48
  T2                 1              133
  T3                 2               97
  T4                 4              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
  NAP1L2 MUTATED     3   0   3   1
  NAP1L2 WILD-TYPE 172  67 159   6
D24V5, multiclass
    clus
vv   NAP1L2 MUTATED NAP1L2 WILD-TYPE
  N0              3              172
  N1              0               67
  N2              3              159
  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"
D24V6, binary
                  cls
clus                 0   1
  NAP1L2 MUTATED     2   5
  NAP1L2 WILD-TYPE 138 365
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      2    5
  NAP1L2 WILD-TYPE  138  365
        clus
vv       NAP1L2 MUTATED NAP1L2 WILD-TYPE
  FEMALE              2              138
  MALE                5              365
[1] 2 2
[1] FALSE
D24V7, binary
                  cls
clus                 0   1
  NAP1L2 MUTATED     2   5
  NAP1L2 WILD-TYPE 144 269
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      2    5
  NAP1L2 WILD-TYPE  144  269
     clus
vv    NAP1L2 MUTATED NAP1L2 WILD-TYPE
  NO               2              144
  YES              5              269
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  NAP1L2 MUTATED                                       6
  NAP1L2 WILD-TYPE                                   496
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  NAP1L2 MUTATED                                                             0
  NAP1L2 WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  NAP1L2 MUTATED                                                     1
  NAP1L2 WILD-TYPE                                                   6
D24V8, multiclass
                                                             clus
vv                                                            NAP1L2 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    6
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      1
                                                             clus
vv                                                            NAP1L2 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    496
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V9, continuous
D24V10, continuous
D24V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NAP1L2 MUTATED                                  0     0
  NAP1L2 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NAP1L2 MUTATED                           1     5
  NAP1L2 WILD-TYPE                        36   441
D24V12, multiclass
                                  clus
vv                                 NAP1L2 MUTATED NAP1L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               36
  WHITE                                         5              441
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, binary
                  cls
clus                 0   1
  NAP1L2 MUTATED     3   3
  NAP1L2 WILD-TYPE  23 445
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      3    3
  NAP1L2 WILD-TYPE   23  445
                        clus
vv                       NAP1L2 MUTATED NAP1L2 WILD-TYPE
  HISPANIC OR LATINO                  3               23
  NOT HISPANIC OR LATINO              3              445
[1] 2 2
[1] FALSE

Clustering(25) Variable = KEAP1 MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2               0   1
  KEAP1 MUTATED    12  10
  KEAP1 WILD-TYPE 281 207
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             488 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             10             207 
$`KEAP1 MUTATED`
TCGA-BA-7269 TCGA-BB-7870 TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-5359 TCGA-CN-6010 
       41.85        66.28        55.86        51.29        12.39        50.07 
TCGA-CN-6012 TCGA-CR-6492 TCGA-CV-5434 TCGA-CV-5978 TCGA-CV-7238 TCGA-CV-7248 
       48.00        15.75       108.95         7.07        47.47        17.13 
TCGA-CV-A6JU TCGA-DQ-7588 TCGA-HD-A633 TCGA-KU-A66S TCGA-P3-A6T0 TCGA-T2-A6WX 
        3.62        14.04        13.84        13.35        19.00         6.87 
TCGA-UF-A71E TCGA-UF-A7JF TCGA-UF-A7JO TCGA-UF-A7JT 
       49.45        55.43        20.75        32.65 

$`KEAP1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
       12.62         4.01        29.42        28.11        20.45        30.18 
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-BB-4217 TCGA-BB-4223 
        2.27        11.05        13.38        20.48         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       33.70        50.20        24.66        38.40        71.05        20.52 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       25.71        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       12.69        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-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 
       46.32         8.58        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-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       56.94        30.67        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       34.13         6.74         9.07         9.24        52.08        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        32.22        35.05        38.89         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       32.48        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-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       24.39        20.88        19.53        48.20        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-6221 
       11.21         4.24        41.19        15.75        32.38        32.88 
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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       38.76        70.13        64.87        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       50.01        39.52        34.52        36.99        18.54        16.90 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        6.02        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       12.46        22.78         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        29.82 
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         7.10 
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 
       87.55        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 
       23.05        86.83        48.59        60.49        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       126.15       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-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
       77.16         4.73        36.00        31.36        26.20        18.97 
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        36.13 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       18.41        57.47        35.54        17.85       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-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
       29.79         6.48        28.01        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
       22.52        10.42        10.42        10.55        18.84        34.36 
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-5629 
       12.10        12.79        11.11        58.45        37.25        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       33.86        18.02        46.32        46.45        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
       40.24        40.04        39.12        41.59        37.18        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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.61        21.11        20.94         0.07        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
       21.93        27.48        27.48        14.66        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
       22.85         0.36         4.27         3.65         6.90        34.75 
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-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       15.48        18.15        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-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       16.08        17.98        15.78        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       36.82        47.01        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        18.64        21.07 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       19.73        12.72        16.96        15.91         7.10        32.45 
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-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        48.03        44.65        74.47        17.95        24.30 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JV TCGA-UP-A6WW 
       29.46        18.05        13.94        22.36         2.96        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  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           21.14 
[1] "3.6 - 109.0 (26.7)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1"  
D25V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  KEAP1 MUTATED         0        1         3        14         2
  KEAP1 WILD-TYPE      25       74        79       234         9
D25V3, multiclass
           clus
vv          KEAP1 MUTATED KEAP1 WILD-TYPE
  STAGE I               0              25
  STAGE II              1              74
  STAGE III             3              79
  STAGE IVA            14             234
  STAGE IVB             2               9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KEAP1 MUTATED       1   3   1  15
  KEAP1 WILD-TYPE    47 131  98 153
D25V4, multiclass
       clus
vv      KEAP1 MUTATED KEAP1 WILD-TYPE
  T0+T1             1              47
  T2                3             131
  T3                1              98
  T4               15             153
[1] 4 2
[1] TRUE
[1] "dimension of 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  64 156   6
D25V5, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  N0            10             165
  N1             3              64
  N2             6             156
  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"
D25V6, binary
                 cls
clus                0   1
  KEAP1 MUTATED     9  13
  KEAP1 WILD-TYPE 131 357
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      9   13
  KEAP1 WILD-TYPE  131  357
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  FEMALE             9             131
  MALE              13             357
[1] 2 2
[1] FALSE
D25V7, binary
                 cls
clus                0   1
  KEAP1 MUTATED     2  17
  KEAP1 WILD-TYPE 144 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      2   17
  KEAP1 WILD-TYPE  144  257
     clus
vv    KEAP1 MUTATED KEAP1 WILD-TYPE
  NO              2             144
  YES            17             257
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  KEAP1 MUTATED                                      20
  KEAP1 WILD-TYPE                                   482
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  KEAP1 MUTATED                                                             0
  KEAP1 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  KEAP1 MUTATED                                                     2
  KEAP1 WILD-TYPE                                                   5
D25V8, multiclass
                                                             clus
vv                                                            KEAP1 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  20
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     2
                                                             clus
vv                                                            KEAP1 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   482
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V9, continuous
D25V10, continuous
D25V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KEAP1 MUTATED                                  0     0
  KEAP1 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KEAP1 MUTATED                           3    19
  KEAP1 WILD-TYPE                        34   427
D25V12, multiclass
                                  clus
vv                                 KEAP1 MUTATED KEAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    3              34
  WHITE                                       19             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"
D25V13, binary
                 cls
clus                0   1
  KEAP1 MUTATED     0  18
  KEAP1 WILD-TYPE  26 430
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      0   18
  KEAP1 WILD-TYPE   26  430
                        clus
vv                       KEAP1 MUTATED KEAP1 WILD-TYPE
  HISPANIC OR LATINO                 0              26
  NOT HISPANIC OR LATINO            18             430
[1] 2 2
[1] FALSE

Clustering(26) Variable = KDM6A MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED    11   6
  KDM6A WILD-TYPE 282 211
  KDM6A MUTATED KDM6A WILD-TYPE 
             17             493 
  KDM6A MUTATED KDM6A WILD-TYPE 
              6             211 
$`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        87.55         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         0.07        28.47         6.25        47.01 

$`KDM6A WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF 
       30.18        27.95        11.54         7.10         5.69         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 
        2.27        11.05        13.38        20.48         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       33.70        50.20        66.28        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       20.52        25.71        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-4727 
        6.28        12.69        55.86        38.04         4.67        51.29 
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-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       73.61        13.05        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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       32.22        35.05        38.89         3.68        17.42        32.48 
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-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        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-6221 TCGA-CQ-6222 
        4.24        41.19        15.75        32.38        32.88        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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
       70.13        64.87        53.52        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       43.10        77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
       39.52        34.52        36.99        18.54        16.90         6.02 
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-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        29.82        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         7.10         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-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-6936 
       21.07        62.43         9.60        90.12         2.14         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       126.15       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-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       12.92        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 
       47.47        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 
       95.34         4.96        47.97         2.10        36.13        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       57.47        35.54        17.85       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-A45R 
       22.19        35.93        30.48        27.98        21.01       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
      159.65        35.47         1.05         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-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        5.98         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-7082 
       21.24        23.47        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.55        18.84        34.36        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-D6-8569 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        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       37.25        30.94        33.86        18.02        14.04        46.32 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       46.45        20.45        37.58        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       41.59        37.18        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-H7-7774 
       18.94        24.95         0.46        17.85        11.80        13.38 
TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7831 
       15.16        13.61        21.11        20.94        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       27.48        27.48        14.66        22.03        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
        0.36        13.84         4.27         3.65         6.90        34.75 
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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       15.48        13.35        18.15        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI 
        7.96        30.05         1.84        12.62        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       16.08        17.98        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        18.64        21.07 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       19.73        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       32.45        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        49.51        48.03        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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  KDM6A MUTATED KDM6A WILD-TYPE 
           0.07            0.07 
  KDM6A MUTATED KDM6A WILD-TYPE 
         169.38          210.97 
  KDM6A MUTATED KDM6A WILD-TYPE 
          24.95           21.07 
[1] "0.1 - 169.4 (24.9)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.5"
D26V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  KDM6A MUTATED         1        5         1         8         0
  KDM6A WILD-TYPE      24       70        81       240        11
D26V3, multiclass
           clus
vv          KDM6A MUTATED KDM6A WILD-TYPE
  STAGE I               1              24
  STAGE II              5              70
  STAGE III             1              81
  STAGE IVA             8             240
  STAGE IVB             0              11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KDM6A MUTATED       3   6   1   5
  KDM6A WILD-TYPE    45 128  98 163
D26V4, multiclass
       clus
vv      KDM6A MUTATED KDM6A WILD-TYPE
  T0+T1             3              45
  T2                6             128
  T3                1              98
  T4                5             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
  KDM6A MUTATED     7   2   4   0
  KDM6A WILD-TYPE 168  65 158   7
D26V5, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  N0             7             168
  N1             2              65
  N2             4             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"
D26V6, binary
                 cls
clus                0   1
  KDM6A MUTATED     4  13
  KDM6A WILD-TYPE 136 357
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      4   13
  KDM6A WILD-TYPE  136  357
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE             4             136
  MALE              13             357
[1] 2 2
[1] FALSE
D26V7, binary
                 cls
clus                0   1
  KDM6A MUTATED     6   7
  KDM6A WILD-TYPE 140 267
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      6    7
  KDM6A WILD-TYPE  140  267
     clus
vv    KDM6A MUTATED KDM6A WILD-TYPE
  NO              6             140
  YES             7             267
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  KDM6A MUTATED                                      17
  KDM6A WILD-TYPE                                   485
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  KDM6A MUTATED                                                             0
  KDM6A WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  KDM6A MUTATED                                                     0
  KDM6A WILD-TYPE                                                   7
D26V8, multiclass
                                                             clus
vv                                                            KDM6A MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  17
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
                                                             clus
vv                                                            KDM6A WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   485
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V9, continuous
D26V10, continuous
D26V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM6A MUTATED                                  0     0
  KDM6A WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED                           3    14
  KDM6A WILD-TYPE                        34   432
D26V12, multiclass
                                  clus
vv                                 KDM6A MUTATED KDM6A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    3              34
  WHITE                                       14             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"
D26V13, binary
                 cls
clus                0   1
  KDM6A MUTATED     0  17
  KDM6A WILD-TYPE  26 431
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      0   17
  KDM6A WILD-TYPE   26  431
                        clus
vv                       KDM6A MUTATED KDM6A WILD-TYPE
  HISPANIC OR LATINO                 0              26
  NOT HISPANIC OR LATINO            17             431
[1] 2 2
[1] FALSE

Clustering(27) Variable = RHOA MUTATION ANALYSIS
D27V1, survival
                sevent
clus2              0   1
  RHOA MUTATED     5   5
  RHOA WILD-TYPE 288 212
  RHOA MUTATED RHOA WILD-TYPE 
            10            500 
  RHOA MUTATED RHOA WILD-TYPE 
             5            212 
$`RHOA MUTATED`
TCGA-BB-8596 TCGA-BB-A5HZ TCGA-CN-6998 TCGA-CN-A6V3 TCGA-CV-7102 TCGA-CV-7410 
       71.05        27.19        11.74        24.39         1.84       210.97 
TCGA-DQ-5625 TCGA-F7-A624 TCGA-KU-A66S TCGA-TN-A7HL 
       37.25        12.43        13.35        20.35 

$`RHOA WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        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-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       36.72        33.70        50.20        66.28        24.66        38.40 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        25.71        10.55        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
       12.69        55.86        38.04         4.67        51.29        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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       32.22        35.05        38.89         3.68        17.42        32.48 
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-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 
       12.07         2.70        23.44        19.82        20.88        19.53 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        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-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       15.75        32.38        32.88        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       13.25         4.24        14.99        38.76        70.13        64.87 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       53.52        16.73        43.04        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        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-6472 
       37.87        26.27        58.42        50.01        39.52        34.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
       36.99        18.54        16.90         6.02        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        29.82        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         7.10         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        87.55 
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       126.15       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7103 
       18.81        12.66         7.99         9.01         5.26        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        47.47        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-7409 TCGA-CV-7411 
       36.13        18.41        57.47        35.54        17.85        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-7082 TCGA-CX-7085 TCGA-CX-7086 
       19.92        22.52        10.42        10.42        10.55        18.84 
TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       34.36        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-5629 
       13.94        12.10        12.79        11.11        58.45        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
       33.86        18.02        14.04        46.32        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       37.58        40.24        40.04        39.12        41.59        37.18 
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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.61        21.11        20.94         0.07        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
       21.93        27.48        27.48        14.66        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.85         0.36        13.84         4.27         3.65         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
       34.75        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-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       19.04        15.48        18.15        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-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-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       18.64        21.07        19.73        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 
       15.91         7.10        32.45        13.55        13.25        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        49.51        48.03        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-UF-A7JV TCGA-UP-A6WW 
       13.94        20.75        22.36        32.65         2.96        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  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          21.14 
[1] "1.8 - 211.0 (22.4)" "0.1 - 180.2 (21.1)"
[1] "hr=" "1.4"
D27V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  RHOA MUTATED         0        1         2         6         0
  RHOA WILD-TYPE      25       74        80       242        11
D27V3, multiclass
           clus
vv          RHOA MUTATED RHOA WILD-TYPE
  STAGE I              0             25
  STAGE II             1             74
  STAGE III            2             80
  STAGE IVA            6            242
  STAGE IVB            0             11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  RHOA MUTATED       1   2   4   2
  RHOA WILD-TYPE    47 132  95 166
D27V4, multiclass
       clus
vv      RHOA MUTATED RHOA WILD-TYPE
  T0+T1            1             47
  T2               2            132
  T3               4             95
  T4               2            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
  RHOA MUTATED     0   3   4   0
  RHOA WILD-TYPE 175  64 158   7
D27V5, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  N0            0            175
  N1            3             64
  N2            4            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"
D27V6, binary
                cls
clus               0   1
  RHOA MUTATED     4   6
  RHOA WILD-TYPE 136 364
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      4    6
  RHOA WILD-TYPE  136  364
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  FEMALE            4            136
  MALE              6            364
[1] 2 2
[1] FALSE
D27V7, binary
                cls
clus               0   1
  RHOA MUTATED     2   7
  RHOA WILD-TYPE 144 267
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      2    7
  RHOA WILD-TYPE  144  267
     clus
vv    RHOA MUTATED RHOA WILD-TYPE
  NO             2            144
  YES            7            267
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  RHOA MUTATED                                       9
  RHOA WILD-TYPE                                   493
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  RHOA MUTATED                                                             0
  RHOA WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  RHOA MUTATED                                                     1
  RHOA WILD-TYPE                                                   6
D27V8, multiclass
                                                             clus
vv                                                            RHOA MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  9
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    1
                                                             clus
vv                                                            RHOA WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  493
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V9, continuous
D27V10, continuous
D27V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RHOA MUTATED                                  0     0
  RHOA WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RHOA MUTATED                           0    10
  RHOA WILD-TYPE                        37   436
D27V12, multiclass
                                  clus
vv                                 RHOA MUTATED RHOA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             37
  WHITE                                      10            436
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V13, binary
                cls
clus               0   1
  RHOA MUTATED     0  10
  RHOA WILD-TYPE  26 438
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      0   10
  RHOA WILD-TYPE   26  438
                        clus
vv                       RHOA MUTATED RHOA WILD-TYPE
  HISPANIC OR LATINO                0             26
  NOT HISPANIC OR LATINO           10            438
[1] 2 2
[1] FALSE

Clustering(28) Variable = CREBBP MUTATION ANALYSIS
D28V1, survival
                  sevent
clus2                0   1
  CREBBP MUTATED    20  15
  CREBBP WILD-TYPE 273 202
  CREBBP MUTATED CREBBP WILD-TYPE 
              35              475 
  CREBBP MUTATED CREBBP WILD-TYPE 
              15              202 
$`CREBBP MUTATED`
TCGA-BA-4074 TCGA-BA-6869 TCGA-BA-A6D8 TCGA-BB-A5HY TCGA-CN-4736 TCGA-CN-5369 
       15.19        21.17        27.95        10.55        12.99        12.49 
TCGA-CN-6988 TCGA-CN-A6V3 TCGA-CQ-5333 TCGA-CQ-7071 TCGA-CQ-A4CI TCGA-CR-6478 
       10.45        24.39        11.21        43.10        31.23         6.02 
TCGA-CR-6481 TCGA-CV-5432 TCGA-CV-6951 TCGA-CV-6962 TCGA-CV-7429 TCGA-CV-7434 
       10.22       129.21        30.08         4.14         3.52         7.17 
TCGA-CV-7568 TCGA-CV-A45Z TCGA-CV-A6JE TCGA-DQ-7592 TCGA-DQ-7594 TCGA-F7-A624 
       30.48        48.20        35.34        37.58        40.04        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-A71D TCGA-UF-A7JA TCGA-UF-A7JJ 
       32.45        20.35        48.03        74.47        18.05 

$`CREBBP WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
        9.30        13.64        37.28         9.07        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       42.35        57.93        17.10        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
       68.48        15.52        14.83         3.55        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA 
       41.85        29.42        28.11        20.45        30.18        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-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       13.38        20.48         6.15       105.90         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.41        18.38        22.42        36.72        33.70        50.20 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU 
       66.28        24.66        38.40        71.05        20.52        25.71 
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-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       38.04         4.67        51.29        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-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        34.13         6.74         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       11.08        32.22        35.05        38.89         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       32.48        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-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 
       54.58        70.45        62.37        45.99        10.42         4.24 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 
       41.19        15.75        32.38        32.88        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       56.58        13.25         4.24        14.99        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7072 
       64.87        53.52        16.73        43.04        41.88        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       14.14        12.46        84.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
       26.27        58.42        50.01        39.52        34.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       18.54        16.90        11.90        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-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 
       29.82        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         5.13         5.95        35.41        29.95        48.39 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
      139.43        17.16       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        87.55        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-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       15.09         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
        8.42        28.34         2.50        64.83       126.15       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        47.47        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-7409 
        2.10        36.13        18.41        57.47        35.54        17.85 
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-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7437 
      156.49        16.27        84.49        19.76       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-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-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
       15.25         5.98         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-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 
       10.42        10.55        18.84        34.36        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-5629 TCGA-DQ-5630 TCGA-DQ-5631 
       11.11        58.45        37.25        30.94        33.86        18.02 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7595 
       14.04        46.32        46.45        20.45        40.24        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       41.59        37.18        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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       15.16        13.61        21.11        20.94         0.07        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       25.74        21.93        27.48        27.48        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        6.90        34.75        15.95        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       19.04        15.48        13.35        18.15        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-A5Q6 TCGA-P3-A5QA 
       15.42         7.13        16.08        17.98        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-A6V9 
       21.21        23.15         7.30        21.47         9.34        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-TN-A7HI 
       21.07        19.73        16.96        15.91         7.10        13.55 
TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       13.25        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK 
       44.65        17.95        24.30        55.43        29.46        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  CREBBP MUTATED CREBBP WILD-TYPE 
            3.52             0.07 
  CREBBP MUTATED CREBBP WILD-TYPE 
          129.21           210.97 
  CREBBP MUTATED CREBBP WILD-TYPE 
           18.05            21.21 
[1] "3.5 - 129.2 (18.1)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.2"
D28V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  CREBBP MUTATED         0        4         6        18         0
  CREBBP WILD-TYPE      25       71        76       230        11
D28V3, multiclass
           clus
vv          CREBBP MUTATED CREBBP WILD-TYPE
  STAGE I                0               25
  STAGE II               4               71
  STAGE III              6               76
  STAGE IVA             18              230
  STAGE IVB              0               11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CREBBP MUTATED       2   7   6  14
  CREBBP WILD-TYPE    46 127  93 154
D28V4, multiclass
       clus
vv      CREBBP MUTATED CREBBP WILD-TYPE
  T0+T1              2               46
  T2                 7              127
  T3                 6               93
  T4                14              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
  CREBBP MUTATED    10   5  10   0
  CREBBP WILD-TYPE 165  62 152   7
D28V5, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  N0             10              165
  N1              5               62
  N2             10              152
  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"
D28V6, binary
                  cls
clus                 0   1
  CREBBP MUTATED    11  24
  CREBBP WILD-TYPE 129 346
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     11   24
  CREBBP WILD-TYPE  129  346
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  FEMALE             11              129
  MALE               24              346
[1] 2 2
[1] FALSE
D28V7, binary
                  cls
clus                 0   1
  CREBBP MUTATED     8  19
  CREBBP WILD-TYPE 138 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED      8   19
  CREBBP WILD-TYPE  138  255
     clus
vv    CREBBP MUTATED CREBBP WILD-TYPE
  NO               8              138
  YES             19              255
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  CREBBP MUTATED                                      34
  CREBBP WILD-TYPE                                   468
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  CREBBP MUTATED                                                             0
  CREBBP WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  CREBBP MUTATED                                                     1
  CREBBP WILD-TYPE                                                   6
D28V8, multiclass
                                                             clus
vv                                                            CREBBP MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   34
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      1
                                                             clus
vv                                                            CREBBP WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    468
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V9, continuous
D28V10, continuous
D28V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CREBBP MUTATED                                  1     0
  CREBBP WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CREBBP MUTATED                           1    32
  CREBBP WILD-TYPE                        36   414
D28V12, multiclass
                                  clus
vv                                 CREBBP MUTATED CREBBP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               36
  WHITE                                        32              414
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, binary
                  cls
clus                 0   1
  CREBBP MUTATED     1  30
  CREBBP WILD-TYPE  25 418
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED      1   30
  CREBBP WILD-TYPE   25  418
                        clus
vv                       CREBBP MUTATED CREBBP WILD-TYPE
  HISPANIC OR LATINO                  1               25
  NOT HISPANIC OR LATINO             30              418
[1] 2 2
[1] FALSE

Clustering(29) Variable = NUDT11 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2                0   1
  NUDT11 MUTATED     6   2
  NUDT11 WILD-TYPE 287 215
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               8              502 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               2              215 
$`NUDT11 MUTATED`
TCGA-BA-5151 TCGA-CN-4727 TCGA-CN-A63U TCGA-CV-7103 TCGA-CV-7245 TCGA-CV-7247 
       23.74        51.29        31.69        52.31        26.20        18.97 
TCGA-HD-7229 TCGA-HD-7754 
        0.07        25.74 

$`NUDT11 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       42.35        57.93        17.10        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       68.48        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        4.01        41.85        29.42        28.11        20.45        30.18 
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-BB-4217 TCGA-BB-4223 
        2.27        11.05        13.38        20.48         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       33.70        50.20        66.28        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       20.52        25.71        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-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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       32.22        35.05        38.89         3.68        17.42        32.48 
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-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
       21.21         7.40        22.32        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        23.44        19.82        24.39        20.88 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       19.53        48.20        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-6221 TCGA-CQ-6222 TCGA-CQ-6223 
       41.19        15.75        32.38        32.88        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       56.58        13.25         4.24        14.99        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
       64.87        53.52        16.73        43.04        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       34.52        36.99        18.54        16.90         6.02        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        29.82        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         7.10         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 
       87.55        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       126.15 
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-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
        1.84        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-7248 
       77.16         4.73        47.47        36.00        31.36        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        36.13 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       18.41        57.47        35.54        17.85       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-7082 TCGA-CX-7085 TCGA-CX-7086 
       19.92        22.52        10.42        10.42        10.55        18.84 
TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       34.36        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        11.11        58.45        37.25 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       30.94        33.86        18.02        14.04        46.32        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45        37.58        40.24        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       37.18        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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7753 
       13.38        15.16        13.61        21.11        20.94        28.47 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
       21.93        27.48        27.48        14.66        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.85         0.36        13.84         4.27         3.65         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
       34.75        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       19.04        15.48        13.35        18.15        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-A5Q6 TCGA-P3-A5QA 
       15.42         7.13        16.08        17.98        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-RS-A6TO TCGA-RS-A6TP 
       12.72        18.64        21.07        19.73        12.72        16.96 
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-A71D 
       20.35        64.80        54.67         2.83        49.51        48.03 
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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        17.03        20.55        14.56 

  NUDT11 MUTATED NUDT11 WILD-TYPE 
            0.07             0.07 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           52.31           210.97 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           25.97            21.07 
[1] "0.1 - 52.3 (26.0)"  "0.1 - 211.0 (21.1)"
[1] "hr=" "1.7"
D29V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  NUDT11 MUTATED         0        0         1         7         0
  NUDT11 WILD-TYPE      25       75        81       241        11
D29V3, multiclass
           clus
vv          NUDT11 MUTATED NUDT11 WILD-TYPE
  STAGE I                0               25
  STAGE II               0               75
  STAGE III              1               81
  STAGE IVA              7              241
  STAGE IVB              0               11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  NUDT11 MUTATED       0   2   2   4
  NUDT11 WILD-TYPE    48 132  97 164
D29V4, multiclass
       clus
vv      NUDT11 MUTATED NUDT11 WILD-TYPE
  T0+T1              0               48
  T2                 2              132
  T3                 2               97
  T4                 4              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
  NUDT11 MUTATED     5   0   3   0
  NUDT11 WILD-TYPE 170  67 159   7
D29V5, multiclass
    clus
vv   NUDT11 MUTATED NUDT11 WILD-TYPE
  N0              5              170
  N1              0               67
  N2              3              159
  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
  NUDT11 MUTATED     0   8
  NUDT11 WILD-TYPE 140 362
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      0    8
  NUDT11 WILD-TYPE  140  362
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  FEMALE              0              140
  MALE                8              362
[1] 2 2
[1] FALSE
D29V7, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     0   4
  NUDT11 WILD-TYPE 146 270
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      0    4
  NUDT11 WILD-TYPE  146  270
     clus
vv    NUDT11 MUTATED NUDT11 WILD-TYPE
  NO               0              146
  YES              4              270
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  NUDT11 MUTATED                                       8
  NUDT11 WILD-TYPE                                   494
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  NUDT11 MUTATED                                                             0
  NUDT11 WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  NUDT11 MUTATED                                                     0
  NUDT11 WILD-TYPE                                                   7
D29V8, multiclass
                                                             clus
vv                                                            NUDT11 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    8
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
                                                             clus
vv                                                            NUDT11 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    494
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V9, continuous
D29V10, continuous
D29V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUDT11 MUTATED                                  0     0
  NUDT11 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUDT11 MUTATED                           0     8
  NUDT11 WILD-TYPE                        37   438
D29V12, multiclass
                                  clus
vv                                 NUDT11 MUTATED NUDT11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               37
  WHITE                                         8              438
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V13, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     1   7
  NUDT11 WILD-TYPE  25 441
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      1    7
  NUDT11 WILD-TYPE   25  441
                        clus
vv                       NUDT11 MUTATED NUDT11 WILD-TYPE
  HISPANIC OR LATINO                  1               25
  NOT HISPANIC OR LATINO              7              441
[1] 2 2
[1] FALSE

Clustering(30) Variable = EMG1 MUTATION ANALYSIS
D30V1, survival
                sevent
clus2              0   1
  EMG1 MUTATED     3   1
  EMG1 WILD-TYPE 290 216
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            506 
  EMG1 MUTATED EMG1 WILD-TYPE 
             1            216 
$`EMG1 MUTATED`
TCGA-CN-5369 TCGA-CR-7367 TCGA-CV-5440 TCGA-CV-6003 
       12.49        47.34       107.51        54.74 

$`EMG1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        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-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       36.72        33.70        50.20        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       71.05        20.52        25.71        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-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       51.29        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-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-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       34.13         6.74         9.07         9.24        52.08        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        32.22        35.05        38.89         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       32.48        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-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       24.39        20.88        19.53        48.20        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-6221 
       11.21         4.24        41.19        15.75        32.38        32.88 
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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       38.76        70.13        64.87        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       50.01        39.52        34.52        36.99        18.54        16.90 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        6.02        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        29.82 
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         7.10 
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-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       87.55        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       126.15       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        47.47        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-7409 
        2.10        36.13        18.41        57.47        35.54        17.85 
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-7082 
       21.24        23.47        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.55        18.84        34.36        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        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       58.45        37.25        30.94        33.86        18.02        14.04 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       46.32        46.45        20.45        37.58        40.24        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       39.12        41.59        37.18        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-A6C4 TCGA-H7-A6C5 
       20.25        12.43        13.38        15.16        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       20.94         0.07        28.47        25.74        21.93        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
       27.48        14.66        22.03        12.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
       13.84         4.27         3.65         6.90        34.75        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        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-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       16.08        17.98        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        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       21.07        19.73        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
        7.10        32.45        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        49.51        48.03        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-UF-A7JV TCGA-UP-A6WW 
       13.94        20.75        22.36        32.65         2.96        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  EMG1 MUTATED EMG1 WILD-TYPE 
         12.49           0.07 
  EMG1 MUTATED EMG1 WILD-TYPE 
        107.51         210.97 
  EMG1 MUTATED EMG1 WILD-TYPE 
         51.04          21.09 
[1] "12.5 - 107.5 (51.0)" "0.1 - 211.0 (21.1)" 
[1] "hr=" "2.8"
D30V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  EMG1 MUTATED         0        0         1         3         0
  EMG1 WILD-TYPE      25       75        81       245        11
D30V3, multiclass
           clus
vv          EMG1 MUTATED EMG1 WILD-TYPE
  STAGE I              0             25
  STAGE II             0             75
  STAGE III            1             81
  STAGE IVA            3            245
  STAGE IVB            0             11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  EMG1 MUTATED       0   1   0   3
  EMG1 WILD-TYPE    48 133  99 165
D30V4, multiclass
       clus
vv      EMG1 MUTATED EMG1 WILD-TYPE
  T0+T1            0             48
  T2               1            133
  T3               0             99
  T4               3            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
  EMG1 MUTATED     1   2   1   0
  EMG1 WILD-TYPE 174  65 161   7
D30V5, multiclass
    clus
vv   EMG1 MUTATED EMG1 WILD-TYPE
  N0            1            174
  N1            2             65
  N2            1            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"
D30V6, binary
                cls
clus               0   1
  EMG1 MUTATED     2   2
  EMG1 WILD-TYPE 138 368
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      2    2
  EMG1 WILD-TYPE  138  368
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  FEMALE            2            138
  MALE              2            368
[1] 2 2
[1] FALSE
D30V7, binary
                cls
clus               0   1
  EMG1 MUTATED     2   2
  EMG1 WILD-TYPE 144 272
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      2    2
  EMG1 WILD-TYPE  144  272
     clus
vv    EMG1 MUTATED EMG1 WILD-TYPE
  NO             2            144
  YES            2            272
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  EMG1 MUTATED                                       4
  EMG1 WILD-TYPE                                   498
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  EMG1 MUTATED                                                             0
  EMG1 WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  EMG1 MUTATED                                                     0
  EMG1 WILD-TYPE                                                   7
D30V8, multiclass
                                                             clus
vv                                                            EMG1 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  4
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
                                                             clus
vv                                                            EMG1 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  498
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V9, continuous
[1] "Remove cluster labels:" "EMG1 MUTATED"          
clus
  EMG1 MUTATED EMG1 WILD-TYPE 
             1            285 
    TCGA-BA-4074     TCGA-BA-4075     TCGA-BA-4076     TCGA-BA-4077 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-4078     TCGA-BA-5149     TCGA-BA-5151     TCGA-BA-5555 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-5556     TCGA-BA-6868     TCGA-BA-6869     TCGA-BA-6870 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-6871     TCGA-BA-6872     TCGA-BA-6873     TCGA-BA-7269 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-A4IF     TCGA-BA-A4IH     TCGA-BA-A4II     TCGA-BA-A6D8 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-A6DA     TCGA-BA-A6DD     TCGA-BA-A6DE     TCGA-BA-A6DG 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-A6DI     TCGA-BA-A6DJ     TCGA-BA-A6DL     TCGA-BB-4217 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BB-4225     TCGA-BB-4227     TCGA-BB-4228     TCGA-BB-7862 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BB-7864     TCGA-BB-7870     TCGA-BB-7871     TCGA-BB-8596 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BB-A5HY     TCGA-BB-A6UM     TCGA-BB-A6UO     TCGA-CN-4726 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-4727     TCGA-CN-4728     TCGA-CN-4729     TCGA-CN-4730 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-4731     TCGA-CN-4735     TCGA-CN-4736     TCGA-CN-4738 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-4739     TCGA-CN-4740     TCGA-CN-4741     TCGA-CN-4742 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-5355     TCGA-CN-5358     TCGA-CN-5359     TCGA-CN-5360 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-5361     TCGA-CN-5363     TCGA-CN-5365     TCGA-CN-5366 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-5367     TCGA-CN-5373     TCGA-CN-5374     TCGA-CN-6010 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-6011     TCGA-CN-6012     TCGA-CN-6016     TCGA-CN-6017 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-6019     TCGA-CN-6021     TCGA-CN-6023     TCGA-CN-6024 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-6988     TCGA-CN-6989     TCGA-CN-6992     TCGA-CN-6994 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-6997     TCGA-CN-6998     TCGA-CN-A498     TCGA-CN-A49B 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-A49C     TCGA-CN-A63T     TCGA-CN-A63U     TCGA-CN-A63V 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-A641     TCGA-CN-A642     TCGA-CN-A6UY     TCGA-CN-A6V3 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-A6V6     TCGA-CQ-5323     TCGA-CQ-5324     TCGA-CQ-5325 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-5326     TCGA-CQ-5330     TCGA-CQ-5331     TCGA-CQ-5332 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-5333     TCGA-CQ-6218     TCGA-CQ-6219     TCGA-CQ-6221 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-6222     TCGA-CQ-6223     TCGA-CQ-6224     TCGA-CQ-6227 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-6228     TCGA-CQ-7063     TCGA-CQ-7072     TCGA-CQ-A4C6 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-A4C7     TCGA-CQ-A4C9     TCGA-CQ-A4CB     TCGA-CQ-A4CG 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-A4CI     TCGA-CR-5247     TCGA-CR-5248     TCGA-CR-5250 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-6467     TCGA-CR-6471     TCGA-CR-6473     TCGA-CR-6474 
"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-7368     TCGA-CR-7369 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7370     TCGA-CR-7371     TCGA-CR-7373     TCGA-CR-7374 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7376     TCGA-CR-7377     TCGA-CR-7379     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-7392     TCGA-CR-7394     TCGA-CR-7395 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7398     TCGA-CR-7399     TCGA-CR-7401     TCGA-CR-7402 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-6436     TCGA-CV-6441     TCGA-CV-6933     TCGA-CV-6934 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-6940     TCGA-CV-6941     TCGA-CV-6945     TCGA-CV-6952 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-6961     TCGA-CV-7095     TCGA-CV-7097     TCGA-CV-7235 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7242     TCGA-CV-7245     TCGA-CV-7248     TCGA-CV-7250 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7254     TCGA-CV-7261     TCGA-CV-7263     TCGA-CV-7406 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7410     TCGA-CV-7418     TCGA-CV-7422     TCGA-CV-7424 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7427     TCGA-CV-7430     TCGA-CV-7432     TCGA-CV-7433 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7434     TCGA-CV-7440     TCGA-CV-7446     TCGA-CV-7568 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-A45Y     TCGA-CV-A45Z     TCGA-CV-A460     TCGA-CV-A464 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-A468     TCGA-CV-A6JD     TCGA-CV-A6JN     TCGA-CV-A6JO 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-A6JU     TCGA-CV-A6JZ     TCGA-CV-A6K1     TCGA-CV-A6K2 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CX-7082     TCGA-CX-7085     TCGA-CX-7086     TCGA-CX-7219 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CX-A4AQ     TCGA-D6-6516     TCGA-D6-6517     TCGA-D6-6823 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-D6-6824     TCGA-D6-6825     TCGA-D6-6827     TCGA-D6-8568 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-D6-8569     TCGA-D6-A4Z9     TCGA-D6-A4ZB     TCGA-D6-A6EK 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-D6-A6EP     TCGA-DQ-5625     TCGA-DQ-5629     TCGA-DQ-5630 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-DQ-5631     TCGA-DQ-7588     TCGA-DQ-7589     TCGA-DQ-7590 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-DQ-7591     TCGA-DQ-7592     TCGA-DQ-7593     TCGA-DQ-7595 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-F7-7848     TCGA-F7-8489     TCGA-F7-A50G     TCGA-F7-A50I 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-F7-A50J     TCGA-F7-A61S     TCGA-F7-A61V     TCGA-F7-A61W 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-F7-A620     TCGA-F7-A623     TCGA-H7-7774     TCGA-H7-A6C4 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-H7-A6C5     TCGA-HD-7753     TCGA-HD-7754     TCGA-HD-7832 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HD-8634     TCGA-HD-8635     TCGA-HD-A634     TCGA-HD-A6I0 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HL-7533     TCGA-IQ-7631     TCGA-IQ-7632     TCGA-IQ-A61E 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-IQ-A61G     TCGA-IQ-A61H     TCGA-IQ-A61K     TCGA-IQ-A6SH 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KU-A66S     TCGA-KU-A6H7     TCGA-KU-A6H8     TCGA-MT-A51W 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-MT-A51X     TCGA-MT-A67D     TCGA-MZ-A6I9     TCGA-MZ-A7D7 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-P3-A5Q6     TCGA-P3-A6SW     TCGA-P3-A6SX     TCGA-P3-A6T0 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-P3-A6T4     TCGA-P3-A6T5     TCGA-P3-A6T7     TCGA-P3-A6T8 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-QK-A6IG     TCGA-QK-A6II     TCGA-QK-A6IJ     TCGA-RS-A6TP 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-T2-A6WZ     TCGA-T2-A6X0     TCGA-T2-A6X2     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-A71D 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-UF-A7J9     TCGA-UF-A7JC     TCGA-UF-A7JD     TCGA-UF-A7JF 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-UF-A7JH     TCGA-UF-A7JJ     TCGA-UF-A7JS     TCGA-WA-A7GZ 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-WA-A7H4 
"EMG1 WILD-TYPE" 
D30V10, continuous
[1] "Remove cluster labels:" "EMG1 MUTATED"          
clus
  EMG1 MUTATED EMG1 WILD-TYPE 
             2            272 
    TCGA-BA-4074     TCGA-BA-4075     TCGA-BA-4076     TCGA-BA-4077 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-4078     TCGA-BA-5149     TCGA-BA-5151     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-6871 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-6872     TCGA-BA-6873     TCGA-BA-7269     TCGA-BA-A6DA 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BA-A6DG     TCGA-BB-4225     TCGA-BB-4228     TCGA-BB-7871 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BB-8596     TCGA-BB-A5HY     TCGA-BB-A6UM     TCGA-BB-A6UO 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-4727     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-6021     TCGA-CN-6023 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-6024     TCGA-CN-6989     TCGA-CN-6992     TCGA-CN-6994 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-6997     TCGA-CN-6998     TCGA-CN-A498     TCGA-CN-A49B 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-A49C     TCGA-CN-A63T     TCGA-CN-A63U     TCGA-CN-A63V 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CN-A641     TCGA-CN-A6UY     TCGA-CN-A6V3     TCGA-CN-A6V6 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-5323     TCGA-CQ-5324     TCGA-CQ-5325     TCGA-CQ-5330 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-5331     TCGA-CQ-5333     TCGA-CQ-6218     TCGA-CQ-6219 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-6221     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-7063     TCGA-CQ-7072 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-A4C6     TCGA-CQ-A4C7     TCGA-CQ-A4C9     TCGA-CQ-A4CB 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CQ-A4CI     TCGA-CR-5247     TCGA-CR-5248     TCGA-CR-5250 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-6467     TCGA-CR-6471     TCGA-CR-6473     TCGA-CR-6474 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-6477     TCGA-CR-6478     TCGA-CR-6482     TCGA-CR-6487 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-6491     TCGA-CR-6492     TCGA-CR-6493     TCGA-CR-7364 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7365     TCGA-CR-7368     TCGA-CR-7369     TCGA-CR-7370 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7371     TCGA-CR-7373     TCGA-CR-7374     TCGA-CR-7376 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7377     TCGA-CR-7383     TCGA-CR-7385     TCGA-CR-7386 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7388     TCGA-CR-7389     TCGA-CR-7390     TCGA-CR-7391 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7392     TCGA-CR-7394     TCGA-CR-7395     TCGA-CR-7397 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CR-7399     TCGA-CR-7401     TCGA-CR-7402     TCGA-CV-5430 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-5431     TCGA-CV-5432     TCGA-CV-5435     TCGA-CV-5436 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-5443     TCGA-CV-5966     TCGA-CV-5970     TCGA-CV-5976 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-6433     TCGA-CV-6436     TCGA-CV-6441     TCGA-CV-6934 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-6935     TCGA-CV-6936     TCGA-CV-6940     TCGA-CV-6941 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-6943     TCGA-CV-6945     TCGA-CV-6952     TCGA-CV-6954 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-6960     TCGA-CV-6961     TCGA-CV-7091     TCGA-CV-7095 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7097     TCGA-CV-7099     TCGA-CV-7100     TCGA-CV-7101 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7102     TCGA-CV-7180     TCGA-CV-7183     TCGA-CV-7235 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7242     TCGA-CV-7245     TCGA-CV-7248     TCGA-CV-7250 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7254     TCGA-CV-7261     TCGA-CV-7406     TCGA-CV-7410 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7418     TCGA-CV-7422     TCGA-CV-7424     TCGA-CV-7427 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7430     TCGA-CV-7432     TCGA-CV-7433     TCGA-CV-7434 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-7435     TCGA-CV-7440     TCGA-CV-7446     TCGA-CV-7568 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-A45Q     TCGA-CV-A45Y     TCGA-CV-A45Z     TCGA-CV-A460 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-A461     TCGA-CV-A464     TCGA-CV-A468     TCGA-CV-A6JD 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-A6JE     TCGA-CV-A6JN     TCGA-CV-A6JO     TCGA-CV-A6JU 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CV-A6JY     TCGA-CV-A6JZ     TCGA-CV-A6K1     TCGA-CV-A6K2 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CX-7086     TCGA-CX-7219     TCGA-D6-6516     TCGA-D6-6517 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-D6-6823     TCGA-D6-6824     TCGA-D6-6825     TCGA-D6-6827 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-D6-8568     TCGA-D6-8569     TCGA-D6-A4Z9     TCGA-D6-A4ZB 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-D6-A6EK     TCGA-D6-A6EP     TCGA-D6-A74Q     TCGA-DQ-5625 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-DQ-5629     TCGA-DQ-5630     TCGA-DQ-5631     TCGA-DQ-7588 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-DQ-7589     TCGA-DQ-7590     TCGA-DQ-7591     TCGA-DQ-7592 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-DQ-7593     TCGA-DQ-7595     TCGA-F7-7848     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-A6C4     TCGA-H7-A6C5     TCGA-H7-A76A 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HD-8634     TCGA-HD-8635     TCGA-HD-A634     TCGA-HD-A6I0 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HL-7533     TCGA-IQ-7631     TCGA-IQ-7632     TCGA-IQ-A61E 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-IQ-A61G     TCGA-IQ-A6SH     TCGA-KU-A66S     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-RS-A6TP     TCGA-TN-A7HI     TCGA-TN-A7HL 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-UF-A718     TCGA-UF-A71B     TCGA-UF-A71D     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" 
D30V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EMG1 MUTATED                                  0     0
  EMG1 WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EMG1 MUTATED                           0     4
  EMG1 WILD-TYPE                        37   442
D30V12, multiclass
                                  clus
vv                                 EMG1 MUTATED EMG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             37
  WHITE                                       4            442
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V13, binary
                cls
clus               0   1
  EMG1 MUTATED     0   4
  EMG1 WILD-TYPE  26 444
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      0    4
  EMG1 WILD-TYPE   26  444
                        clus
vv                       EMG1 MUTATED EMG1 WILD-TYPE
  HISPANIC OR LATINO                0             26
  NOT HISPANIC OR LATINO            4            444
[1] 2 2
[1] FALSE

Clustering(31) Variable = SMAD4 MUTATION ANALYSIS
D31V1, survival
                 sevent
clus2               0   1
  SMAD4 MUTATED     6   7
  SMAD4 WILD-TYPE 287 210
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             13             497 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              7             210 
$`SMAD4 MUTATED`
TCGA-BA-5555 TCGA-BB-A6UO TCGA-CN-4723 TCGA-CN-5364 TCGA-CN-A6V1 TCGA-CQ-6222 
       17.10         8.81        55.86        16.21        19.82        66.28 
TCGA-CR-7365 TCGA-CV-7097 TCGA-CV-7406 TCGA-HD-8635 TCGA-P3-A6T5 TCGA-P3-A6T7 
       39.16        12.66        57.47        22.85        29.00        16.01 
TCGA-UF-A7JC 
       17.95 

$`SMAD4 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       23.74        42.35        57.93        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       68.48        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        4.01        41.85        29.42        28.11        20.45        30.18 
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-BB-4217 TCGA-BB-4223 
        2.27        11.05        13.38        20.48         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       33.70        50.20        66.28        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-C9-A47Z 
       20.52        25.71        10.55        27.19        12.92         6.28 
TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       12.69        38.04         4.67        51.29        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-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
        8.32        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-6021 
       47.44        28.04        19.07        34.13         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        9.24        52.08        11.08        10.45        32.22        35.05 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 
       38.89         3.68        17.42        32.48        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-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
        2.70        23.44        24.39        20.88        19.53        48.20 
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-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.38        32.88        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
       14.99        38.76        70.13        64.87        53.52        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       43.04        41.88        43.10        77.56        44.48        11.61 
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-6472 TCGA-CR-6473 TCGA-CR-6474 
       58.42        50.01        39.52        34.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       16.90         6.02        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-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-7394 TCGA-CR-7395 
       29.82        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         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-5436 
      139.43        17.16       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       17.95       107.51        87.55        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-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-7099 TCGA-CV-7100 
       64.83       126.15       111.16        18.81         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        47.47        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-7407 
       11.87        47.97         2.10        36.13        18.41        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       17.85       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-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-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 
       10.42        10.55        18.84        34.36        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-5629 TCGA-DQ-5630 TCGA-DQ-5631 
       11.11        58.45        37.25        30.94        33.86        18.02 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       14.04        46.32        46.45        20.45        37.58        40.24 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       40.04        39.12        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-A6C4 
       11.80        20.25        12.43        13.38        15.16        13.61 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       21.11        20.94         0.07        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 
       27.48        27.48        14.66        22.03        12.66         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
       13.84         4.27         3.65         6.90        34.75        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        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-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       16.08        17.98        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-A6T6 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       12.99        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        18.64        21.07        19.73 
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-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-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD 
       49.51        48.03        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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       32.65         2.96        17.03        20.55        14.56 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
           8.81            0.07 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          66.28          210.97 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          19.82           21.17 
[1] "8.8 - 66.3 (19.8)"  "0.1 - 211.0 (21.2)"
[1] "hr=" "1.3"
D31V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  SMAD4 MUTATED         0        2         1        10         0
  SMAD4 WILD-TYPE      25       73        81       238        11
D31V3, multiclass
           clus
vv          SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE I               0              25
  STAGE II              2              73
  STAGE III             1              81
  STAGE IVA            10             238
  STAGE IVB             0              11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SMAD4 MUTATED       1   4   3   5
  SMAD4 WILD-TYPE    47 130  96 163
D31V4, multiclass
       clus
vv      SMAD4 MUTATED SMAD4 WILD-TYPE
  T0+T1             1              47
  T2                4             130
  T3                3              96
  T4                5             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
  SMAD4 MUTATED     4   1   7   0
  SMAD4 WILD-TYPE 171  66 155   7
D31V5, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  N0             4             171
  N1             1              66
  N2             7             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"
D31V6, binary
                 cls
clus                0   1
  SMAD4 MUTATED     3  10
  SMAD4 WILD-TYPE 137 360
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      3   10
  SMAD4 WILD-TYPE  137  360
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  FEMALE             3             137
  MALE              10             360
[1] 2 2
[1] FALSE
D31V7, binary
                 cls
clus                0   1
  SMAD4 MUTATED     5   6
  SMAD4 WILD-TYPE 141 268
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      5    6
  SMAD4 WILD-TYPE  141  268
     clus
vv    SMAD4 MUTATED SMAD4 WILD-TYPE
  NO              5             141
  YES             6             268
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  SMAD4 MUTATED                                      13
  SMAD4 WILD-TYPE                                   489
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  SMAD4 MUTATED                                                             0
  SMAD4 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  SMAD4 MUTATED                                                     0
  SMAD4 WILD-TYPE                                                   7
D31V8, multiclass
                                                             clus
vv                                                            SMAD4 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  13
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
                                                             clus
vv                                                            SMAD4 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   489
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V9, continuous
D31V10, continuous
D31V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMAD4 MUTATED                                  0     0
  SMAD4 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SMAD4 MUTATED                           1    12
  SMAD4 WILD-TYPE                        36   434
D31V12, multiclass
                                  clus
vv                                 SMAD4 MUTATED SMAD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              36
  WHITE                                       12             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"
D31V13, binary
                 cls
clus                0   1
  SMAD4 MUTATED     0  11
  SMAD4 WILD-TYPE  26 437
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      0   11
  SMAD4 WILD-TYPE   26  437
                        clus
vv                       SMAD4 MUTATED SMAD4 WILD-TYPE
  HISPANIC OR LATINO                 0              26
  NOT HISPANIC OR LATINO            11             437
[1] 2 2
[1] FALSE

Clustering(32) Variable = CUL3 MUTATION ANALYSIS
D32V1, survival
                sevent
clus2              0   1
  CUL3 MUTATED     8   6
  CUL3 WILD-TYPE 285 211
  CUL3 MUTATED CUL3 WILD-TYPE 
            14            496 
  CUL3 MUTATED CUL3 WILD-TYPE 
             6            211 
$`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-UF-A71B 
        6.38        49.51 

$`CUL3 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       65.59        68.48        15.52        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        4.01        41.85        29.42        28.11        20.45        30.18 
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-BB-4217 TCGA-BB-4223 
        2.27        11.05        13.38        20.48         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       33.70        50.20        66.28        24.66        38.40        71.05 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       25.71        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
       12.69        55.86        38.04         4.67        51.29        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-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-6020 TCGA-CN-6021 TCGA-CN-6022 
       47.44        28.04        19.07         6.74         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       52.08        11.08        10.45        35.05        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       17.42        32.48        11.74        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-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       24.39        20.88        19.53        48.20        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-6221 
       11.21         4.24        41.19        15.75        32.38        32.88 
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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       38.76        70.13        64.87        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 
       50.01        39.52        34.52        36.99        18.54         6.02 
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        29.82 
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         7.10 
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-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
       17.16       108.95        19.20        17.95       107.51        87.55 
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-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        2.50         4.14        64.83       126.15       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        47.47        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-7409 TCGA-CV-7410 
       36.13        18.41        57.47        35.54        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 
       89.33         9.67         0.46        22.85        25.08         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-A6JN 
       56.61         7.07        15.25         5.98        35.34        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-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
       22.52        10.42        10.42        10.55        18.84        34.36 
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-5629 
       12.10        12.79        11.11        58.45        37.25        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
       33.86        18.02        14.04        46.32        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       37.58        40.24        40.04        39.12        41.59        37.18 
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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       15.16        13.61        21.11        20.94         0.07        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       25.74        21.93        27.48        27.48        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 
       13.84        19.04        15.48        13.35        18.15        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-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-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-RS-A6TO 
        9.34        12.72        18.64        21.07        19.73        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI 
       16.96         6.87        15.91         7.10        32.45        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71D 
       13.25        20.35        64.80        54.67         2.83        48.03 
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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        17.03        20.55        14.56 

  CUL3 MUTATED CUL3 WILD-TYPE 
          6.38           0.07 
  CUL3 MUTATED CUL3 WILD-TYPE 
        129.21         210.97 
  CUL3 MUTATED CUL3 WILD-TYPE 
         30.28          21.07 
[1] "6.4 - 129.2 (30.3)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.3"
D32V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  CUL3 MUTATED         0        0         5         7         0
  CUL3 WILD-TYPE      25       75        77       241        11
D32V3, multiclass
           clus
vv          CUL3 MUTATED CUL3 WILD-TYPE
  STAGE I              0             25
  STAGE II             0             75
  STAGE III            5             77
  STAGE IVA            7            241
  STAGE IVB            0             11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CUL3 MUTATED       1   0   5   6
  CUL3 WILD-TYPE    47 134  94 162
D32V4, multiclass
       clus
vv      CUL3 MUTATED CUL3 WILD-TYPE
  T0+T1            1             47
  T2               0            134
  T3               5             94
  T4               6            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
  CUL3 MUTATED     7   2   3   0
  CUL3 WILD-TYPE 168  65 159   7
D32V5, multiclass
    clus
vv   CUL3 MUTATED CUL3 WILD-TYPE
  N0            7            168
  N1            2             65
  N2            3            159
  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
  CUL3 MUTATED     2  12
  CUL3 WILD-TYPE 138 358
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL3 MUTATED      2   12
  CUL3 WILD-TYPE  138  358
        clus
vv       CUL3 MUTATED CUL3 WILD-TYPE
  FEMALE            2            138
  MALE             12            358
[1] 2 2
[1] FALSE
D32V7, binary
                cls
clus               0   1
  CUL3 MUTATED     5   7
  CUL3 WILD-TYPE 141 267
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL3 MUTATED      5    7
  CUL3 WILD-TYPE  141  267
     clus
vv    CUL3 MUTATED CUL3 WILD-TYPE
  NO             5            141
  YES            7            267
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  CUL3 MUTATED                                      14
  CUL3 WILD-TYPE                                   488
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  CUL3 MUTATED                                                             0
  CUL3 WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  CUL3 MUTATED                                                     0
  CUL3 WILD-TYPE                                                   7
D32V8, multiclass
                                                             clus
vv                                                            CUL3 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                 14
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
                                                             clus
vv                                                            CUL3 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  488
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V9, continuous
D32V10, continuous
D32V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CUL3 MUTATED                                  0     0
  CUL3 WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CUL3 MUTATED                           3    10
  CUL3 WILD-TYPE                        34   436
D32V12, multiclass
                                  clus
vv                                 CUL3 MUTATED CUL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   3             34
  WHITE                                      10            436
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V13, binary
                cls
clus               0   1
  CUL3 MUTATED     0  12
  CUL3 WILD-TYPE  26 436
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL3 MUTATED      0   12
  CUL3 WILD-TYPE   26  436
                        clus
vv                       CUL3 MUTATED CUL3 WILD-TYPE
  HISPANIC OR LATINO                0             26
  NOT HISPANIC OR LATINO           12            436
[1] 2 2
[1] FALSE

Clustering(33) Variable = TIGD4 MUTATION ANALYSIS
D33V1, survival
                 sevent
clus2               0   1
  TIGD4 MUTATED     4   3
  TIGD4 WILD-TYPE 289 214
  TIGD4 MUTATED TIGD4 WILD-TYPE 
              7             503 
  TIGD4 MUTATED TIGD4 WILD-TYPE 
              3             214 
$`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-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        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-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       36.72        33.70        50.20        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       71.05        20.52        25.71        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-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       51.29        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-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        34.13         6.74         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       11.08        10.45        32.22        35.05        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        32.48        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       17.29        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-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       24.39        20.88        19.53        48.20        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-6221 
       11.21         4.24        41.19        15.75        32.38        32.88 
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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       38.76        70.13        64.87        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       50.01        39.52        34.52        36.99        18.54        16.90 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        6.02        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-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 
       29.82        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         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-5436 
      139.43        17.16       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       17.95       107.51        87.55        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-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-7089 
       10.98         7.13         8.42        28.34         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      126.15       111.16        18.81        12.66         7.99         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-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        47.47        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        36.13        18.41        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       17.85       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-7432 TCGA-CV-7433 TCGA-CV-7434 
       56.48       156.49         3.52        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-7082 
       21.24        23.47        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        34.36        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        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       37.25        30.94        33.86        18.02        14.04        46.32 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       46.45        20.45        37.58        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       41.59        37.18        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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       15.16        13.61        21.11        20.94         0.07        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       25.74        21.93        27.48        27.48        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 
       13.84        19.04        15.48        13.35        18.15        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-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-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-RS-A6TO 
        9.34        12.72        18.64        21.07        19.73        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI 
       16.96         6.87        15.91         7.10        32.45        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-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       48.03        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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       32.65         2.96        17.03        20.55        14.56 

  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           21.21 
[1] "2.5 - 29.7 (13.4)"  "0.1 - 211.0 (21.2)"
[1] "hr=" "1.8"
D33V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  TIGD4 MUTATED         0        3         2         2         0
  TIGD4 WILD-TYPE      25       72        80       246        11
D33V3, multiclass
           clus
vv          TIGD4 MUTATED TIGD4 WILD-TYPE
  STAGE I               0              25
  STAGE II              3              72
  STAGE III             2              80
  STAGE IVA             2             246
  STAGE IVB             0              11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TIGD4 MUTATED       0   3   2   2
  TIGD4 WILD-TYPE    48 131  97 166
D33V4, multiclass
       clus
vv      TIGD4 MUTATED TIGD4 WILD-TYPE
  T0+T1             0              48
  T2                3             131
  T3                2              97
  T4                2             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
  TIGD4 MUTATED     3   2   0   0
  TIGD4 WILD-TYPE 172  65 162   7
D33V5, multiclass
    clus
vv   TIGD4 MUTATED TIGD4 WILD-TYPE
  N0             3             172
  N1             2              65
  N2             0             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"
D33V6, binary
                 cls
clus                0   1
  TIGD4 MUTATED     1   6
  TIGD4 WILD-TYPE 139 364
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD4 MUTATED      1    6
  TIGD4 WILD-TYPE  139  364
        clus
vv       TIGD4 MUTATED TIGD4 WILD-TYPE
  FEMALE             1             139
  MALE               6             364
[1] 2 2
[1] FALSE
D33V7, binary
                 cls
clus                0   1
  TIGD4 MUTATED     1   4
  TIGD4 WILD-TYPE 145 270
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD4 MUTATED      1    4
  TIGD4 WILD-TYPE  145  270
     clus
vv    TIGD4 MUTATED TIGD4 WILD-TYPE
  NO              1             145
  YES             4             270
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  TIGD4 MUTATED                                       7
  TIGD4 WILD-TYPE                                   495
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  TIGD4 MUTATED                                                             0
  TIGD4 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  TIGD4 MUTATED                                                     0
  TIGD4 WILD-TYPE                                                   7
D33V8, multiclass
                                                             clus
vv                                                            TIGD4 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   7
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
                                                             clus
vv                                                            TIGD4 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   495
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V9, continuous
D33V10, continuous
D33V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TIGD4 MUTATED                                  0     0
  TIGD4 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TIGD4 MUTATED                           1     6
  TIGD4 WILD-TYPE                        36   440
D33V12, multiclass
                                  clus
vv                                 TIGD4 MUTATED TIGD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              36
  WHITE                                        6             440
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V13, binary
                 cls
clus                0   1
  TIGD4 MUTATED     0   7
  TIGD4 WILD-TYPE  26 441
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD4 MUTATED      0    7
  TIGD4 WILD-TYPE   26  441
                        clus
vv                       TIGD4 MUTATED TIGD4 WILD-TYPE
  HISPANIC OR LATINO                 0              26
  NOT HISPANIC OR LATINO             7             441
[1] 2 2
[1] FALSE

Clustering(34) Variable = MYH9 MUTATION ANALYSIS
D34V1, survival
                sevent
clus2              0   1
  MYH9 MUTATED    12  10
  MYH9 WILD-TYPE 281 207
  MYH9 MUTATED MYH9 WILD-TYPE 
            22            488 
  MYH9 MUTATED MYH9 WILD-TYPE 
            10            207 
$`MYH9 MUTATED`
TCGA-BA-5153 TCGA-BA-A4IH TCGA-BA-A6DJ TCGA-BB-7861 TCGA-CN-6013 TCGA-CN-A6V6 
       57.93        20.45        13.38        22.42        23.90        20.88 
TCGA-CQ-7067 TCGA-CR-7386 TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6960 TCGA-CV-6961 
       16.73        47.01        30.08        53.95        28.34         2.50 
TCGA-CV-7437 TCGA-CV-A45Q TCGA-CV-A463 TCGA-CV-A6JT TCGA-F7-A620 TCGA-IQ-7630 
       16.64       169.38         0.76        28.01        17.85        15.95 
TCGA-P3-A6T2 TCGA-QK-A6VB TCGA-T2-A6X2 TCGA-UF-A7JJ 
       75.55        21.07        32.45        18.05 

$`MYH9 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       23.74        42.35        17.10        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       68.48        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 
        4.01        41.85        29.42        28.11        30.18        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-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       11.05        20.48         6.15       105.90         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 
        4.41        18.38        36.72        33.70        50.20        66.28 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY 
       24.66        38.40        71.05        20.52        25.71        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-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       38.04         4.67        51.29        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-6021 TCGA-CN-6022 
       28.04        19.07        34.13         6.74         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
       52.08        11.08        10.45        32.22        35.05        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        3.68        17.42        32.48        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-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       23.44        19.82        24.39        19.53        48.20        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-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.88        66.28        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
       14.99        38.76        70.13        64.87        53.52        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       50.01        39.52        34.52        36.99        18.54        16.90 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        6.02        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        29.82 
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         7.10 
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        87.55        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       126.15       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 
       47.47        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        36.13 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       18.41        57.47        35.54        17.85       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-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-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-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       48.20        60.43        67.86        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JU 
        5.98        35.34         6.38        29.79         6.48         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
       21.24        23.47        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.55        18.84        34.36        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        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       58.45        37.25        30.94        33.86        18.02        14.04 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       46.32        46.45        20.45        37.58        40.24        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       39.12        41.59        37.18        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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       12.43        13.38        15.16        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65         6.90        34.75        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-A66S TCGA-KU-A66T 
       13.68        13.84        19.04        15.48        13.35        18.15 
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-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-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       19.00        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-A6VC TCGA-RS-A6TO TCGA-RS-A6TP 
        9.34        12.72        18.64        19.73        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
        6.87        15.91         7.10        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       64.80        54.67         2.83        49.51        48.03        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-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       13.94        20.75        22.36        32.65         2.96        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  MYH9 MUTATED MYH9 WILD-TYPE 
          0.76           0.07 
  MYH9 MUTATED MYH9 WILD-TYPE 
        169.38         210.97 
  MYH9 MUTATED MYH9 WILD-TYPE 
        21.745         21.140 
[1] "0.8 - 169.4 (21.7)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D34V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  MYH9 MUTATED         1        4         5        10         0
  MYH9 WILD-TYPE      24       71        77       238        11
D34V3, multiclass
           clus
vv          MYH9 MUTATED MYH9 WILD-TYPE
  STAGE I              1             24
  STAGE II             4             71
  STAGE III            5             77
  STAGE IVA           10            238
  STAGE IVB            0             11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MYH9 MUTATED       2   7   5   7
  MYH9 WILD-TYPE    46 127  94 161
D34V4, multiclass
       clus
vv      MYH9 MUTATED MYH9 WILD-TYPE
  T0+T1            2             46
  T2               7            127
  T3               5             94
  T4               7            161
[1] 4 2
[1] TRUE
[1] "dimension of 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    10   3   6   0
  MYH9 WILD-TYPE 165  64 156   7
D34V5, multiclass
    clus
vv   MYH9 MUTATED MYH9 WILD-TYPE
  N0           10            165
  N1            3             64
  N2            6            156
  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
  MYH9 MUTATED     4  18
  MYH9 WILD-TYPE 136 352
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH9 MUTATED      4   18
  MYH9 WILD-TYPE  136  352
        clus
vv       MYH9 MUTATED MYH9 WILD-TYPE
  FEMALE            4            136
  MALE             18            352
[1] 2 2
[1] FALSE
D34V7, binary
                cls
clus               0   1
  MYH9 MUTATED     5  12
  MYH9 WILD-TYPE 141 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH9 MUTATED      5   12
  MYH9 WILD-TYPE  141  262
     clus
vv    MYH9 MUTATED MYH9 WILD-TYPE
  NO             5            141
  YES           12            262
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  MYH9 MUTATED                                      21
  MYH9 WILD-TYPE                                   481
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  MYH9 MUTATED                                                             0
  MYH9 WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  MYH9 MUTATED                                                     1
  MYH9 WILD-TYPE                                                   6
D34V8, multiclass
                                                             clus
vv                                                            MYH9 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                 21
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    1
                                                             clus
vv                                                            MYH9 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  481
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V9, continuous
D34V10, continuous
D34V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYH9 MUTATED                                  0     1
  MYH9 WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MYH9 MUTATED                           1    18
  MYH9 WILD-TYPE                        36   428
D34V12, multiclass
                                  clus
vv                                 MYH9 MUTATED MYH9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             36
  WHITE                                      18            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"
D34V13, binary
                cls
clus               0   1
  MYH9 MUTATED     2  17
  MYH9 WILD-TYPE  24 431
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH9 MUTATED      2   17
  MYH9 WILD-TYPE   24  431
                        clus
vv                       MYH9 MUTATED MYH9 WILD-TYPE
  HISPANIC OR LATINO                2             24
  NOT HISPANIC OR LATINO           17            431
[1] 2 2
[1] FALSE

Clustering(35) Variable = C3ORF59 MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                 0   1
  C3ORF59 MUTATED     7   4
  C3ORF59 WILD-TYPE 286 213
  C3ORF59 MUTATED C3ORF59 WILD-TYPE 
               11               499 
  C3ORF59 MUTATED C3ORF59 WILD-TYPE 
                4               213 
$`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 TCGA-HL-7533 
       29.79        10.42        12.43         0.36        34.75 

$`C3ORF59 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        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-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       36.72        33.70        50.20        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       71.05        20.52        25.71        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-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       51.29        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-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        34.13         6.74         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       11.08        10.45        32.22        35.05        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        32.48        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-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       19.82        20.88        19.53        48.20        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-6221 
       11.21         4.24        41.19        15.75        32.38        32.88 
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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       38.76        70.13        64.87        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       50.01        39.52        34.52        36.99        18.54        16.90 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        6.02        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-7372 TCGA-CR-7373 TCGA-CR-7374 
       40.93        35.84         3.45        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-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       32.78        27.06        12.89        29.82        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         7.10         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        87.55 
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       126.15       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        47.47        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-7409 TCGA-CV-7410 
        2.10        36.13        18.41        35.54        17.85       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-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 
        0.07       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-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-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ 
       22.52        10.42        10.55        18.84        34.36        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-5629 TCGA-DQ-5630 
       12.79        11.11        58.45        37.25        30.94        33.86 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       18.02        14.04        46.32        46.45        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
       40.24        40.04        39.12        41.59        37.18        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-A6C4 
       17.85        11.80        20.25        13.38        15.16        13.61 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       21.11        20.94         0.07        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       27.48        27.48        14.66        22.03        12.66        22.85 
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-A66S 
        5.29        13.68        13.84        19.04        15.48        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        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-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       17.98        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        18.64        21.07 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       19.73        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       32.45        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        49.51        48.03        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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  C3ORF59 MUTATED C3ORF59 WILD-TYPE 
             0.36              0.07 
  C3ORF59 MUTATED C3ORF59 WILD-TYPE 
            57.47            210.97 
  C3ORF59 MUTATED C3ORF59 WILD-TYPE 
            29.79             21.07 
[1] "0.4 - 57.5 (29.8)"  "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D35V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  C3ORF59 MUTATED         0        2         1         6         0
  C3ORF59 WILD-TYPE      25       73        81       242        11
D35V3, multiclass
           clus
vv          C3ORF59 MUTATED C3ORF59 WILD-TYPE
  STAGE I                 0                25
  STAGE II                2                73
  STAGE III               1                81
  STAGE IVA               6               242
  STAGE IVB               0                11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C3ORF59 MUTATED       0   2   2   5
  C3ORF59 WILD-TYPE    48 132  97 163
D35V4, multiclass
       clus
vv      C3ORF59 MUTATED C3ORF59 WILD-TYPE
  T0+T1               0                48
  T2                  2               132
  T3                  2                97
  T4                  5               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
  C3ORF59 MUTATED     2   3   3   0
  C3ORF59 WILD-TYPE 173  64 159   7
D35V5, multiclass
    clus
vv   C3ORF59 MUTATED C3ORF59 WILD-TYPE
  N0               2               173
  N1               3                64
  N2               3               159
  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
  C3ORF59 MUTATED     3   8
  C3ORF59 WILD-TYPE 137 362
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF59 MUTATED      3    8
  C3ORF59 WILD-TYPE  137  362
        clus
vv       C3ORF59 MUTATED C3ORF59 WILD-TYPE
  FEMALE               3               137
  MALE                 8               362
[1] 2 2
[1] FALSE
D35V7, binary
                   cls
clus                  0   1
  C3ORF59 MUTATED     2   7
  C3ORF59 WILD-TYPE 144 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF59 MUTATED      2    7
  C3ORF59 WILD-TYPE  144  267
     clus
vv    C3ORF59 MUTATED C3ORF59 WILD-TYPE
  NO                2               144
  YES               7               267
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  C3ORF59 MUTATED                                      11
  C3ORF59 WILD-TYPE                                   491
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  C3ORF59 MUTATED                                                             0
  C3ORF59 WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  C3ORF59 MUTATED                                                     0
  C3ORF59 WILD-TYPE                                                   7
D35V8, multiclass
                                                             clus
vv                                                            C3ORF59 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    11
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            C3ORF59 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     491
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V9, continuous
D35V10, continuous
D35V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C3ORF59 MUTATED                                  0     0
  C3ORF59 WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C3ORF59 MUTATED                           1    10
  C3ORF59 WILD-TYPE                        36   436
D35V12, multiclass
                                  clus
vv                                 C3ORF59 MUTATED C3ORF59 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                36
  WHITE                                         10               436
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V13, binary
                   cls
clus                  0   1
  C3ORF59 MUTATED     0  11
  C3ORF59 WILD-TYPE  26 437
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF59 MUTATED      0   11
  C3ORF59 WILD-TYPE   26  437
                        clus
vv                       C3ORF59 MUTATED C3ORF59 WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO              11               437
[1] 2 2
[1] FALSE

Clustering(36) Variable = HUWE1 MUTATION ANALYSIS
D36V1, survival
                 sevent
clus2               0   1
  HUWE1 MUTATED    24  21
  HUWE1 WILD-TYPE 269 196
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             45             465 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             21             196 
$`HUWE1 MUTATED`
TCGA-BA-5557 TCGA-BB-A6UO TCGA-CN-A63Y TCGA-CN-A642 TCGA-CQ-5330 TCGA-CQ-5332 
       20.48         8.81        16.57         2.70        62.37        10.42 
TCGA-CQ-5334 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CB TCGA-CR-5248 TCGA-CR-6471 
        4.24        43.04        43.10        29.36        54.67        39.52 
TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7374 TCGA-CV-5442 
       34.52        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-A6T5 TCGA-QK-A652 TCGA-QK-A6II TCGA-RS-A6TO 
       27.48        12.62        29.00        21.21         9.34        12.72 
TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-UF-A7JT 
        6.87        32.45        32.65 

$`HUWE1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         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-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       68.48        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        4.01        41.85        29.42        28.11        20.45        30.18 
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-BB-4217 TCGA-BB-4223 
        2.27        11.05        13.38        20.48         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       33.70        50.20        66.28        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-C9-A47Z 
       20.52        25.71        10.55        27.19        12.92         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
       12.69        55.86        38.04         4.67        51.29        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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       32.22        35.05        38.89         3.68        17.42        32.48 
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-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
       12.07        23.44        19.82        24.39        20.88        19.53 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6221 
       45.99        11.21        41.19        15.75        32.38        32.88 
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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 
       38.76        70.13        64.87        53.52        16.73        41.88 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE 
       77.56        44.48        11.61        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-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
        6.02        11.90        10.22        11.34         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-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 
       35.84         3.09        24.95        29.23        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        29.82        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         7.10         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-5443 
       76.24        19.20        17.95       107.51        87.55        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-6962 
       65.82        10.98         7.13         8.42        28.34         4.14 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      126.15       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        47.47        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-7407 
       11.87        47.97         2.10        36.13        18.41        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       17.85       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-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-7446 TCGA-CV-A45O TCGA-CV-A45P 
      153.86        16.64         6.38        35.93        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-A464 
        6.51        88.87        48.20        60.43        67.86        56.61 
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-A6K0 TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7085 
        3.62        21.24        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 
       18.84        34.36        51.12        13.25         9.60        23.05 
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-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       12.36         7.63        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       12.79        11.11        30.94        33.86        18.02        14.04 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       46.32        46.45        20.45        37.58        40.24        40.04 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       39.12        37.18        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       18.94        24.95        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       13.38        15.16        13.61        21.11        20.94         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 
       13.84        19.04        15.48        13.35        18.15        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-A5Q6 TCGA-P3-A5QA 
       15.42         7.13        16.08        17.98        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-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       18.97         2.04        12.99        16.01        13.15        21.07 
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        18.64        21.07 
TCGA-QK-A6VC TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-TN-A7HJ 
       19.73        16.96        15.91         7.10        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D 
       20.35        64.80        54.67         2.83        49.51        48.03 
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-A7JV 
       29.46        18.05        13.94        20.75        22.36         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

  HUWE1 MUTATED HUWE1 WILD-TYPE 
           0.46            0.07 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
          76.50          210.97 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
          23.47           21.07 
[1] "0.5 - 76.5 (23.5)"  "0.1 - 211.0 (21.1)"
[1] "hr=" "1.3"
D36V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  HUWE1 MUTATED         1        6         9        20         1
  HUWE1 WILD-TYPE      24       69        73       228        10
D36V3, multiclass
           clus
vv          HUWE1 MUTATED HUWE1 WILD-TYPE
  STAGE I               1              24
  STAGE II              6              69
  STAGE III             9              73
  STAGE IVA            20             228
  STAGE IVB             1              10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HUWE1 MUTATED       4   9   6  18
  HUWE1 WILD-TYPE    44 125  93 150
D36V4, multiclass
       clus
vv      HUWE1 MUTATED HUWE1 WILD-TYPE
  T0+T1             4              44
  T2                9             125
  T3                6              93
  T4               18             150
[1] 4 2
[1] TRUE
[1] "dimension of 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  10   1
  HUWE1 WILD-TYPE 158  61 152   6
D36V5, multiclass
    clus
vv   HUWE1 MUTATED HUWE1 WILD-TYPE
  N0            17             158
  N1             6              61
  N2            10             152
  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"
D36V6, binary
                 cls
clus                0   1
  HUWE1 MUTATED    19  26
  HUWE1 WILD-TYPE 121 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED     19   26
  HUWE1 WILD-TYPE  121  344
        clus
vv       HUWE1 MUTATED HUWE1 WILD-TYPE
  FEMALE            19             121
  MALE              26             344
[1] 2 2
[1] FALSE
D36V7, binary
                 cls
clus                0   1
  HUWE1 MUTATED    12  24
  HUWE1 WILD-TYPE 134 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED     12   24
  HUWE1 WILD-TYPE  134  250
     clus
vv    HUWE1 MUTATED HUWE1 WILD-TYPE
  NO             12             134
  YES            24             250
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  HUWE1 MUTATED                                      45
  HUWE1 WILD-TYPE                                   457
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  HUWE1 MUTATED                                                             0
  HUWE1 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  HUWE1 MUTATED                                                     0
  HUWE1 WILD-TYPE                                                   7
D36V8, multiclass
                                                             clus
vv                                                            HUWE1 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  45
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
                                                             clus
vv                                                            HUWE1 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   457
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V9, continuous
D36V10, continuous
D36V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HUWE1 MUTATED                                  0     2
  HUWE1 WILD-TYPE                                2     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HUWE1 MUTATED                           0    40
  HUWE1 WILD-TYPE                        37   406
D36V12, multiclass
                                  clus
vv                                 HUWE1 MUTATED HUWE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              37
  WHITE                                       40             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"
D36V13, binary
                 cls
clus                0   1
  HUWE1 MUTATED     4  39
  HUWE1 WILD-TYPE  22 409
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED      4   39
  HUWE1 WILD-TYPE   22  409
                        clus
vv                       HUWE1 MUTATED HUWE1 WILD-TYPE
  HISPANIC OR LATINO                 4              22
  NOT HISPANIC OR LATINO            39             409
[1] 2 2
[1] FALSE

Clustering(37) Variable = SLC9A6 MUTATION ANALYSIS
D37V1, survival
                  sevent
clus2                0   1
  SLC9A6 MUTATED     1   4
  SLC9A6 WILD-TYPE 292 213
  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
               5              505 
  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
               4              213 
$`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-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        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-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       36.72        33.70        50.20        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       71.05        20.52        25.71        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-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       51.29        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-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       27.58        73.61        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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       34.13         6.74         9.07         9.24        52.08        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        32.22        35.05        38.89         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       32.48        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-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       24.39        20.88        19.53        48.20        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-6221 
       11.21         4.24        41.19        15.75        32.38        32.88 
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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       38.76        70.13        64.87        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       50.01        39.52        34.52        36.99        18.54        16.90 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        6.02        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-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 
       29.82        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         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-5436 
      139.43        17.16       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       17.95       107.51        87.55        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-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-6953 TCGA-CV-6954 TCGA-CV-6955 
       42.38        15.09        30.08        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 
      126.15       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        47.47        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        36.13        18.41        57.47 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       35.54        17.85       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-7440 TCGA-CV-7446 
       19.76         7.17       153.86        16.64        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-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 
       10.42        10.55        18.84        34.36        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-5629 TCGA-DQ-5630 TCGA-DQ-5631 
       11.11        58.45        37.25        30.94        33.86        18.02 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       14.04        46.32        46.45        20.45        37.58        40.24 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       40.04        39.12        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-A6C4 
       11.80        20.25        12.43        13.38        15.16        13.61 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       21.11        20.94         0.07        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       27.48        27.48        14.66        22.03        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
        0.36        13.84         4.27         3.65         6.90        34.75 
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-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
        0.07         5.29        13.68        13.84        19.04        15.48 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        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-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       16.08        17.98        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-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       29.00        12.99        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        18.64        21.07 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       19.73        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       32.45        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        49.51        48.03        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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  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            21.21 
[1] "6.1 - 33.6 (13.1)"  "0.1 - 211.0 (21.2)"
[1] "hr=" "3.4"
D37V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  SLC9A6 MUTATED         1        0         0         4         0
  SLC9A6 WILD-TYPE      24       75        82       244        11
D37V3, multiclass
           clus
vv          SLC9A6 MUTATED SLC9A6 WILD-TYPE
  STAGE I                1               24
  STAGE II               0               75
  STAGE III              0               82
  STAGE IVA              4              244
  STAGE IVB              0               11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SLC9A6 MUTATED       1   1   2   1
  SLC9A6 WILD-TYPE    47 133  97 167
D37V4, multiclass
       clus
vv      SLC9A6 MUTATED SLC9A6 WILD-TYPE
  T0+T1              1               47
  T2                 1              133
  T3                 2               97
  T4                 1              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
  SLC9A6 MUTATED     0   0   4   0
  SLC9A6 WILD-TYPE 175  67 158   7
D37V5, multiclass
    clus
vv   SLC9A6 MUTATED SLC9A6 WILD-TYPE
  N0              0              175
  N1              0               67
  N2              4              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"
D37V6, binary
                  cls
clus                 0   1
  SLC9A6 MUTATED     3   2
  SLC9A6 WILD-TYPE 137 368
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A6 MUTATED      3    2
  SLC9A6 WILD-TYPE  137  368
        clus
vv       SLC9A6 MUTATED SLC9A6 WILD-TYPE
  FEMALE              3              137
  MALE                2              368
[1] 2 2
[1] FALSE
D37V7, binary
                  cls
clus                 0   1
  SLC9A6 MUTATED     1   4
  SLC9A6 WILD-TYPE 145 270
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A6 MUTATED      1    4
  SLC9A6 WILD-TYPE  145  270
     clus
vv    SLC9A6 MUTATED SLC9A6 WILD-TYPE
  NO               1              145
  YES              4              270
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  SLC9A6 MUTATED                                       5
  SLC9A6 WILD-TYPE                                   497
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  SLC9A6 MUTATED                                                             0
  SLC9A6 WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  SLC9A6 MUTATED                                                     0
  SLC9A6 WILD-TYPE                                                   7
D37V8, multiclass
                                                             clus
vv                                                            SLC9A6 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    5
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
                                                             clus
vv                                                            SLC9A6 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    497
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V9, continuous
D37V10, continuous
[1] "Remove cluster labels:" "SLC9A6 MUTATED"        
clus
  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
               2              272 
      TCGA-BA-4074       TCGA-BA-4075       TCGA-BA-4076       TCGA-BA-4077 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-BA-4078       TCGA-BA-5149       TCGA-BA-5151       TCGA-BA-5556 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-BA-6868       TCGA-BA-6869       TCGA-BA-6870       TCGA-BA-6871 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-BA-6872       TCGA-BA-6873       TCGA-BA-7269       TCGA-BA-A6DA 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-BA-A6DG       TCGA-BB-4225       TCGA-BB-4228       TCGA-BB-7871 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-BB-8596       TCGA-BB-A5HY       TCGA-BB-A6UM       TCGA-BB-A6UO 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CN-4727       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-6021       TCGA-CN-6023       TCGA-CN-6024 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CN-6989       TCGA-CN-6992       TCGA-CN-6994       TCGA-CN-6997 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CN-6998       TCGA-CN-A498       TCGA-CN-A49B       TCGA-CN-A49C 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CN-A63T       TCGA-CN-A63U       TCGA-CN-A63V       TCGA-CN-A641 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CN-A6UY       TCGA-CN-A6V3       TCGA-CN-A6V6       TCGA-CQ-5323 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CQ-5324       TCGA-CQ-5325       TCGA-CQ-5330       TCGA-CQ-5331 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CQ-5333       TCGA-CQ-6218       TCGA-CQ-6219       TCGA-CQ-6221 
"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-7063       TCGA-CQ-7072       TCGA-CQ-A4C6 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CQ-A4C7       TCGA-CQ-A4C9       TCGA-CQ-A4CB       TCGA-CQ-A4CI 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-5247       TCGA-CR-5248       TCGA-CR-5250       TCGA-CR-6467 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-6471       TCGA-CR-6473       TCGA-CR-6474       TCGA-CR-6477 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-6478       TCGA-CR-6482       TCGA-CR-6487       TCGA-CR-6491 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-6492       TCGA-CR-6493       TCGA-CR-7364       TCGA-CR-7365 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-7367       TCGA-CR-7368       TCGA-CR-7369       TCGA-CR-7370 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-7371       TCGA-CR-7373       TCGA-CR-7374       TCGA-CR-7376 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-7377       TCGA-CR-7383       TCGA-CR-7385       TCGA-CR-7386 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-7388       TCGA-CR-7389       TCGA-CR-7390       TCGA-CR-7391 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-7392       TCGA-CR-7394       TCGA-CR-7395       TCGA-CR-7397 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CR-7399       TCGA-CR-7401       TCGA-CR-7402       TCGA-CV-5430 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-5431       TCGA-CV-5432       TCGA-CV-5435       TCGA-CV-5436 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-5440       TCGA-CV-5443       TCGA-CV-5966       TCGA-CV-5970 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-5976       TCGA-CV-6433       TCGA-CV-6436       TCGA-CV-6441 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-6934       TCGA-CV-6935       TCGA-CV-6936       TCGA-CV-6940 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-6941       TCGA-CV-6943       TCGA-CV-6945       TCGA-CV-6954 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-6960       TCGA-CV-6961       TCGA-CV-7091       TCGA-CV-7095 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7097       TCGA-CV-7099       TCGA-CV-7100       TCGA-CV-7101 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7102       TCGA-CV-7180       TCGA-CV-7183       TCGA-CV-7235 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7242       TCGA-CV-7245       TCGA-CV-7248       TCGA-CV-7250 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7254       TCGA-CV-7261       TCGA-CV-7406       TCGA-CV-7410 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7418       TCGA-CV-7422       TCGA-CV-7424       TCGA-CV-7427 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7430       TCGA-CV-7432       TCGA-CV-7433       TCGA-CV-7434 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7435       TCGA-CV-7440       TCGA-CV-7446       TCGA-CV-7568 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-A45Q       TCGA-CV-A45Y       TCGA-CV-A45Z       TCGA-CV-A460 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-A461       TCGA-CV-A464       TCGA-CV-A468       TCGA-CV-A6JD 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-A6JE       TCGA-CV-A6JN       TCGA-CV-A6JO       TCGA-CV-A6JU 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-A6JY       TCGA-CV-A6JZ       TCGA-CV-A6K1       TCGA-CV-A6K2 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CX-7086       TCGA-CX-7219       TCGA-D6-6516       TCGA-D6-6517 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-D6-6823       TCGA-D6-6824       TCGA-D6-6825       TCGA-D6-6827 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-D6-8568       TCGA-D6-8569       TCGA-D6-A4Z9       TCGA-D6-A4ZB 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-D6-A6EK       TCGA-D6-A6EP       TCGA-D6-A74Q       TCGA-DQ-5625 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-DQ-5629       TCGA-DQ-5630       TCGA-DQ-5631       TCGA-DQ-7588 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-DQ-7589       TCGA-DQ-7590       TCGA-DQ-7591       TCGA-DQ-7592 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-DQ-7593       TCGA-DQ-7595       TCGA-F7-7848       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-A6C4       TCGA-H7-A6C5       TCGA-H7-A76A 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-HD-8634       TCGA-HD-8635       TCGA-HD-A634       TCGA-HD-A6I0 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-HL-7533       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-A66S       TCGA-KU-A6H7 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-KU-A6H8       TCGA-MT-A51W       TCGA-MT-A51X       TCGA-MT-A67D 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-MZ-A6I9       TCGA-MZ-A7D7       TCGA-P3-A6SX       TCGA-P3-A6T0 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-P3-A6T4       TCGA-P3-A6T8       TCGA-QK-A6IG       TCGA-QK-A6II 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-QK-A6IJ       TCGA-RS-A6TP       TCGA-TN-A7HI       TCGA-TN-A7HL 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-UF-A718       TCGA-UF-A71B       TCGA-UF-A71D       TCGA-UF-A7J9 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-UF-A7JC       TCGA-UF-A7JD       TCGA-UF-A7JF       TCGA-UF-A7JH 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-UF-A7JJ       TCGA-UF-A7JS       TCGA-WA-A7GZ       TCGA-WA-A7H4 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
D37V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC9A6 MUTATED                                  0     0
  SLC9A6 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLC9A6 MUTATED                           0     5
  SLC9A6 WILD-TYPE                        37   441
D37V12, multiclass
                                  clus
vv                                 SLC9A6 MUTATED SLC9A6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               37
  WHITE                                         5              441
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, binary
                  cls
clus                 0   1
  SLC9A6 MUTATED     0   5
  SLC9A6 WILD-TYPE  26 443
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A6 MUTATED      0    5
  SLC9A6 WILD-TYPE   26  443
                        clus
vv                       SLC9A6 MUTATED SLC9A6 WILD-TYPE
  HISPANIC OR LATINO                  0               26
  NOT HISPANIC OR LATINO              5              443
[1] 2 2
[1] FALSE

Clustering(38) Variable = ZNF623 MUTATION ANALYSIS
D38V1, survival
                  sevent
clus2                0   1
  ZNF623 MUTATED     8   3
  ZNF623 WILD-TYPE 285 214
  ZNF623 MUTATED ZNF623 WILD-TYPE 
              11              499 
  ZNF623 MUTATED ZNF623 WILD-TYPE 
               3              214 
$`ZNF623 MUTATED`
TCGA-BA-5152 TCGA-BA-A6DA TCGA-BB-4223 TCGA-BB-4225 TCGA-CN-4727 TCGA-CN-4736 
       42.35        11.54       105.90         4.60        51.29        12.99 
TCGA-CN-5356 TCGA-CN-6020 TCGA-CQ-7069 TCGA-CV-7432 TCGA-QK-A6VC 
       46.32         6.74        41.88        84.49        19.73 

$`ZNF623 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       23.74        57.93        17.10        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       68.48        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        4.01        41.85        29.42        28.11        20.45        30.18 
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-BB-4217 TCGA-BB-4224 TCGA-BB-4227 
       11.05        13.38        20.48         6.15         9.14         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 
       18.38        22.42        36.72        33.70        50.20        66.28 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY 
       24.66        38.40        71.05        20.52        25.71        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-4737 TCGA-CN-4738 TCGA-CN-4739 
       52.14        55.56        57.11        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 
       27.58        73.61        13.05        42.02         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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
       34.13         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       32.22        35.05        38.89         3.68        17.42        32.48 
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-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        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-6221 TCGA-CQ-6222 
        4.24        41.19        15.75        32.38        32.88        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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 
       70.13        64.87        53.52        16.73        43.04        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       34.52        36.99        18.54        16.90         6.02        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        29.82        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         7.10         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 
       87.55        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       126.15 
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        47.47        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        36.13        18.41        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       17.85       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-7433 TCGA-CV-7434 
       56.48       156.49         3.52        16.27        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-7082 
       21.24        23.47        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.55        18.84        34.36        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        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       58.45        37.25        30.94        33.86        18.02        14.04 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       46.32        46.45        20.45        37.58        40.24        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       39.12        41.59        37.18        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-A6C4 TCGA-H7-A6C5 
       20.25        12.43        13.38        15.16        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       20.94         0.07        28.47        25.74        21.93        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
       27.48        14.66        22.03        12.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
       13.84         4.27         3.65         6.90        34.75        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        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-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       16.08        17.98        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        18.64 
TCGA-QK-A6VB TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       21.07        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       32.45        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        49.51        48.03        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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  ZNF623 MUTATED ZNF623 WILD-TYPE 
            4.60             0.07 
  ZNF623 MUTATED ZNF623 WILD-TYPE 
          105.90           210.97 
  ZNF623 MUTATED ZNF623 WILD-TYPE 
           41.88            21.11 
[1] "4.6 - 105.9 (41.9)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.9"
D38V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  ZNF623 MUTATED         0        2         2         5         0
  ZNF623 WILD-TYPE      25       73        80       243        11
D38V3, multiclass
           clus
vv          ZNF623 MUTATED ZNF623 WILD-TYPE
  STAGE I                0               25
  STAGE II               2               73
  STAGE III              2               80
  STAGE IVA              5              243
  STAGE IVB              0               11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF623 MUTATED       1   4   1   4
  ZNF623 WILD-TYPE    47 130  98 164
D38V4, multiclass
       clus
vv      ZNF623 MUTATED ZNF623 WILD-TYPE
  T0+T1              1               47
  T2                 4              130
  T3                 1               98
  T4                 4              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
  ZNF623 MUTATED     5   2   2   0
  ZNF623 WILD-TYPE 170  65 160   7
D38V5, multiclass
    clus
vv   ZNF623 MUTATED ZNF623 WILD-TYPE
  N0              5              170
  N1              2               65
  N2              2              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"
D38V6, binary
                  cls
clus                 0   1
  ZNF623 MUTATED     4   7
  ZNF623 WILD-TYPE 136 363
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF623 MUTATED      4    7
  ZNF623 WILD-TYPE  136  363
        clus
vv       ZNF623 MUTATED ZNF623 WILD-TYPE
  FEMALE              4              136
  MALE                7              363
[1] 2 2
[1] FALSE
D38V7, binary
                  cls
clus                 0   1
  ZNF623 MUTATED     2   8
  ZNF623 WILD-TYPE 144 266
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF623 MUTATED      2    8
  ZNF623 WILD-TYPE  144  266
     clus
vv    ZNF623 MUTATED ZNF623 WILD-TYPE
  NO               2              144
  YES              8              266
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  ZNF623 MUTATED                                      11
  ZNF623 WILD-TYPE                                   491
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  ZNF623 MUTATED                                                             0
  ZNF623 WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  ZNF623 MUTATED                                                     0
  ZNF623 WILD-TYPE                                                   7
D38V8, multiclass
                                                             clus
vv                                                            ZNF623 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   11
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
                                                             clus
vv                                                            ZNF623 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    491
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V9, continuous
D38V10, continuous
D38V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF623 MUTATED                                  0     0
  ZNF623 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF623 MUTATED                           2     9
  ZNF623 WILD-TYPE                        35   437
D38V12, multiclass
                                  clus
vv                                 ZNF623 MUTATED ZNF623 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               35
  WHITE                                         9              437
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, binary
                  cls
clus                 0   1
  ZNF623 MUTATED     0  11
  ZNF623 WILD-TYPE  26 437
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF623 MUTATED      0   11
  ZNF623 WILD-TYPE   26  437
                        clus
vv                       ZNF623 MUTATED ZNF623 WILD-TYPE
  HISPANIC OR LATINO                  0               26
  NOT HISPANIC OR LATINO             11              437
[1] 2 2
[1] FALSE

Clustering(39) Variable = MLL4 MUTATION ANALYSIS
D39V1, survival
                sevent
clus2              0   1
  MLL4 MUTATED    10  10
  MLL4 WILD-TYPE 283 207
  MLL4 MUTATED MLL4 WILD-TYPE 
            20            490 
  MLL4 MUTATED MLL4 WILD-TYPE 
            10            207 
$`MLL4 MUTATED`
TCGA-BA-5151 TCGA-BA-A4II TCGA-BA-A6DF TCGA-BA-A6DJ TCGA-BB-7863 TCGA-CN-5360 
       23.74        30.18         7.82        13.38        33.70        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-HD-8634 TCGA-MT-A67A 
       12.66        30.05 

$`MLL4 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       42.35        57.93        17.10        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       68.48        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 
        4.01        41.85        29.42        28.11        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-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       20.48         6.15       105.90         9.14         4.60         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 
       18.38        22.42        36.72        50.20        66.28        24.66 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ 
       38.40        71.05        20.52        25.71        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-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
        4.67        51.29        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-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-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        34.13         6.74         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       11.08        10.45        32.22        35.05        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A 
       17.42        32.48        11.74        35.01        25.41        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       29.72        21.21        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        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-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       15.75        32.38        32.88        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       13.25         4.24        14.99        38.76        70.13        64.87 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       53.52        16.73        43.04        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        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-6472 
       37.87        26.27        58.42        50.01        39.52        34.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
       36.99        18.54        16.90         6.02        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-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        29.82        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         7.10         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        87.55        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-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
       20.52        21.90        26.43        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       12.03        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       126.15       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        47.47 
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-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
       11.87        47.97         2.10        36.13        18.41        57.47 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       35.54        17.85       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-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 
       10.42        10.55        18.84        34.36        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        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       58.45        37.25        30.94        33.86        18.02        14.04 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       46.32        46.45        20.45        37.58        40.24        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       39.12        41.59        37.18        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
       31.13        18.94        24.95         0.46        17.85        20.25 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       13.38        15.16        13.61        21.11        20.94         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       28.47        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       22.03        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 
       13.84        19.04        15.48        13.35        18.15        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-A5Q6 TCGA-P3-A5QA 
       15.42         7.13        16.08        17.98        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-RS-A6TO TCGA-RS-A6TP 
       12.72        18.64        21.07        19.73        12.72        16.96 
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-A71D 
       20.35        64.80        54.67         2.83        49.51        48.03 
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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        17.03        20.55        14.56 

  MLL4 MUTATED MLL4 WILD-TYPE 
          3.45           0.07 
  MLL4 MUTATED MLL4 WILD-TYPE 
        169.38         210.97 
  MLL4 MUTATED MLL4 WILD-TYPE 
         13.02          21.19 
[1] "3.5 - 169.4 (13.0)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.3"
D39V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  MLL4 MUTATED         2        5         3         7         1
  MLL4 WILD-TYPE      23       70        79       241        10
D39V3, multiclass
           clus
vv          MLL4 MUTATED MLL4 WILD-TYPE
  STAGE I              2             23
  STAGE II             5             70
  STAGE III            3             79
  STAGE IVA            7            241
  STAGE IVB            1             10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MLL4 MUTATED       2   6   4   6
  MLL4 WILD-TYPE    46 128  95 162
D39V4, multiclass
       clus
vv      MLL4 MUTATED MLL4 WILD-TYPE
  T0+T1            2             46
  T2               6            128
  T3               4             95
  T4               6            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
  MLL4 MUTATED    10   1   3   1
  MLL4 WILD-TYPE 165  66 159   6
D39V5, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  N0           10            165
  N1            1             66
  N2            3            159
  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"
D39V6, binary
                cls
clus               0   1
  MLL4 MUTATED     9  11
  MLL4 WILD-TYPE 131 359
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED      9   11
  MLL4 WILD-TYPE  131  359
        clus
vv       MLL4 MUTATED MLL4 WILD-TYPE
  FEMALE            9            131
  MALE             11            359
[1] 2 2
[1] FALSE
D39V7, binary
                cls
clus               0   1
  MLL4 MUTATED     6  10
  MLL4 WILD-TYPE 140 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED      6   10
  MLL4 WILD-TYPE  140  264
     clus
vv    MLL4 MUTATED MLL4 WILD-TYPE
  NO             6            140
  YES           10            264
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  MLL4 MUTATED                                      20
  MLL4 WILD-TYPE                                   482
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  MLL4 MUTATED                                                             0
  MLL4 WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  MLL4 MUTATED                                                     0
  MLL4 WILD-TYPE                                                   7
D39V8, multiclass
                                                             clus
vv                                                            MLL4 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                 20
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
                                                             clus
vv                                                            MLL4 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  482
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V9, continuous
D39V10, continuous
D39V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL4 MUTATED                                  0     1
  MLL4 WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MLL4 MUTATED                           1    18
  MLL4 WILD-TYPE                        36   428
D39V12, multiclass
                                  clus
vv                                 MLL4 MUTATED MLL4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             36
  WHITE                                      18            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"
D39V13, binary
                cls
clus               0   1
  MLL4 MUTATED     1  19
  MLL4 WILD-TYPE  25 429
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED      1   19
  MLL4 WILD-TYPE   25  429
                        clus
vv                       MLL4 MUTATED MLL4 WILD-TYPE
  HISPANIC OR LATINO                1             25
  NOT HISPANIC OR LATINO           19            429
[1] 2 2
[1] FALSE

Clustering(40) Variable = CTCF MUTATION ANALYSIS
D40V1, survival
                sevent
clus2              0   1
  CTCF MUTATED     8   8
  CTCF WILD-TYPE 285 209
  CTCF MUTATED CTCF WILD-TYPE 
            16            494 
  CTCF MUTATED CTCF WILD-TYPE 
             8            209 
$`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-HL-7533 TCGA-QK-A6IH 
       12.43        13.38        34.75        21.47 

$`CTCF WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       42.35        57.93        17.10        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       68.48        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        4.01        41.85        29.42        28.11        20.45        30.18 
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-4223 TCGA-BB-4224 
       11.05        13.38        20.48         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       50.20        66.28        24.66        38.40        71.05        20.52 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       25.71        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
       12.69        55.86        38.04         4.67        51.29        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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       32.22        35.05        38.89         3.68        17.42        32.48 
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-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        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-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       32.38        32.88        66.28        46.95        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        4.24        38.76        70.13        64.87        53.52        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       43.04        41.88        43.10        77.56        44.48        11.61 
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-6472 TCGA-CR-6473 TCGA-CR-6474 
       58.42        50.01        39.52        34.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       16.90         6.02        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-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       19.92        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 
       29.82        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         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-5436 
      139.43        17.16       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       17.95       107.51        87.55        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-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-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 
      126.15       111.16        18.81        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        5.26        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 
      130.88        77.16         4.73        47.47        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7255 
       18.97        17.13        95.34         4.96        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
       36.13        18.41        57.47        35.54        17.85       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-A45W 
       21.01       169.38       180.16       159.65        35.47        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-7082 TCGA-CX-7085 TCGA-CX-7086 
       19.92        22.52        10.42        10.42        10.55        18.84 
TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       34.36        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        11.11        58.45        37.25 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       30.94        33.86        18.02        14.04        46.32        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45        37.58        40.24        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       37.18        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-H7-8501 
       24.95         0.46        17.85        11.80        20.25        15.16 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.61        21.11        20.94         0.07        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
       21.93        27.48        27.48        14.66        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.85         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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       15.48        13.35        18.15        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-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-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.21        23.15         7.30         9.34        12.72        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       21.07        19.73        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
        7.10        32.45        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        49.51        48.03        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-UF-A7JV TCGA-UP-A6WW 
       13.94        20.75        22.36        32.65         2.96        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  CTCF MUTATED CTCF WILD-TYPE 
          1.05           0.07 
  CTCF MUTATED CTCF WILD-TYPE 
         54.58         210.97 
  CTCF MUTATED CTCF WILD-TYPE 
        12.905         21.210 
[1] "1.1 - 54.6 (12.9)"  "0.1 - 211.0 (21.2)"
[1] "hr=" "1.9"
D40V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  CTCF MUTATED         0        4         0        10         1
  CTCF WILD-TYPE      25       71        82       238        10
D40V3, multiclass
           clus
vv          CTCF MUTATED CTCF WILD-TYPE
  STAGE I              0             25
  STAGE II             4             71
  STAGE III            0             82
  STAGE IVA           10            238
  STAGE IVB            1             10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CTCF MUTATED       1   5   3   6
  CTCF WILD-TYPE    47 129  96 162
D40V4, multiclass
       clus
vv      CTCF MUTATED CTCF WILD-TYPE
  T0+T1            1             47
  T2               5            129
  T3               3             96
  T4               6            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
  CTCF MUTATED     7   0   6   0
  CTCF WILD-TYPE 168  67 156   7
D40V5, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  N0            7            168
  N1            0             67
  N2            6            156
  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"
D40V6, binary
                cls
clus               0   1
  CTCF MUTATED     8   8
  CTCF WILD-TYPE 132 362
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED      8    8
  CTCF WILD-TYPE  132  362
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  FEMALE            8            132
  MALE              8            362
[1] 2 2
[1] FALSE
D40V7, binary
                cls
clus               0   1
  CTCF MUTATED     4   8
  CTCF WILD-TYPE 142 266
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED      4    8
  CTCF WILD-TYPE  142  266
     clus
vv    CTCF MUTATED CTCF WILD-TYPE
  NO             4            142
  YES            8            266
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  CTCF MUTATED                                      16
  CTCF WILD-TYPE                                   486
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  CTCF MUTATED                                                             0
  CTCF WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  CTCF MUTATED                                                     0
  CTCF WILD-TYPE                                                   7
D40V8, multiclass
                                                             clus
vv                                                            CTCF MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                 16
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
                                                             clus
vv                                                            CTCF WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  486
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V9, continuous
D40V10, continuous
D40V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTCF MUTATED                                  0     1
  CTCF WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CTCF MUTATED                           1    14
  CTCF WILD-TYPE                        36   432
D40V12, multiclass
                                  clus
vv                                 CTCF MUTATED CTCF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             36
  WHITE                                      14            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"
D40V13, binary
                cls
clus               0   1
  CTCF MUTATED     0  16
  CTCF WILD-TYPE  26 432
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED      0   16
  CTCF WILD-TYPE   26  432
                        clus
vv                       CTCF MUTATED CTCF WILD-TYPE
  HISPANIC OR LATINO                0             26
  NOT HISPANIC OR LATINO           16            432
[1] 2 2
[1] FALSE

Clustering(41) Variable = NCOR1 MUTATION ANALYSIS
D41V1, survival
                 sevent
clus2               0   1
  NCOR1 MUTATED    11   7
  NCOR1 WILD-TYPE 282 210
  NCOR1 MUTATED NCOR1 WILD-TYPE 
             18             492 
  NCOR1 MUTATED NCOR1 WILD-TYPE 
              7             210 
$`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-DQ-7595 TCGA-F7-A624 TCGA-MT-A67F TCGA-MZ-A7D7 TCGA-QK-A6VB 
        6.38        39.12        12.43        12.62        17.98        21.07 

$`NCOR1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        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-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       36.72        33.70        50.20        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       71.05        20.52        25.71        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-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       51.29        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-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        34.13         6.74         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       11.08        10.45        32.22        38.89         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       32.48        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-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       24.39        20.88        19.53        48.20        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-6221 TCGA-CQ-6222 
        4.24        41.19        15.75        32.38        32.88        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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
       70.13        64.87        53.52        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       43.10        77.56        44.48        11.61        23.24        29.36 
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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       34.52        36.99        18.54        16.90         6.02        11.90 
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        29.82        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         7.10         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        87.55 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       76.50        91.53        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-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       126.15       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-7247 TCGA-CV-7248 TCGA-CV-7250 
       47.47        36.00        31.36        18.97        17.13        95.34 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
       11.87        47.97         2.10        36.13        18.41        57.47 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 
       17.85       210.97        89.33         9.67        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-A45O TCGA-CV-A45P 
       16.64         6.38        22.19        35.93        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-A6JN 
       56.61         7.07        15.25         5.98        35.34        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-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
       22.52        10.42        10.42        10.55        18.84        34.36 
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-5629 
       12.10        12.79        11.11        58.45        37.25        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
       33.86        18.02        14.04        46.32        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
       37.58        40.24        40.04        41.59        37.18        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-A6C4 
       17.85        11.80        20.25        13.38        15.16        13.61 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       21.11        20.94         0.07        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       27.48        27.48        14.66        22.03        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
        0.36        13.84         4.27         3.65         6.90        34.75 
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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       15.48        13.35        18.15        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
        7.96        30.05         1.84         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       16.08        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        18.64        19.73 
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-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-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       49.51        48.03        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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36        32.65         2.96        17.03        20.55        14.56 

  NCOR1 MUTATED NCOR1 WILD-TYPE 
           0.46            0.07 
  NCOR1 MUTATED NCOR1 WILD-TYPE 
         156.49          210.97 
  NCOR1 MUTATED NCOR1 WILD-TYPE 
         23.635          21.140 
[1] "0.5 - 156.5 (23.6)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D41V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  NCOR1 MUTATED         0        3         1        10         0
  NCOR1 WILD-TYPE      25       72        81       238        11
D41V3, multiclass
           clus
vv          NCOR1 MUTATED NCOR1 WILD-TYPE
  STAGE I               0              25
  STAGE II              3              72
  STAGE III             1              81
  STAGE IVA            10             238
  STAGE IVB             0              11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NCOR1 MUTATED       0   4   3   8
  NCOR1 WILD-TYPE    48 130  96 160
D41V4, multiclass
       clus
vv      NCOR1 MUTATED NCOR1 WILD-TYPE
  T0+T1             0              48
  T2                4             130
  T3                3              96
  T4                8             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
  NCOR1 MUTATED     6   1   3   0
  NCOR1 WILD-TYPE 169  66 159   7
D41V5, multiclass
    clus
vv   NCOR1 MUTATED NCOR1 WILD-TYPE
  N0             6             169
  N1             1              66
  N2             3             159
  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
  NCOR1 MUTATED     6  12
  NCOR1 WILD-TYPE 134 358
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOR1 MUTATED      6   12
  NCOR1 WILD-TYPE  134  358
        clus
vv       NCOR1 MUTATED NCOR1 WILD-TYPE
  FEMALE             6             134
  MALE              12             358
[1] 2 2
[1] FALSE
D41V7, binary
                 cls
clus                0   1
  NCOR1 MUTATED     6   8
  NCOR1 WILD-TYPE 140 266
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOR1 MUTATED      6    8
  NCOR1 WILD-TYPE  140  266
     clus
vv    NCOR1 MUTATED NCOR1 WILD-TYPE
  NO              6             140
  YES             8             266
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  NCOR1 MUTATED                                      18
  NCOR1 WILD-TYPE                                   484
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  NCOR1 MUTATED                                                             0
  NCOR1 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  NCOR1 MUTATED                                                     0
  NCOR1 WILD-TYPE                                                   7
D41V8, multiclass
                                                             clus
vv                                                            NCOR1 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  18
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
                                                             clus
vv                                                            NCOR1 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   484
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V9, continuous
D41V10, continuous
D41V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCOR1 MUTATED                                  0     0
  NCOR1 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NCOR1 MUTATED                           2    16
  NCOR1 WILD-TYPE                        35   430
D41V12, multiclass
                                  clus
vv                                 NCOR1 MUTATED NCOR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              35
  WHITE                                       16             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"
D41V13, binary
                 cls
clus                0   1
  NCOR1 MUTATED     2  16
  NCOR1 WILD-TYPE  24 432
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOR1 MUTATED      2   16
  NCOR1 WILD-TYPE   24  432
                        clus
vv                       NCOR1 MUTATED NCOR1 WILD-TYPE
  HISPANIC OR LATINO                 2              24
  NOT HISPANIC OR LATINO            16             432
[1] 2 2
[1] FALSE

Clustering(42) Variable = PTPN14 MUTATION ANALYSIS
D42V1, survival
                  sevent
clus2                0   1
  PTPN14 MUTATED    12   3
  PTPN14 WILD-TYPE 281 214
  PTPN14 MUTATED PTPN14 WILD-TYPE 
              15              495 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
               3              214 
$`PTPN14 MUTATED`
TCGA-CN-4727 TCGA-CN-5363 TCGA-CN-A63U TCGA-CQ-5327 TCGA-CQ-7071 TCGA-CQ-A4C6 
       51.29         8.32        31.69        54.58        43.10        44.48 
TCGA-CR-7365 TCGA-CV-5430 TCGA-CV-5441 TCGA-CV-A6JD TCGA-D6-6516 TCGA-D6-A6EN 
       39.16       139.43        87.55         5.98        25.41        22.59 
TCGA-D6-A6ES TCGA-DQ-7588 TCGA-MT-A67F 
       12.79        14.04        12.62 

$`PTPN14 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        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-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       36.72        33.70        50.20        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       71.05        20.52        25.71        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-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       71.31        69.70        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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       32.22        35.05        38.89         3.68        17.42        32.48 
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-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
       21.21         7.40        22.32        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        23.44        19.82        24.39        20.88 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 
       19.53        48.20        52.37        21.50         2.93        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-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       15.75        32.38        32.88        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       13.25         4.24        14.99        38.76        70.13        64.87 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C7 
       53.52        16.73        43.04        41.88        77.56        11.61 
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-6472 TCGA-CR-6473 TCGA-CR-6474 
       58.42        50.01        39.52        34.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       16.90         6.02        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-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-7394 TCGA-CR-7395 
       29.82        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         5.13         5.95        35.41        29.95        48.39 
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-5966 TCGA-CV-5970 
      107.51        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       126.15 
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        47.47        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        36.13        18.41        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       17.85       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-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-7082 
       21.24        23.47        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 
       10.55        18.84        34.36        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-A6EO 
       25.32        17.72        12.36        28.77         7.63        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
       13.94        12.10        11.11        58.45        37.25        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       33.86        18.02        46.32        46.45        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
       40.24        40.04        39.12        41.59        37.18        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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.61        21.11        20.94         0.07        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
       21.93        27.48        27.48        14.66        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.85         0.36        13.84         4.27         3.65         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
       34.75        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       19.04        15.48        13.35        18.15        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-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-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-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       18.64        21.07        19.73        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       15.91         7.10        32.45        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       64.80        54.67         2.83        49.51        48.03        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-UF-A7JV 
       18.05        13.94        20.75        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

  PTPN14 MUTATED PTPN14 WILD-TYPE 
            5.98             0.07 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
          139.43           210.97 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
           31.69            21.07 
[1] "6.0 - 139.4 (31.7)" "0.1 - 211.0 (21.1)"
[1] "hr=" "2.6"
D42V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  PTPN14 MUTATED         1        1         2         8         1
  PTPN14 WILD-TYPE      24       74        80       240        10
D42V3, multiclass
           clus
vv          PTPN14 MUTATED PTPN14 WILD-TYPE
  STAGE I                1               24
  STAGE II               1               74
  STAGE III              2               80
  STAGE IVA              8              240
  STAGE IVB              1               10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PTPN14 MUTATED       1   3   2   7
  PTPN14 WILD-TYPE    47 131  97 161
D42V4, multiclass
       clus
vv      PTPN14 MUTATED PTPN14 WILD-TYPE
  T0+T1              1               47
  T2                 3              131
  T3                 2               97
  T4                 7              161
[1] 4 2
[1] TRUE
[1] "dimension of 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   2   4   1
  PTPN14 WILD-TYPE 169  65 158   6
D42V5, multiclass
    clus
vv   PTPN14 MUTATED PTPN14 WILD-TYPE
  N0              6              169
  N1              2               65
  N2              4              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"
D42V6, binary
                  cls
clus                 0   1
  PTPN14 MUTATED     4  11
  PTPN14 WILD-TYPE 136 359
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED      4   11
  PTPN14 WILD-TYPE  136  359
        clus
vv       PTPN14 MUTATED PTPN14 WILD-TYPE
  FEMALE              4              136
  MALE               11              359
[1] 2 2
[1] FALSE
D42V7, binary
                  cls
clus                 0   1
  PTPN14 MUTATED     3  10
  PTPN14 WILD-TYPE 143 264
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED      3   10
  PTPN14 WILD-TYPE  143  264
     clus
vv    PTPN14 MUTATED PTPN14 WILD-TYPE
  NO               3              143
  YES             10              264
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  PTPN14 MUTATED                                      15
  PTPN14 WILD-TYPE                                   487
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  PTPN14 MUTATED                                                             0
  PTPN14 WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  PTPN14 MUTATED                                                     0
  PTPN14 WILD-TYPE                                                   7
D42V8, multiclass
                                                             clus
vv                                                            PTPN14 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   15
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
                                                             clus
vv                                                            PTPN14 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    487
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V9, continuous
D42V10, continuous
D42V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPN14 MUTATED                                  0     2
  PTPN14 WILD-TYPE                                2     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PTPN14 MUTATED                           1    12
  PTPN14 WILD-TYPE                        36   434
D42V12, multiclass
                                  clus
vv                                 PTPN14 MUTATED PTPN14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               36
  WHITE                                        12              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"
D42V13, binary
                  cls
clus                 0   1
  PTPN14 MUTATED     1  14
  PTPN14 WILD-TYPE  25 434
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED      1   14
  PTPN14 WILD-TYPE   25  434
                        clus
vv                       PTPN14 MUTATED PTPN14 WILD-TYPE
  HISPANIC OR LATINO                  1               25
  NOT HISPANIC OR LATINO             14              434
[1] 2 2
[1] FALSE

Clustering(43) Variable = ITGB1 MUTATION ANALYSIS
D43V1, survival
                 sevent
clus2               0   1
  ITGB1 MUTATED     7   6
  ITGB1 WILD-TYPE 286 211
  ITGB1 MUTATED ITGB1 WILD-TYPE 
             13             497 
  ITGB1 MUTATED ITGB1 WILD-TYPE 
              6             211 
$`ITGB1 MUTATED`
TCGA-BB-7871 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CR-7368 TCGA-CR-7380 TCGA-CV-6003 
       24.66        10.42         4.24        40.93        19.92        54.74 
TCGA-CV-6953 TCGA-CV-6962 TCGA-CV-7252 TCGA-D6-6516 TCGA-F7-A623 TCGA-HD-A6I0 
       53.95         4.14         4.96        25.41        20.25         6.90 
TCGA-QK-A6VB 
       21.07 

$`ITGB1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        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-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 
       36.72        33.70        50.20        66.28        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       20.52        25.71        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-4727 
        6.28        12.69        55.86        38.04         4.67        51.29 
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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       34.13         6.74         9.07         9.24        52.08        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        32.22        35.05        38.89         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       32.48        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-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       24.39        20.88        19.53        48.20        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
        2.93        54.58        70.45        62.37        45.99        11.21 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6223 
       41.19        15.75        32.38        32.88        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       56.58        13.25         4.24        14.99        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
       64.87        53.52        16.73        43.04        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       34.52        36.99        18.54        16.90         6.02        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-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
        9.17        34.06        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        29.82        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         7.10         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        87.55        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-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-7089 
       10.98         7.13         8.42        28.34         2.50        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      126.15       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        47.47        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        36.13        18.41        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       17.85       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-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-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 
       10.42        10.55        18.84        34.36        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        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       58.45        37.25        30.94        33.86        18.02        14.04 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       46.32        46.45        20.45        37.58        40.24        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       39.12        41.59        37.18        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-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       12.43        13.38        15.16        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65        34.75        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-A66S TCGA-KU-A66T 
       13.68        13.84        19.04        15.48        13.35        18.15 
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-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-A6VC TCGA-RS-A6TO 
       21.47         9.34        12.72        18.64        19.73        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI 
       16.96         6.87        15.91         7.10        32.45        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-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       48.03        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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       32.65         2.96        17.03        20.55        14.56 

  ITGB1 MUTATED ITGB1 WILD-TYPE 
           4.14            0.07 
  ITGB1 MUTATED ITGB1 WILD-TYPE 
          54.74          210.97 
  ITGB1 MUTATED ITGB1 WILD-TYPE 
          20.25           21.21 
[1] "4.1 - 54.7 (20.2)"  "0.1 - 211.0 (21.2)"
[1] "hr=" "1.4"
D43V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  ITGB1 MUTATED         1        0         3         8         1
  ITGB1 WILD-TYPE      24       75        79       240        10
D43V3, multiclass
           clus
vv          ITGB1 MUTATED ITGB1 WILD-TYPE
  STAGE I               1              24
  STAGE II              0              75
  STAGE III             3              79
  STAGE IVA             8             240
  STAGE IVB             1              10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ITGB1 MUTATED       2   1   3   7
  ITGB1 WILD-TYPE    46 133  96 161
D43V4, multiclass
       clus
vv      ITGB1 MUTATED ITGB1 WILD-TYPE
  T0+T1             2              46
  T2                1             133
  T3                3              96
  T4                7             161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ITGB1 MUTATED     6   3   3   0
  ITGB1 WILD-TYPE 169  64 159   7
D43V5, multiclass
    clus
vv   ITGB1 MUTATED ITGB1 WILD-TYPE
  N0             6             169
  N1             3              64
  N2             3             159
  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
  ITGB1 MUTATED     4   9
  ITGB1 WILD-TYPE 136 361
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB1 MUTATED      4    9
  ITGB1 WILD-TYPE  136  361
        clus
vv       ITGB1 MUTATED ITGB1 WILD-TYPE
  FEMALE             4             136
  MALE               9             361
[1] 2 2
[1] FALSE
D43V7, binary
                 cls
clus                0   1
  ITGB1 MUTATED     2   8
  ITGB1 WILD-TYPE 144 266
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB1 MUTATED      2    8
  ITGB1 WILD-TYPE  144  266
     clus
vv    ITGB1 MUTATED ITGB1 WILD-TYPE
  NO              2             144
  YES             8             266
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  ITGB1 MUTATED                                      13
  ITGB1 WILD-TYPE                                   489
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  ITGB1 MUTATED                                                             0
  ITGB1 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  ITGB1 MUTATED                                                     0
  ITGB1 WILD-TYPE                                                   7
D43V8, multiclass
                                                             clus
vv                                                            ITGB1 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  13
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
                                                             clus
vv                                                            ITGB1 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   489
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V9, continuous
D43V10, continuous
D43V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITGB1 MUTATED                                  0     0
  ITGB1 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ITGB1 MUTATED                           1    12
  ITGB1 WILD-TYPE                        36   434
D43V12, multiclass
                                  clus
vv                                 ITGB1 MUTATED ITGB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              36
  WHITE                                       12             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"
D43V13, binary
                 cls
clus                0   1
  ITGB1 MUTATED     1  12
  ITGB1 WILD-TYPE  25 436
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB1 MUTATED      1   12
  ITGB1 WILD-TYPE   25  436
                        clus
vv                       ITGB1 MUTATED ITGB1 WILD-TYPE
  HISPANIC OR LATINO                 1              25
  NOT HISPANIC OR LATINO            12             436
[1] 2 2
[1] FALSE

Clustering(44) Variable = IRS4 MUTATION ANALYSIS
D44V1, survival
                sevent
clus2              0   1
  IRS4 MUTATED     9   8
  IRS4 WILD-TYPE 284 209
  IRS4 MUTATED IRS4 WILD-TYPE 
            17            493 
  IRS4 MUTATED IRS4 WILD-TYPE 
             8            209 
$`IRS4 MUTATED`
TCGA-BA-6868 TCGA-CN-4741 TCGA-CR-7388 TCGA-CR-7398 TCGA-CV-6953 TCGA-CV-7245 
       15.52        73.61        27.06         5.13        53.95        26.20 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7427 TCGA-CV-7568 TCGA-CV-A468 TCGA-DQ-7593 
       17.13        47.97       156.49        30.48        15.25        40.24 
TCGA-F7-A50J TCGA-QK-A6IF TCGA-QK-A6V9 TCGA-TN-A7HL TCGA-UF-A7JJ 
       31.13        23.15        18.64        20.35        18.05 

$`IRS4 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       65.59        68.48        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        4.01        41.85        29.42        28.11        20.45        30.18 
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-BB-4217 TCGA-BB-4223 
        2.27        11.05        13.38        20.48         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       33.70        50.20        66.28        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       20.52        25.71        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-4727 
        6.28        12.69        55.86        38.04         4.67        51.29 
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-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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       32.22        35.05        38.89         3.68        17.42        32.48 
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-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        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-6221 TCGA-CQ-6222 
        4.24        41.19        15.75        32.38        32.88        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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
       70.13        64.87        53.52        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       43.10        77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
       39.52        34.52        36.99        18.54        16.90         6.02 
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-7389 TCGA-CR-7390 TCGA-CR-7391 
       17.13        32.78        47.01        12.89        29.82        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         7.10         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        87.55 
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-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
        6.08        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       126.15       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-7247 TCGA-CV-7250 
        4.73        47.47        36.00        31.36        18.97        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
        4.96        11.87         2.10        36.13        18.41        57.47 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       35.54        17.85       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-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       14.89        56.48         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-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-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-7082 TCGA-CX-7085 
       23.47        19.92        22.52        10.42        10.42        10.55 
TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       18.84        34.36        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        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       37.25        30.94        33.86        18.02        14.04        46.32 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       46.45        20.45        37.58        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V 
       37.18        21.63        20.25         3.02        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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       15.16        13.61        21.11        20.94         0.07        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       25.74        21.93        27.48        27.48        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 
       13.84        19.04        15.48        13.35        18.15        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-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-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-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       13.15        21.07        21.21         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       12.72        21.07        19.73        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 
       15.91         7.10        32.45        13.55        13.25        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        49.51        48.03        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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  IRS4 MUTATED IRS4 WILD-TYPE 
          5.13           0.07 
  IRS4 MUTATED IRS4 WILD-TYPE 
        156.49         210.97 
  IRS4 MUTATED IRS4 WILD-TYPE 
         26.20          21.07 
[1] "5.1 - 156.5 (26.2)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D44V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  IRS4 MUTATED         0        4         2         7         0
  IRS4 WILD-TYPE      25       71        80       241        11
D44V3, multiclass
           clus
vv          IRS4 MUTATED IRS4 WILD-TYPE
  STAGE I              0             25
  STAGE II             4             71
  STAGE III            2             80
  STAGE IVA            7            241
  STAGE IVB            0             11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  IRS4 MUTATED       0   4   3   6
  IRS4 WILD-TYPE    48 130  96 162
D44V4, multiclass
       clus
vv      IRS4 MUTATED IRS4 WILD-TYPE
  T0+T1            0             48
  T2               4            130
  T3               3             96
  T4               6            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
  IRS4 MUTATED     6   0   3   0
  IRS4 WILD-TYPE 169  67 159   7
D44V5, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  N0            6            169
  N1            0             67
  N2            3            159
  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
  IRS4 MUTATED     7  10
  IRS4 WILD-TYPE 133 360
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      7   10
  IRS4 WILD-TYPE  133  360
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  FEMALE            7            133
  MALE             10            360
[1] 2 2
[1] FALSE
D44V7, binary
                cls
clus               0   1
  IRS4 MUTATED     3   9
  IRS4 WILD-TYPE 143 265
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      3    9
  IRS4 WILD-TYPE  143  265
     clus
vv    IRS4 MUTATED IRS4 WILD-TYPE
  NO             3            143
  YES            9            265
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  IRS4 MUTATED                                      17
  IRS4 WILD-TYPE                                   485
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  IRS4 MUTATED                                                             0
  IRS4 WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  IRS4 MUTATED                                                     0
  IRS4 WILD-TYPE                                                   7
D44V8, multiclass
                                                             clus
vv                                                            IRS4 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                 17
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
                                                             clus
vv                                                            IRS4 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  485
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V9, continuous
D44V10, continuous
D44V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IRS4 MUTATED                                  0     0
  IRS4 WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IRS4 MUTATED                           2    13
  IRS4 WILD-TYPE                        35   433
D44V12, multiclass
                                  clus
vv                                 IRS4 MUTATED IRS4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   2             35
  WHITE                                      13            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"
D44V13, binary
                cls
clus               0   1
  IRS4 MUTATED     2  13
  IRS4 WILD-TYPE  24 435
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      2   13
  IRS4 WILD-TYPE   24  435
                        clus
vv                       IRS4 MUTATED IRS4 WILD-TYPE
  HISPANIC OR LATINO                2             24
  NOT HISPANIC OR LATINO           13            435
[1] 2 2
[1] FALSE

Clustering(45) Variable = SRPX MUTATION ANALYSIS
D45V1, survival
                sevent
clus2              0   1
  SRPX MUTATED     3   4
  SRPX WILD-TYPE 290 213
  SRPX MUTATED SRPX WILD-TYPE 
             7            503 
  SRPX MUTATED SRPX WILD-TYPE 
             4            213 
$`SRPX MUTATED`
TCGA-BA-4074 TCGA-BA-7269 TCGA-CN-4742 TCGA-CV-7425 TCGA-CV-7568 TCGA-F7-A620 
       15.19        41.85        13.05        56.48        30.48        17.85 
TCGA-MT-A67G 
        6.25 

$`SRPX WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
        9.30        13.64        37.28         9.07        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       42.35        57.93        17.10        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       68.48        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
        4.01        29.42        28.11        20.45        30.18        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-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       11.05        13.38        20.48         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       50.20        66.28        24.66        38.40        71.05        20.52 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       25.71        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
       12.69        55.86        38.04         4.67        51.29        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-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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        9.07         9.24        52.08        11.08        10.45        32.22 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       35.05        38.89         3.68        17.42        32.48        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-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        23.44        19.82        24.39        20.88 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       19.53        48.20        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-6221 TCGA-CQ-6222 TCGA-CQ-6223 
       41.19        15.75        32.38        32.88        66.28        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       56.58        13.25         4.24        14.99        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
       64.87        53.52        16.73        43.04        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       34.52        36.99        18.54        16.90         6.02        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        29.82        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         7.10         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 
       87.55        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       126.15 
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        47.47        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        36.13        18.41        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       17.85       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-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-A45O 
      153.86        16.64         6.38        22.19        35.93        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-7082 TCGA-CX-7085 
       23.47        19.92        22.52        10.42        10.42        10.55 
TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       18.84        34.36        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        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       37.25        30.94        33.86        18.02        14.04        46.32 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       46.45        20.45        37.58        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       41.59        37.18        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       18.94        24.95         0.46        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       13.38        15.16        13.61        21.11        20.94         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       28.47        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       22.03        12.66        22.85         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        3.65         6.90        34.75        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-A66S TCGA-KU-A66T 
       13.68        13.84        19.04        15.48        13.35        18.15 
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-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       12.62        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-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-RS-A6TO 
        9.34        12.72        18.64        21.07        19.73        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI 
       16.96         6.87        15.91         7.10        32.45        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-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       48.03        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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       32.65         2.96        17.03        20.55        14.56 

  SRPX MUTATED SRPX WILD-TYPE 
          6.25           0.07 
  SRPX MUTATED SRPX WILD-TYPE 
         56.48         210.97 
  SRPX MUTATED SRPX WILD-TYPE 
         17.85          21.17 
[1] "6.2 - 56.5 (17.9)"  "0.1 - 211.0 (21.2)"
[1] "hr=" "1.5"
D45V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  SRPX MUTATED         0        0         3         4         0
  SRPX WILD-TYPE      25       75        79       244        11
D45V3, multiclass
           clus
vv          SRPX MUTATED SRPX WILD-TYPE
  STAGE I              0             25
  STAGE II             0             75
  STAGE III            3             79
  STAGE IVA            4            244
  STAGE IVB            0             11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  SRPX MUTATED       1   2   2   2
  SRPX WILD-TYPE    47 132  97 166
D45V4, multiclass
       clus
vv      SRPX MUTATED SRPX WILD-TYPE
  T0+T1            1             47
  T2               2            132
  T3               2             97
  T4               2            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
  SRPX MUTATED     0   2   3   0
  SRPX WILD-TYPE 175  65 159   7
D45V5, multiclass
    clus
vv   SRPX MUTATED SRPX WILD-TYPE
  N0            0            175
  N1            2             65
  N2            3            159
  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
  SRPX MUTATED     4   3
  SRPX WILD-TYPE 136 367
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      4    3
  SRPX WILD-TYPE  136  367
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  FEMALE            4            136
  MALE              3            367
[1] 2 2
[1] FALSE
D45V7, binary
                cls
clus               0   1
  SRPX MUTATED     1   3
  SRPX WILD-TYPE 145 271
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      1    3
  SRPX WILD-TYPE  145  271
     clus
vv    SRPX MUTATED SRPX WILD-TYPE
  NO             1            145
  YES            3            271
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  SRPX MUTATED                                       7
  SRPX WILD-TYPE                                   495
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  SRPX MUTATED                                                             0
  SRPX WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  SRPX MUTATED                                                     0
  SRPX WILD-TYPE                                                   7
D45V8, multiclass
                                                             clus
vv                                                            SRPX MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  7
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
                                                             clus
vv                                                            SRPX WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  495
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V9, continuous
D45V10, continuous
D45V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SRPX MUTATED                                  0     0
  SRPX WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SRPX MUTATED                           0     7
  SRPX WILD-TYPE                        37   439
D45V12, multiclass
                                  clus
vv                                 SRPX MUTATED SRPX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             37
  WHITE                                       7            439
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V13, binary
                cls
clus               0   1
  SRPX MUTATED     0   7
  SRPX WILD-TYPE  26 441
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      0    7
  SRPX WILD-TYPE   26  441
                        clus
vv                       SRPX MUTATED SRPX WILD-TYPE
  HISPANIC OR LATINO                0             26
  NOT HISPANIC OR LATINO            7            441
[1] 2 2
[1] FALSE

Clustering(46) Variable = KIAA1949 MUTATION ANALYSIS
D46V1, survival
                    sevent
clus2                  0   1
  KIAA1949 MUTATED     5   1
  KIAA1949 WILD-TYPE 288 216
  KIAA1949 MUTATED KIAA1949 WILD-TYPE 
                 6                504 
  KIAA1949 MUTATED KIAA1949 WILD-TYPE 
                 1                216 
$`KIAA1949 MUTATED`
TCGA-CQ-7063 TCGA-CQ-7072 TCGA-CV-6961 TCGA-DQ-7589 TCGA-F7-A624 TCGA-QK-A6VB 
       70.13        77.56         2.50        46.32        12.43        21.07 

$`KIAA1949 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        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-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       36.72        33.70        50.20        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       71.05        20.52        25.71        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-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       51.29        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-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        34.13         6.74         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       11.08        10.45        32.22        35.05        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        32.48        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-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       19.82        24.39        20.88        19.53        48.20        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-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.88        66.28        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       14.99        38.76        64.87        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
       39.52        34.52        36.99        18.54        16.90         6.02 
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        29.82 
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         7.10 
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        87.55        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       126.15 
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        47.47        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        36.13        18.41        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       17.85       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-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-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 
       10.42        10.55        18.84        34.36        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-5629 TCGA-DQ-5630 TCGA-DQ-5631 
       11.11        58.45        37.25        30.94        33.86        18.02 
TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       14.04        46.45        20.45        37.58        40.24        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       39.12        41.59        37.18        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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       20.25        13.38        15.16        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
        4.27         3.65         6.90        34.75        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-A66S 
        5.29        13.68        13.84        19.04        15.48        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        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-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       17.98        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        18.64        19.73 
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-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-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       49.51        48.03        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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36        32.65         2.96        17.03        20.55        14.56 

  KIAA1949 MUTATED KIAA1949 WILD-TYPE 
              2.50               0.07 
  KIAA1949 MUTATED KIAA1949 WILD-TYPE 
             77.56             210.97 
  KIAA1949 MUTATED KIAA1949 WILD-TYPE 
            33.695             21.140 
[1] "2.5 - 77.6 (33.7)"  "0.1 - 211.0 (21.1)"
[1] "hr=" "3.1"
D46V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  KIAA1949 MUTATED         1        3         0         1         0
  KIAA1949 WILD-TYPE      24       72        82       247        11
D46V3, multiclass
           clus
vv          KIAA1949 MUTATED KIAA1949 WILD-TYPE
  STAGE I                  1                 24
  STAGE II                 3                 72
  STAGE III                0                 82
  STAGE IVA                1                247
  STAGE IVB                0                 11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA1949 MUTATED       1   3   0   1
  KIAA1949 WILD-TYPE    47 131  99 167
D46V4, multiclass
       clus
vv      KIAA1949 MUTATED KIAA1949 WILD-TYPE
  T0+T1                1                 47
  T2                   3                131
  T3                   0                 99
  T4                   1                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
  KIAA1949 MUTATED     3   0   0   0
  KIAA1949 WILD-TYPE 172  67 162   7
D46V5, multiclass
    clus
vv   KIAA1949 MUTATED KIAA1949 WILD-TYPE
  N0                3                172
  N1                0                 67
  N2                0                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"
D46V6, binary
                    cls
clus                   0   1
  KIAA1949 MUTATED     1   5
  KIAA1949 WILD-TYPE 139 365
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1949 MUTATED      1    5
  KIAA1949 WILD-TYPE  139  365
        clus
vv       KIAA1949 MUTATED KIAA1949 WILD-TYPE
  FEMALE                1                139
  MALE                  5                365
[1] 2 2
[1] FALSE
D46V7, binary
                    cls
clus                   0   1
  KIAA1949 MUTATED     2   4
  KIAA1949 WILD-TYPE 144 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1949 MUTATED      2    4
  KIAA1949 WILD-TYPE  144  270
     clus
vv    KIAA1949 MUTATED KIAA1949 WILD-TYPE
  NO                 2                144
  YES                4                270
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  KIAA1949 MUTATED                                       6
  KIAA1949 WILD-TYPE                                   496
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  KIAA1949 MUTATED                                                             0
  KIAA1949 WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  KIAA1949 MUTATED                                                     0
  KIAA1949 WILD-TYPE                                                   7
D46V8, multiclass
                                                             clus
vv                                                            KIAA1949 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      6
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            KIAA1949 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      496
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V9, continuous
D46V10, continuous
D46V11, continuous
[1] "Remove cluster labels:" "KIAA1949 MUTATED"      
clus
  KIAA1949 MUTATED KIAA1949 WILD-TYPE 
                 2                398 
        TCGA-BA-4074         TCGA-BA-4075         TCGA-BA-4078 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-BA-5149         TCGA-BA-5151         TCGA-BA-5152 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-BA-5555         TCGA-BA-5556         TCGA-BA-5557 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-BA-5558         TCGA-BA-5559         TCGA-BA-6869 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-BA-6872         TCGA-BA-6873         TCGA-BA-7269 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-BA-A4IG         TCGA-BA-A4IH         TCGA-BA-A4II 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-BA-A6D8         TCGA-BA-A6DA         TCGA-BA-A6DB 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-BA-A6DD         TCGA-BA-A6DE         TCGA-BA-A6DF 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-BA-A6DJ         TCGA-BB-7861         TCGA-BB-7862 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-BB-7863         TCGA-BB-7864         TCGA-BB-7870 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-BB-7871         TCGA-BB-7872         TCGA-BB-8601 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-BB-A5HU         TCGA-BB-A5HY         TCGA-BB-A5HZ 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-C9-A47Z         TCGA-CN-4723         TCGA-CN-4725 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-4726         TCGA-CN-4727         TCGA-CN-4728 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-4729         TCGA-CN-4730         TCGA-CN-4731 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-4733         TCGA-CN-4734         TCGA-CN-4735 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-4737         TCGA-CN-4738         TCGA-CN-4739 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-4740         TCGA-CN-4741         TCGA-CN-4742 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-5355         TCGA-CN-5356         TCGA-CN-5358 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-5359         TCGA-CN-5360         TCGA-CN-5361 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-5363         TCGA-CN-5364         TCGA-CN-5365 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-5366         TCGA-CN-5367         TCGA-CN-5369 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-5370         TCGA-CN-5373         TCGA-CN-6010 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-6011         TCGA-CN-6012         TCGA-CN-6013 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-6016         TCGA-CN-6017         TCGA-CN-6018 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-6019         TCGA-CN-6020         TCGA-CN-6022 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-6023         TCGA-CN-6024         TCGA-CN-6988 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-6989         TCGA-CN-6992         TCGA-CN-6994 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-6995         TCGA-CN-6996         TCGA-CN-6997 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-6998         TCGA-CN-A497         TCGA-CN-A498 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-A499         TCGA-CN-A49A         TCGA-CN-A49B 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-A63T         TCGA-CN-A63U         TCGA-CN-A63V 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-A63W         TCGA-CN-A63Y         TCGA-CN-A640 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-A641         TCGA-CN-A642         TCGA-CN-A6UY 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CN-A6V1         TCGA-CN-A6V3         TCGA-CN-A6V6 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CQ-5323         TCGA-CQ-5324         TCGA-CQ-5325 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CQ-5326         TCGA-CQ-5327         TCGA-CQ-5329 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CQ-5330         TCGA-CQ-5332         TCGA-CQ-5333 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CQ-5334         TCGA-CQ-6218         TCGA-CQ-6219 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CQ-6220         TCGA-CQ-6222         TCGA-CQ-6223 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CQ-6224         TCGA-CQ-6225         TCGA-CQ-6227 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CQ-6228         TCGA-CQ-6229         TCGA-CQ-7064 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CQ-7065         TCGA-CQ-7067         TCGA-CQ-7068 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CQ-7069         TCGA-CQ-7071         TCGA-CQ-A4C6 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CQ-A4C7         TCGA-CQ-A4C9         TCGA-CQ-A4CB 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CQ-A4CD         TCGA-CQ-A4CE         TCGA-CQ-A4CG 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CQ-A4CH         TCGA-CQ-A4CI         TCGA-CR-6467 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CR-6470         TCGA-CR-6471         TCGA-CR-6474 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CR-6484         TCGA-CR-6488         TCGA-CR-6491 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CR-6492         TCGA-CR-6493         TCGA-CR-7364 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CR-7365         TCGA-CR-7367         TCGA-CR-7368 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CR-7369         TCGA-CR-7371         TCGA-CR-7372 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CR-7373         TCGA-CR-7376         TCGA-CR-7377 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CR-7379         TCGA-CR-7380         TCGA-CR-7382 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CR-7383         TCGA-CR-7386         TCGA-CR-7390 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CR-7391         TCGA-CR-7392         TCGA-CR-7393 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CR-7394         TCGA-CR-7397         TCGA-CR-7398 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CR-7399         TCGA-CR-7401         TCGA-CV-5430 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-5431         TCGA-CV-5432         TCGA-CV-5434 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-5435         TCGA-CV-5436         TCGA-CV-5439 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-5440         TCGA-CV-5441         TCGA-CV-5442 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-5443         TCGA-CV-5444         TCGA-CV-5966 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-5970         TCGA-CV-5971         TCGA-CV-5973 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-5976         TCGA-CV-5977         TCGA-CV-5978 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-5979         TCGA-CV-6003         TCGA-CV-6433 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-6436         TCGA-CV-6441         TCGA-CV-6933 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-6934         TCGA-CV-6935         TCGA-CV-6936 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-6939         TCGA-CV-6940         TCGA-CV-6941 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-6945         TCGA-CV-6948         TCGA-CV-6950 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-6951         TCGA-CV-6952         TCGA-CV-6953 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-6954         TCGA-CV-6956         TCGA-CV-6959 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-6960         TCGA-CV-7089         TCGA-CV-7091 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-7095         TCGA-CV-7101         TCGA-CV-7102 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-7103         TCGA-CV-7104         TCGA-CV-7178 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-7180         TCGA-CV-7183         TCGA-CV-7236 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-7242         TCGA-CV-7243         TCGA-CV-7245 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-7248         TCGA-CV-7252         TCGA-CV-7254 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-7261         TCGA-CV-7406         TCGA-CV-7409 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-7410         TCGA-CV-7411         TCGA-CV-7414 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-7415         TCGA-CV-7418         TCGA-CV-7421 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-7422         TCGA-CV-7424         TCGA-CV-7429 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-7430         TCGA-CV-7432         TCGA-CV-7433 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-7434         TCGA-CV-7435         TCGA-CV-7446 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-A45O         TCGA-CV-A45P         TCGA-CV-A45Q 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-A45R         TCGA-CV-A45T         TCGA-CV-A45U 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-A45W         TCGA-CV-A45X         TCGA-CV-A45Y 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-A45Z         TCGA-CV-A460         TCGA-CV-A461 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-A463         TCGA-CV-A464         TCGA-CV-A465 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-A468         TCGA-CV-A6JD         TCGA-CV-A6JE 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-A6JM         TCGA-CV-A6JN         TCGA-CV-A6JO 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-A6JT         TCGA-CV-A6JU         TCGA-CV-A6JY 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-A6JZ         TCGA-CV-A6K0         TCGA-CV-A6K1 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CV-A6K2         TCGA-CX-7082         TCGA-CX-7085 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-CX-7086         TCGA-CX-7219         TCGA-CX-A4AQ 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-D6-6516         TCGA-D6-6517         TCGA-D6-6823 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-D6-6825         TCGA-D6-6826         TCGA-D6-8568 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-D6-8569         TCGA-D6-A4Z9         TCGA-D6-A4ZB 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-D6-A6EK         TCGA-D6-A6EM         TCGA-D6-A6EN 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-D6-A6EO         TCGA-D6-A6EP         TCGA-D6-A6EQ 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-D6-A6ES         TCGA-D6-A74Q         TCGA-DQ-5624 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-DQ-5625         TCGA-DQ-5629         TCGA-DQ-5630 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-DQ-5631         TCGA-DQ-7588         TCGA-DQ-7592 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-F7-7848         TCGA-F7-A50G         TCGA-F7-A50J 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-F7-A61S         TCGA-F7-A61V         TCGA-F7-A61W 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-F7-A620         TCGA-F7-A623         TCGA-H7-7774 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-H7-8501         TCGA-H7-A6C4         TCGA-H7-A6C5 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-H7-A76A         TCGA-HD-7754         TCGA-HD-7831 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-HD-7832         TCGA-HD-7917         TCGA-HD-8224 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-HD-8314         TCGA-HD-8634         TCGA-HD-8635 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-HD-A4C1         TCGA-HD-A633         TCGA-HD-A634 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-HD-A6HZ         TCGA-HD-A6I0         TCGA-IQ-7630 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-IQ-7631         TCGA-IQ-7632         TCGA-IQ-A61E 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-IQ-A61G         TCGA-IQ-A61H         TCGA-IQ-A61I 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-IQ-A61J         TCGA-IQ-A61K         TCGA-IQ-A61L 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-IQ-A61O         TCGA-IQ-A6SG         TCGA-IQ-A6SH 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-KU-A66S         TCGA-KU-A66T         TCGA-KU-A6H7 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-KU-A6H8         TCGA-MT-A51X         TCGA-MT-A67A 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-MT-A67D         TCGA-MT-A67F         TCGA-MT-A67G 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-MZ-A7D7         TCGA-P3-A5Q6         TCGA-P3-A5QE 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-P3-A5QF         TCGA-P3-A6SX         TCGA-P3-A6T0 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-P3-A6T2         TCGA-P3-A6T3         TCGA-P3-A6T4 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-P3-A6T5         TCGA-P3-A6T7         TCGA-P3-A6T8 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-QK-A652         TCGA-QK-A6IG         TCGA-QK-A6IH 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-QK-A6II         TCGA-QK-A6IJ         TCGA-QK-A6VC 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-RS-A6TO         TCGA-T2-A6WX         TCGA-T2-A6WZ 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-T2-A6X0         TCGA-TN-A7HI         TCGA-TN-A7HJ 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-TN-A7HL         TCGA-UF-A718         TCGA-UF-A719 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-UF-A71A         TCGA-UF-A71B         TCGA-UF-A71D 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-UF-A71E         TCGA-UF-A7J9         TCGA-UF-A7JA 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-UF-A7JC         TCGA-UF-A7JD         TCGA-UF-A7JF 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-UF-A7JH         TCGA-UF-A7JJ         TCGA-UF-A7JK 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-UF-A7JO         TCGA-UF-A7JS         TCGA-UF-A7JT 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
        TCGA-UF-A7JV         TCGA-UP-A6WW 
"KIAA1949 WILD-TYPE" "KIAA1949 WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1949 MUTATED                                  0     0
  KIAA1949 WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1949 MUTATED                           0     6
  KIAA1949 WILD-TYPE                        37   440
D46V12, multiclass
                                  clus
vv                                 KIAA1949 MUTATED KIAA1949 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 37
  WHITE                                           6                440
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V13, binary
                    cls
clus                   0   1
  KIAA1949 MUTATED     0   6
  KIAA1949 WILD-TYPE  26 442
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1949 MUTATED      0    6
  KIAA1949 WILD-TYPE   26  442
                        clus
vv                       KIAA1949 MUTATED KIAA1949 WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO                6                442
[1] 2 2
[1] FALSE

Clustering(47) Variable = NOTCH2 MUTATION ANALYSIS
D47V1, survival
                  sevent
clus2                0   1
  NOTCH2 MUTATED     8  12
  NOTCH2 WILD-TYPE 285 205
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
              20              490 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
              12              205 
$`NOTCH2 MUTATED`
TCGA-BA-6870 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-6018 TCGA-CN-6989 TCGA-CN-A498 
       14.83         4.67        51.29        19.07        32.22        25.41 
TCGA-CR-7364 TCGA-CR-7383 TCGA-CR-7394 TCGA-CV-6003 TCGA-CV-6937 TCGA-CV-7178 
       47.18        17.13        44.25        54.74        20.52        71.21 
TCGA-CV-7427 TCGA-CV-7568 TCGA-CV-A45P TCGA-CX-A4AQ TCGA-DQ-5631 TCGA-MT-A67A 
      156.49        30.48        21.01        51.12        18.02        30.05 
TCGA-P3-A6SX TCGA-P3-A6T0 
       47.01        19.00 

$`NOTCH2 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 
       65.59        68.48        15.52        21.17         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        4.01        41.85        29.42        28.11        20.45        30.18 
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-BB-4217 TCGA-BB-4223 
        2.27        11.05        13.38        20.48         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       33.70        50.20        66.28        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       20.52        25.71        10.55        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4729 
        6.28        12.69        55.86        38.04        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-6019 TCGA-CN-6020 TCGA-CN-6021 
       23.90        47.44        28.04        34.13         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 
        9.24        52.08        11.08        10.45        35.05        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 
        3.68        17.42        32.48        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-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       19.82        24.39        20.88        19.53        48.20        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-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.88        66.28        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
       14.99        38.76        70.13        64.87        53.52        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       43.04        41.88        43.10        77.56        44.48        11.61 
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-6472 TCGA-CR-6473 TCGA-CR-6474 
       58.42        50.01        39.52        34.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       16.90         6.02        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-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-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       26.17        32.78        47.01        27.06        12.89        29.82 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       30.02        46.85        32.65        30.58         7.10         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 
       87.55        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-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
        5.46         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       126.15       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-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       12.92        21.80        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 
       47.47        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        36.13 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       18.41        57.47        35.54        17.85       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-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-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-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-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        34.36        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        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 
       58.45        37.25        30.94        33.86        14.04        46.32 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       46.45        20.45        37.58        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       41.59        37.18        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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       12.43        13.38        15.16        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
        4.27         3.65         6.90        34.75        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-A66S 
        5.29        13.68        13.84        19.04        15.48        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D 
       18.15        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-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T2 
       15.78        71.74        51.25        10.85        36.82        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-RS-A6TO TCGA-RS-A6TP 
       12.72        18.64        21.07        19.73        12.72        16.96 
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-A71D 
       20.35        64.80        54.67         2.83        49.51        48.03 
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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        17.03        20.55        14.56 

  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
            4.67             0.07 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
          156.49           210.97 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
          30.265           21.070 
[1] "4.7 - 156.5 (30.3)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D47V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  NOTCH2 MUTATED         3        2         4         9         0
  NOTCH2 WILD-TYPE      22       73        78       239        11
D47V3, multiclass
           clus
vv          NOTCH2 MUTATED NOTCH2 WILD-TYPE
  STAGE I                3               22
  STAGE II               2               73
  STAGE III              4               78
  STAGE IVA              9              239
  STAGE IVB              0               11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  NOTCH2 MUTATED       3   5   4   6
  NOTCH2 WILD-TYPE    45 129  95 162
D47V4, multiclass
       clus
vv      NOTCH2 MUTATED NOTCH2 WILD-TYPE
  T0+T1              3               45
  T2                 5              129
  T3                 4               95
  T4                 6              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
  NOTCH2 MUTATED     9   2   5   0
  NOTCH2 WILD-TYPE 166  65 157   7
D47V5, multiclass
    clus
vv   NOTCH2 MUTATED NOTCH2 WILD-TYPE
  N0              9              166
  N1              2               65
  N2              5              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"
D47V6, binary
                  cls
clus                 0   1
  NOTCH2 MUTATED    11   9
  NOTCH2 WILD-TYPE 129 361
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED     11    9
  NOTCH2 WILD-TYPE  129  361
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  FEMALE             11              129
  MALE                9              361
[1] 2 2
[1] FALSE
D47V7, binary
                  cls
clus                 0   1
  NOTCH2 MUTATED     6   9
  NOTCH2 WILD-TYPE 140 265
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      6    9
  NOTCH2 WILD-TYPE  140  265
     clus
vv    NOTCH2 MUTATED NOTCH2 WILD-TYPE
  NO               6              140
  YES              9              265
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  NOTCH2 MUTATED                                      20
  NOTCH2 WILD-TYPE                                   482
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  NOTCH2 MUTATED                                                             0
  NOTCH2 WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  NOTCH2 MUTATED                                                     0
  NOTCH2 WILD-TYPE                                                   7
D47V8, multiclass
                                                             clus
vv                                                            NOTCH2 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   20
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
                                                             clus
vv                                                            NOTCH2 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    482
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V9, continuous
D47V10, continuous
D47V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOTCH2 MUTATED                                  0     0
  NOTCH2 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NOTCH2 MUTATED                           1    19
  NOTCH2 WILD-TYPE                        36   427
D47V12, multiclass
                                  clus
vv                                 NOTCH2 MUTATED NOTCH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               36
  WHITE                                        19              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"
D47V13, binary
                  cls
clus                 0   1
  NOTCH2 MUTATED     0  20
  NOTCH2 WILD-TYPE  26 428
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      0   20
  NOTCH2 WILD-TYPE   26  428
                        clus
vv                       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  HISPANIC OR LATINO                  0               26
  NOT HISPANIC OR LATINO             20              428
[1] 2 2
[1] FALSE

Clustering(48) Variable = GAGE2A MUTATION ANALYSIS
D48V1, survival
                  sevent
clus2                0   1
  GAGE2A MUTATED     1   4
  GAGE2A WILD-TYPE 292 213
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               5              505 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               4              213 
$`GAGE2A MUTATED`
TCGA-CQ-6221 TCGA-CV-5434 TCGA-CV-7409 TCGA-CV-7430 TCGA-CV-A45W 
       32.88       108.95        17.85        16.27        45.96 

$`GAGE2A WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        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-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       36.72        33.70        50.20        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       71.05        20.52        25.71        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-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       51.29        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-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        34.13         6.74         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       11.08        10.45        32.22        35.05        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        32.48        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-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       19.82        24.39        20.88        19.53        48.20        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-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       38.76        70.13        64.87        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        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-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       50.01        39.52        34.52        36.99        18.54        16.90 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        6.02        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-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 
       29.82        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         5.13         5.95        35.41        29.95        48.39 
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-5444 TCGA-CV-5966 
      107.51        87.55        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 
      126.15       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        47.47        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        36.13        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-7432 TCGA-CV-7433 TCGA-CV-7434 
       56.48       156.49         3.52        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-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-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-7082 TCGA-CX-7085 
       23.47        19.92        22.52        10.42        10.42        10.55 
TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       18.84        34.36        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        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       37.25        30.94        33.86        18.02        14.04        46.32 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       46.45        20.45        37.58        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       41.59        37.18        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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       12.43        13.38        15.16        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
        4.27         3.65         6.90        34.75        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-A66S 
        5.29        13.68        13.84        19.04        15.48        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        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-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       17.98        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        18.64        21.07 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       19.73        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       32.45        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        49.51        48.03        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-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  GAGE2A MUTATED GAGE2A WILD-TYPE 
           16.27             0.07 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
          108.95           210.97 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
           32.88            21.11 
[1] "16.3 - 109.0 (32.9)" "0.1 - 211.0 (21.1)" 
[1] "hr=" "1.3"
D48V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  GAGE2A MUTATED         0        1         0         2         1
  GAGE2A WILD-TYPE      25       74        82       246        10
D48V3, multiclass
           clus
vv          GAGE2A MUTATED GAGE2A WILD-TYPE
  STAGE I                0               25
  STAGE II               1               74
  STAGE III              0               82
  STAGE IVA              2              246
  STAGE IVB              1               10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  GAGE2A MUTATED       0   2   0   3
  GAGE2A WILD-TYPE    48 132  99 165
D48V4, multiclass
       clus
vv      GAGE2A MUTATED GAGE2A WILD-TYPE
  T0+T1              0               48
  T2                 2              132
  T3                 0               99
  T4                 3              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
  GAGE2A MUTATED     2   0   1   1
  GAGE2A WILD-TYPE 173  67 161   6
D48V5, multiclass
    clus
vv   GAGE2A MUTATED GAGE2A WILD-TYPE
  N0              2              173
  N1              0               67
  N2              1              161
  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"
D48V6, binary
                  cls
clus                 0   1
  GAGE2A MUTATED     0   5
  GAGE2A WILD-TYPE 140 365
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      0    5
  GAGE2A WILD-TYPE  140  365
        clus
vv       GAGE2A MUTATED GAGE2A WILD-TYPE
  FEMALE              0              140
  MALE                5              365
[1] 2 2
[1] FALSE
D48V7, binary
                  cls
clus                 0   1
  GAGE2A MUTATED     3   1
  GAGE2A WILD-TYPE 143 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      3    1
  GAGE2A WILD-TYPE  143  273
     clus
vv    GAGE2A MUTATED GAGE2A WILD-TYPE
  NO               3              143
  YES              1              273
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  GAGE2A MUTATED                                       5
  GAGE2A WILD-TYPE                                   497
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  GAGE2A MUTATED                                                             0
  GAGE2A WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  GAGE2A MUTATED                                                     0
  GAGE2A WILD-TYPE                                                   7
D48V8, multiclass
                                                             clus
vv                                                            GAGE2A MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    5
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      0
                                                             clus
vv                                                            GAGE2A WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    497
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V9, continuous
[1] "Remove cluster labels:" "GAGE2A MUTATED"        
clus
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               2              284 
      TCGA-BA-4074       TCGA-BA-4075       TCGA-BA-4076       TCGA-BA-4077 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BA-4078       TCGA-BA-5149       TCGA-BA-5151       TCGA-BA-5555 
"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-6871       TCGA-BA-6872       TCGA-BA-6873       TCGA-BA-7269 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BA-A4IF       TCGA-BA-A4IH       TCGA-BA-A4II       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-BB-4217 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BB-4225       TCGA-BB-4227       TCGA-BB-4228       TCGA-BB-7862 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BB-7864       TCGA-BB-7870       TCGA-BB-7871       TCGA-BB-8596 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BB-A5HY       TCGA-BB-A6UM       TCGA-BB-A6UO       TCGA-CN-4726 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-4727       TCGA-CN-4728       TCGA-CN-4729       TCGA-CN-4730 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-4731       TCGA-CN-4735       TCGA-CN-4736       TCGA-CN-4738 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-4739       TCGA-CN-4740       TCGA-CN-4741       TCGA-CN-4742 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-5355       TCGA-CN-5358       TCGA-CN-5359       TCGA-CN-5360 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-5361       TCGA-CN-5363       TCGA-CN-5365       TCGA-CN-5366 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-5367       TCGA-CN-5373       TCGA-CN-5374       TCGA-CN-6010 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-6011       TCGA-CN-6012       TCGA-CN-6016       TCGA-CN-6017 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-6019       TCGA-CN-6021       TCGA-CN-6023       TCGA-CN-6024 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-6988       TCGA-CN-6989       TCGA-CN-6992       TCGA-CN-6994 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-6997       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-A6V3 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-A6V6       TCGA-CQ-5323       TCGA-CQ-5324       TCGA-CQ-5325 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-5326       TCGA-CQ-5330       TCGA-CQ-5331       TCGA-CQ-5332 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-5333       TCGA-CQ-6218       TCGA-CQ-6219       TCGA-CQ-6222 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-6223       TCGA-CQ-6224       TCGA-CQ-6227       TCGA-CQ-6228 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-7063       TCGA-CQ-7072       TCGA-CQ-A4C6       TCGA-CQ-A4C7 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-A4C9       TCGA-CQ-A4CB       TCGA-CQ-A4CG       TCGA-CQ-A4CI 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-5247       TCGA-CR-5248       TCGA-CR-5250       TCGA-CR-6467 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-6471       TCGA-CR-6473       TCGA-CR-6474       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-7367       TCGA-CR-7368       TCGA-CR-7369 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7370       TCGA-CR-7371       TCGA-CR-7373       TCGA-CR-7374 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7376       TCGA-CR-7377       TCGA-CR-7379       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-7392       TCGA-CR-7394       TCGA-CR-7395 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7398       TCGA-CR-7399       TCGA-CR-7401       TCGA-CR-7402 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-6436       TCGA-CV-6441       TCGA-CV-6933       TCGA-CV-6934 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-6940       TCGA-CV-6941       TCGA-CV-6945       TCGA-CV-6952 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-6961       TCGA-CV-7095       TCGA-CV-7097       TCGA-CV-7235 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7242       TCGA-CV-7245       TCGA-CV-7248       TCGA-CV-7250 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7254       TCGA-CV-7261       TCGA-CV-7263       TCGA-CV-7406 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7410       TCGA-CV-7418       TCGA-CV-7422       TCGA-CV-7424 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7427       TCGA-CV-7432       TCGA-CV-7433       TCGA-CV-7434 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7440       TCGA-CV-7446       TCGA-CV-7568       TCGA-CV-A45Y 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-A45Z       TCGA-CV-A460       TCGA-CV-A464       TCGA-CV-A468 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-A6JD       TCGA-CV-A6JN       TCGA-CV-A6JO       TCGA-CV-A6JU 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-A6JZ       TCGA-CV-A6K1       TCGA-CV-A6K2       TCGA-CX-7082 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CX-7085       TCGA-CX-7086       TCGA-CX-7219       TCGA-CX-A4AQ 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-D6-6516       TCGA-D6-6517       TCGA-D6-6823       TCGA-D6-6824 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-D6-6825       TCGA-D6-6827       TCGA-D6-8568       TCGA-D6-8569 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-D6-A4Z9       TCGA-D6-A4ZB       TCGA-D6-A6EK       TCGA-D6-A6EP 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-DQ-5625       TCGA-DQ-5629       TCGA-DQ-5630       TCGA-DQ-5631 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-DQ-7588       TCGA-DQ-7589       TCGA-DQ-7590       TCGA-DQ-7591 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-DQ-7592       TCGA-DQ-7593       TCGA-DQ-7595       TCGA-F7-7848 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-F7-8489       TCGA-F7-A50G       TCGA-F7-A50I       TCGA-F7-A50J 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-F7-A61S       TCGA-F7-A61V       TCGA-F7-A61W       TCGA-F7-A620 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-F7-A623       TCGA-H7-7774       TCGA-H7-A6C4       TCGA-H7-A6C5 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-HD-7753       TCGA-HD-7754       TCGA-HD-7832       TCGA-HD-8634 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-HD-8635       TCGA-HD-A634       TCGA-HD-A6I0       TCGA-HL-7533 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-IQ-7631       TCGA-IQ-7632       TCGA-IQ-A61E       TCGA-IQ-A61G 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-IQ-A61H       TCGA-IQ-A61K       TCGA-IQ-A6SH       TCGA-KU-A66S 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-KU-A6H7       TCGA-KU-A6H8       TCGA-MT-A51W       TCGA-MT-A51X 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-MT-A67D       TCGA-MZ-A6I9       TCGA-MZ-A7D7       TCGA-P3-A5Q6 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-P3-A6SW       TCGA-P3-A6SX       TCGA-P3-A6T0       TCGA-P3-A6T4 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-P3-A6T5       TCGA-P3-A6T7       TCGA-P3-A6T8       TCGA-QK-A6IG 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-QK-A6II       TCGA-QK-A6IJ       TCGA-RS-A6TP       TCGA-T2-A6WZ 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-T2-A6X0       TCGA-T2-A6X2       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-A71D       TCGA-UF-A7J9 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-UF-A7JC       TCGA-UF-A7JD       TCGA-UF-A7JF       TCGA-UF-A7JH 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-UF-A7JJ       TCGA-UF-A7JS       TCGA-WA-A7GZ       TCGA-WA-A7H4 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
D48V10, continuous
[1] "Remove cluster labels:" "GAGE2A MUTATED"        
clus
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               2              272 
      TCGA-BA-4074       TCGA-BA-4075       TCGA-BA-4076       TCGA-BA-4077 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BA-4078       TCGA-BA-5149       TCGA-BA-5151       TCGA-BA-5556 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-BA-6868       TCGA-BA-6869       TCGA-BA-6870       TCGA-BA-6871 
"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-BB-4225       TCGA-BB-4228       TCGA-BB-7871 
"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-4727       TCGA-CN-4728       TCGA-CN-4730       TCGA-CN-4736 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-4738       TCGA-CN-4739       TCGA-CN-4741       TCGA-CN-4742 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-5358       TCGA-CN-5359       TCGA-CN-5360       TCGA-CN-5361 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-5363       TCGA-CN-5365       TCGA-CN-5366       TCGA-CN-5367 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-5370       TCGA-CN-6010       TCGA-CN-6011       TCGA-CN-6012 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-6016       TCGA-CN-6017       TCGA-CN-6021       TCGA-CN-6023 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-6024       TCGA-CN-6989       TCGA-CN-6992       TCGA-CN-6994 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CN-6997       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-A6UY       TCGA-CN-A6V3       TCGA-CN-A6V6 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-5323       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-7063       TCGA-CQ-7072       TCGA-CQ-A4C6 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CQ-A4C7       TCGA-CQ-A4C9       TCGA-CQ-A4CB       TCGA-CQ-A4CI 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-5247       TCGA-CR-5248       TCGA-CR-5250       TCGA-CR-6467 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-6471       TCGA-CR-6473       TCGA-CR-6474       TCGA-CR-6477 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-6478       TCGA-CR-6482       TCGA-CR-6487       TCGA-CR-6491 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-6492       TCGA-CR-6493       TCGA-CR-7364       TCGA-CR-7365 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7367       TCGA-CR-7368       TCGA-CR-7369       TCGA-CR-7370 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7371       TCGA-CR-7373       TCGA-CR-7374       TCGA-CR-7376 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7377       TCGA-CR-7383       TCGA-CR-7385       TCGA-CR-7386 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7388       TCGA-CR-7389       TCGA-CR-7390       TCGA-CR-7391 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7392       TCGA-CR-7394       TCGA-CR-7395       TCGA-CR-7397 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CR-7399       TCGA-CR-7401       TCGA-CR-7402       TCGA-CV-5430 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-5431       TCGA-CV-5432       TCGA-CV-5435       TCGA-CV-5436 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-5440       TCGA-CV-5443       TCGA-CV-5966       TCGA-CV-5970 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-5976       TCGA-CV-6433       TCGA-CV-6436       TCGA-CV-6441 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-6934       TCGA-CV-6935       TCGA-CV-6936       TCGA-CV-6940 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-6941       TCGA-CV-6943       TCGA-CV-6945       TCGA-CV-6952 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-6954       TCGA-CV-6960       TCGA-CV-6961       TCGA-CV-7091 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7095       TCGA-CV-7097       TCGA-CV-7099       TCGA-CV-7100 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7101       TCGA-CV-7102       TCGA-CV-7180       TCGA-CV-7183 
"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-7406 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7410       TCGA-CV-7418       TCGA-CV-7422       TCGA-CV-7424 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7427       TCGA-CV-7432       TCGA-CV-7433       TCGA-CV-7434 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-7435       TCGA-CV-7440       TCGA-CV-7446       TCGA-CV-7568 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-A45Q       TCGA-CV-A45Y       TCGA-CV-A45Z       TCGA-CV-A460 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-A461       TCGA-CV-A464       TCGA-CV-A468       TCGA-CV-A6JD 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-A6JE       TCGA-CV-A6JN       TCGA-CV-A6JO       TCGA-CV-A6JU 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CV-A6JY       TCGA-CV-A6JZ       TCGA-CV-A6K1       TCGA-CV-A6K2 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CX-7086       TCGA-CX-7219       TCGA-D6-6516       TCGA-D6-6517 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-D6-6823       TCGA-D6-6824       TCGA-D6-6825       TCGA-D6-6827 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-D6-8568       TCGA-D6-8569       TCGA-D6-A4Z9       TCGA-D6-A4ZB 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-D6-A6EK       TCGA-D6-A6EP       TCGA-D6-A74Q       TCGA-DQ-5625 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-DQ-5629       TCGA-DQ-5630       TCGA-DQ-5631       TCGA-DQ-7588 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-DQ-7589       TCGA-DQ-7590       TCGA-DQ-7591       TCGA-DQ-7592 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-DQ-7593       TCGA-DQ-7595       TCGA-F7-7848       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-A6C4       TCGA-H7-A6C5       TCGA-H7-A76A 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-HD-8634       TCGA-HD-8635       TCGA-HD-A634       TCGA-HD-A6I0 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-HL-7533       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-A66S       TCGA-KU-A6H7 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-KU-A6H8       TCGA-MT-A51W       TCGA-MT-A51X       TCGA-MT-A67D 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-MZ-A6I9       TCGA-MZ-A7D7       TCGA-P3-A6SX       TCGA-P3-A6T0 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-P3-A6T4       TCGA-P3-A6T8       TCGA-QK-A6IG       TCGA-QK-A6II 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-QK-A6IJ       TCGA-RS-A6TP       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-A71D       TCGA-UF-A7J9 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-UF-A7JC       TCGA-UF-A7JD       TCGA-UF-A7JF       TCGA-UF-A7JH 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-UF-A7JJ       TCGA-UF-A7JS       TCGA-WA-A7GZ       TCGA-WA-A7H4 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
D48V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAGE2A MUTATED                                  0     0
  GAGE2A WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GAGE2A MUTATED                           2     3
  GAGE2A WILD-TYPE                        35   443
D48V12, multiclass
                                  clus
vv                                 GAGE2A MUTATED GAGE2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               35
  WHITE                                         3              443
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V13, binary
                  cls
clus                 0   1
  GAGE2A MUTATED     0   5
  GAGE2A WILD-TYPE  26 443
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      0    5
  GAGE2A WILD-TYPE   26  443
                        clus
vv                       GAGE2A MUTATED GAGE2A WILD-TYPE
  HISPANIC OR LATINO                  0               26
  NOT HISPANIC OR LATINO              5              443
[1] 2 2
[1] FALSE

Clustering(49) Variable = LCP1 MUTATION ANALYSIS
D49V1, survival
                sevent
clus2              0   1
  LCP1 MUTATED     7   8
  LCP1 WILD-TYPE 286 209
  LCP1 MUTATED LCP1 WILD-TYPE 
            15            495 
  LCP1 MUTATED LCP1 WILD-TYPE 
             8            209 
$`LCP1 MUTATED`
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-A497 TCGA-CN-A63W TCGA-CV-5436 TCGA-CV-7091 
       12.99        20.55        35.01        12.39        19.20       111.16 
TCGA-CV-7254 TCGA-CV-7414 TCGA-CV-7427 TCGA-D6-6516 TCGA-D6-6823 TCGA-DQ-5629 
       47.97         0.46       156.49        25.41        23.05        30.94 
TCGA-DQ-5630 TCGA-DQ-7595 TCGA-P3-A6T5 
       33.86        39.12        29.00 

$`LCP1 WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        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-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       36.72        33.70        50.20        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       71.05        20.52        25.71        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-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       51.29        56.68        12.89        26.86        32.81        52.14 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       55.56        57.11        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-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       32.22        35.05        38.89         3.68        17.42        32.48 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       11.74        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-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
        2.70        23.44        19.82        24.39        20.88        19.53 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        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-6221 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 
       15.75        32.38        32.88        66.28        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       13.25         4.24        14.99        38.76        70.13        64.87 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       53.52        16.73        43.04        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        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-6472 
       37.87        26.27        58.42        50.01        39.52        34.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
       36.99        18.54        16.90         6.02        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        29.82        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         7.10         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        87.55        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-7095 TCGA-CV-7097 
        2.50         4.14        64.83       126.15        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 
       47.47        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 
       95.34         4.96        11.87         2.10        36.13        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       57.47        35.54        17.85       210.97        89.33         9.67 
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-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       14.89        56.48         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-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 
       10.42        10.55        18.84        34.36        51.12        13.25 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
        9.60         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        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
       37.25        18.02        14.04        46.32        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
       37.58        40.24        40.04        41.59        37.18        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-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.61        21.11        20.94         0.07        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
       21.93        27.48        27.48        14.66        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.85         0.36        13.84         4.27         3.65         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
       34.75        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-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       19.04        15.48        13.35        18.15        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-A5Q6 TCGA-P3-A5QA 
       15.42         7.13        16.08        17.98        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-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       18.97         2.04        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-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       18.64        21.07        19.73        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       15.91         7.10        32.45        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       64.80        54.67         2.83        49.51        48.03        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-UF-A7JV 
       18.05        13.94        20.75        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

  LCP1 MUTATED LCP1 WILD-TYPE 
          0.46           0.07 
  LCP1 MUTATED LCP1 WILD-TYPE 
        156.49         210.97 
  LCP1 MUTATED LCP1 WILD-TYPE 
         29.00          21.07 
[1] "0.5 - 156.5 (29.0)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1"  
D49V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  LCP1 MUTATED         2        3         1         5         0
  LCP1 WILD-TYPE      23       72        81       243        11
D49V3, multiclass
           clus
vv          LCP1 MUTATED LCP1 WILD-TYPE
  STAGE I              2             23
  STAGE II             3             72
  STAGE III            1             81
  STAGE IVA            5            243
  STAGE IVB            0             11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  LCP1 MUTATED       4   4   1   3
  LCP1 WILD-TYPE    44 130  98 165
D49V4, multiclass
       clus
vv      LCP1 MUTATED LCP1 WILD-TYPE
  T0+T1            4             44
  T2               4            130
  T3               1             98
  T4               3            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
  LCP1 MUTATED     4   1   4   0
  LCP1 WILD-TYPE 171  66 158   7
D49V5, multiclass
    clus
vv   LCP1 MUTATED LCP1 WILD-TYPE
  N0            4            171
  N1            1             66
  N2            4            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"
D49V6, binary
                cls
clus               0   1
  LCP1 MUTATED     4  11
  LCP1 WILD-TYPE 136 359
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCP1 MUTATED      4   11
  LCP1 WILD-TYPE  136  359
        clus
vv       LCP1 MUTATED LCP1 WILD-TYPE
  FEMALE            4            136
  MALE             11            359
[1] 2 2
[1] FALSE
D49V7, binary
                cls
clus               0   1
  LCP1 MUTATED     7   5
  LCP1 WILD-TYPE 139 269
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCP1 MUTATED      7    5
  LCP1 WILD-TYPE  139  269
     clus
vv    LCP1 MUTATED LCP1 WILD-TYPE
  NO             7            139
  YES            5            269
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  LCP1 MUTATED                                      15
  LCP1 WILD-TYPE                                   487
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  LCP1 MUTATED                                                             0
  LCP1 WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  LCP1 MUTATED                                                     0
  LCP1 WILD-TYPE                                                   7
D49V8, multiclass
                                                             clus
vv                                                            LCP1 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                 15
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
                                                             clus
vv                                                            LCP1 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  487
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V9, continuous
D49V10, continuous
D49V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LCP1 MUTATED                                  0     0
  LCP1 WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LCP1 MUTATED                           0    13
  LCP1 WILD-TYPE                        37   433
D49V12, multiclass
                                  clus
vv                                 LCP1 MUTATED LCP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             37
  WHITE                                      13            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"
D49V13, binary
                cls
clus               0   1
  LCP1 MUTATED     1  14
  LCP1 WILD-TYPE  25 434
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCP1 MUTATED      1   14
  LCP1 WILD-TYPE   25  434
                        clus
vv                       LCP1 MUTATED LCP1 WILD-TYPE
  HISPANIC OR LATINO                1             25
  NOT HISPANIC OR LATINO           14            434
[1] 2 2
[1] FALSE
