[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/15078978/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/15648706/transformed.cor.cli.txt"

nPatients in clinical file=522, in cluster file=510, common to both=506
[1]  64 506
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           356            150 
  TP53 MUTATED TP53 WILD-TYPE 
           356            150 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
             110              396 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
             110              396 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              94              412 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              94              412 
[1] "NSD1 MUTATION ANALYSIS"
[1] 3
  NSD1 MUTATED NSD1 WILD-TYPE 
            63            443 
  NSD1 MUTATED NSD1 WILD-TYPE 
            63            443 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
             54             452 
  CASP8 MUTATED CASP8 WILD-TYPE 
             54             452 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            28            478 
  HRAS MUTATED HRAS WILD-TYPE 
            28            478 
[1] "TGFBR2 MUTATION ANALYSIS"
[1] 3
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              23              483 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              23              483 
[1] "FAT1 MUTATION ANALYSIS"
[1] 3
  FAT1 MUTATED FAT1 WILD-TYPE 
           113            393 
  FAT1 MUTATED FAT1 WILD-TYPE 
           113            393 
[1] "NOTCH1 MUTATION ANALYSIS"
[1] 3
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              86              420 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              86              420 
[1] "EPHA2 MUTATION ANALYSIS"
[1] 3
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             23             483 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             23             483 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
             24             482 
  HLA-B MUTATED HLA-B WILD-TYPE 
             24             482 
[1] "RAC1 MUTATION ANALYSIS"
[1] 3
  RAC1 MUTATED RAC1 WILD-TYPE 
            15            491 
  RAC1 MUTATED RAC1 WILD-TYPE 
            15            491 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              26              480 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              26              480 
[1] "ZNF750 MUTATION ANALYSIS"
[1] 3
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              19              487 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              19              487 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            14            492 
  PTEN MUTATED PTEN WILD-TYPE 
            14            492 
[1] "HLA-A MUTATION ANALYSIS"
[1] 3
  HLA-A MUTATED HLA-A WILD-TYPE 
             22             484 
  HLA-A MUTATED HLA-A WILD-TYPE 
             22             484 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           17           489 
  RB1 MUTATED RB1 WILD-TYPE 
           17           489 
[1] "MAPK1 MUTATION ANALYSIS"
[1] 3
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             497 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             497 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
             17             489 
  KDM6A MUTATED KDM6A WILD-TYPE 
             17             489 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
             39             467 
  EP300 MUTATED EP300 WILD-TYPE 
             39             467 
[1] "RASA1 MUTATION ANALYSIS"
[1] 3
  RASA1 MUTATED RASA1 WILD-TYPE 
             17             489 
  RASA1 MUTATED RASA1 WILD-TYPE 
             17             489 
[1] "NAP1L2 MUTATION ANALYSIS"
[1] 3
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               7              499 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               7              499 
[1] "CREBBP MUTATION ANALYSIS"
[1] 3
  CREBBP MUTATED CREBBP WILD-TYPE 
              35              471 
  CREBBP MUTATED CREBBP WILD-TYPE 
              35              471 
[1] "CTCF MUTATION ANALYSIS"
[1] 3
  CTCF MUTATED CTCF WILD-TYPE 
            16            490 
  CTCF MUTATED CTCF WILD-TYPE 
            16            490 
[1] "KEAP1 MUTATION ANALYSIS"
[1] 3
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             484 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             484 
[1] "RHOA MUTATION ANALYSIS"
[1] 3
  RHOA MUTATED RHOA WILD-TYPE 
            10            496 
  RHOA MUTATED RHOA WILD-TYPE 
            10            496 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             33             473 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             33             473 
[1] "TIGD4 MUTATION ANALYSIS"
[1] 3
  TIGD4 MUTATED TIGD4 WILD-TYPE 
              7             499 
  TIGD4 MUTATED TIGD4 WILD-TYPE 
              7             499 
[1] "KRT5 MUTATION ANALYSIS"
[1] 3
  KRT5 MUTATED KRT5 WILD-TYPE 
            11            495 
  KRT5 MUTATED KRT5 WILD-TYPE 
            11            495 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             14             492 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             14             492 
[1] "ASXL1 MUTATION ANALYSIS"
[1] 3
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             16             490 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             16             490 
[1] "CES2 MUTATION ANALYSIS"
[1] 3
  CES2 MUTATED CES2 WILD-TYPE 
            11            495 
  CES2 MUTATED CES2 WILD-TYPE 
            11            495 
[1] "IRS4 MUTATION ANALYSIS"
[1] 3
  IRS4 MUTATED IRS4 WILD-TYPE 
            17            489 
  IRS4 MUTATED IRS4 WILD-TYPE 
            17            489 
[1] "ARID2 MUTATION ANALYSIS"
[1] 3
  ARID2 MUTATED ARID2 WILD-TYPE 
             20             486 
  ARID2 MUTATED ARID2 WILD-TYPE 
             20             486 
[1] "CBWD1 MUTATION ANALYSIS"
[1] 3
  CBWD1 MUTATED CBWD1 WILD-TYPE 
              5             501 
  CBWD1 MUTATED CBWD1 WILD-TYPE 
              5             501 
[1] "RGL4 MUTATION ANALYSIS"
[1] 3
  RGL4 MUTATED RGL4 WILD-TYPE 
             7            499 
  RGL4 MUTATED RGL4 WILD-TYPE 
             7            499 
[1] "HUWE1 MUTATION ANALYSIS"
[1] 3
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             45             461 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             45             461 
[1] "HNRNPL MUTATION ANALYSIS"
[1] 3
  HNRNPL MUTATED HNRNPL WILD-TYPE 
              11              495 
  HNRNPL MUTATED HNRNPL WILD-TYPE 
              11              495 
[1] "ITGB1 MUTATION ANALYSIS"
[1] 3
  ITGB1 MUTATED ITGB1 WILD-TYPE 
             14             492 
  ITGB1 MUTATED ITGB1 WILD-TYPE 
             14             492 
[1] "B2M MUTATION ANALYSIS"
[1] 3
  B2M MUTATED B2M WILD-TYPE 
            7           499 
  B2M MUTATED B2M WILD-TYPE 
            7           499 
[1] "LRRC37B MUTATION ANALYSIS"
[1] 3
  LRRC37B MUTATED LRRC37B WILD-TYPE 
               16               490 
  LRRC37B MUTATED LRRC37B WILD-TYPE 
               16               490 
[1] "PPFIA4 MUTATION ANALYSIS"
[1] 3
  PPFIA4 MUTATED PPFIA4 WILD-TYPE 
              14              492 
  PPFIA4 MUTATED PPFIA4 WILD-TYPE 
              14              492 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               9              497 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               9              497 
[1] "VPS33B MUTATION ANALYSIS"
[1] 3
  VPS33B MUTATED VPS33B WILD-TYPE 
               7              499 
  VPS33B MUTATED VPS33B WILD-TYPE 
               7              499 
[1] "C8ORF31 MUTATION ANALYSIS"
[1] 3
  C8ORF31 MUTATED C8ORF31 WILD-TYPE 
                4               502 
  C8ORF31 MUTATED C8ORF31 WILD-TYPE 
                4               502 
[1] "NCOR1 MUTATION ANALYSIS"
[1] 3
  NCOR1 MUTATED NCOR1 WILD-TYPE 
             18             488 
  NCOR1 MUTATED NCOR1 WILD-TYPE 
             18             488 
[1] "SEH1L MUTATION ANALYSIS"
[1] 3
  SEH1L MUTATED SEH1L WILD-TYPE 
              4             502 
  SEH1L MUTATED SEH1L WILD-TYPE 
              4             502 
[1] "CUL3 MUTATION ANALYSIS"
[1] 3
  CUL3 MUTATED CUL3 WILD-TYPE 
            14            492 
  CUL3 MUTATED CUL3 WILD-TYPE 
            14            492 
[1] "NOTCH2 MUTATION ANALYSIS"
[1] 3
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
              19              487 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
              19              487 
[1] "YTHDF1 MUTATION ANALYSIS"
[1] 3
  YTHDF1 MUTATED YTHDF1 WILD-TYPE 
               6              500 
  YTHDF1 MUTATED YTHDF1 WILD-TYPE 
               6              500 
[1] "FOSL2 MUTATION ANALYSIS"
[1] 3
  FOSL2 MUTATED FOSL2 WILD-TYPE 
             10             496 
  FOSL2 MUTATED FOSL2 WILD-TYPE 
             10             496 
[1] "MYH9 MUTATION ANALYSIS"
[1] 3
  MYH9 MUTATED MYH9 WILD-TYPE 
            22            484 
  MYH9 MUTATED MYH9 WILD-TYPE 
            22            484 
[1] "TP63 MUTATION ANALYSIS"
[1] 3
  TP63 MUTATED TP63 WILD-TYPE 
            12            494 
  TP63 MUTATED TP63 WILD-TYPE 
            12            494 
[1] "DYSF MUTATION ANALYSIS"
[1] 3
  DYSF MUTATED DYSF WILD-TYPE 
            21            485 
  DYSF MUTATED DYSF WILD-TYPE 
            21            485 
[1] "TMEM2 MUTATION ANALYSIS"
[1] 3
  TMEM2 MUTATED TMEM2 WILD-TYPE 
             17             489 
  TMEM2 MUTATED TMEM2 WILD-TYPE 
             17             489 
[1] "PTPN14 MUTATION ANALYSIS"
[1] 3
  PTPN14 MUTATED PTPN14 WILD-TYPE 
              14              492 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
              14              492 
[1] "RBM10 MUTATION ANALYSIS"
[1] 3
  RBM10 MUTATED RBM10 WILD-TYPE 
              4             502 
  RBM10 MUTATED RBM10 WILD-TYPE 
              4             502 
[1] "IRF2 MUTATION ANALYSIS"
[1] 3
  IRF2 MUTATED IRF2 WILD-TYPE 
             7            499 
  IRF2 MUTATED IRF2 WILD-TYPE 
             7            499 
[1] "AMPD1 MUTATION ANALYSIS"
[1] 3
  AMPD1 MUTATED AMPD1 WILD-TYPE 
              6             500 
  AMPD1 MUTATED AMPD1 WILD-TYPE 
              6             500 
[1] "ZMYM1 MUTATION ANALYSIS"
[1] 3
  ZMYM1 MUTATED ZMYM1 WILD-TYPE 
              9             497 
  ZMYM1 MUTATED ZMYM1 WILD-TYPE 
              9             497 
[1] "LCP1 MUTATION ANALYSIS"
[1] 3
  LCP1 MUTATED LCP1 WILD-TYPE 
            15            491 
  LCP1 MUTATED LCP1 WILD-TYPE 
            15            491 
[1] "SLC9A6 MUTATION ANALYSIS"
[1] 3
  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
               5              501 
  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
               5              501 
[1] "CCNG2 MUTATION ANALYSIS"
[1] 3
  CCNG2 MUTATED CCNG2 WILD-TYPE 
              3             503 
  CCNG2 MUTATED CCNG2 WILD-TYPE 
              3             503 
[1] "TACR2 MUTATION ANALYSIS"
[1] 3
  TACR2 MUTATED TACR2 WILD-TYPE 
              4             502 
  TACR2 MUTATED TACR2 WILD-TYPE 
              4             502 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "NUMBER_PACK_YEARS_SMOKED"              
[18] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[19] "NUMBER_OF_LYMPH_NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 506 columns.

[1] "Batch" "22"   
[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=186,	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=322,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	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:'DCC_UPLOAD_DATE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'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 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=86,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=25,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 506 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"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "GENDER"                                
 [6] "HISTOLOGICAL_TYPE"                     
 [7] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [8] "NUMBER_PACK_YEARS_SMOKED"              
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[10] "NUMBER_OF_LYMPH_NODES"                 
[11] "RACE"                                  
[12] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=60, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, 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  47 131  98 168 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   48   131    98   168 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  47 131  98 168 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   48   131    98   168 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
174  65 161   7 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
174  65 161   7 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
174  65 161   7 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
174  65 161   7 
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, 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=23, 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   199 156
  TP53 WILD-TYPE 104  45
  TP53 MUTATED TP53 WILD-TYPE 
           355            149 
  TP53 MUTATED TP53 WILD-TYPE 
           156             45 
$`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        53.79        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         7.76        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        23.70        38.04         4.67        40.44        37.84 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       12.89        32.65        21.11        41.10        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       14.33        43.73        27.58        13.05        33.11        34.36 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
        8.58        12.39        35.54         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        22.45        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T 
       11.74        35.01        14.56        12.85        29.72         7.40 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A6V3 TCGA-CQ-5326 
       17.29        11.44         4.41        12.07         9.80         2.93 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 
       46.75        45.80        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        34.75        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        51.29        33.11 
TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       16.73        41.88        64.11        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        32.81        25.81        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        11.51         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        29.85        29.52         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       126.08        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 
       24.99       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 
       22.03         3.62        21.24        23.47        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.42        18.84        34.36        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       23.05        16.14        11.44        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q 
       12.36         7.63        14.30        13.94        12.10        11.11 
TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       58.45        30.94        33.86        18.02        14.04        18.90 
TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
        9.83        10.65        37.18        21.63        20.25         3.02 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 
       18.94        12.62         0.46        17.85        20.25        12.43 
TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7917 
       15.16        13.61        21.11         0.07         0.16         1.22 
TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 
       14.66        12.66        22.85        13.84         3.65        15.95 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       19.33        11.84        13.55        14.47         5.29        11.54 
TCGA-IQ-A61O TCGA-KU-A66T TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A7BN TCGA-MZ-A7D7 
       11.84        18.15        10.75        14.37        15.42        17.98 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       15.78        56.75        47.01        19.00        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        2.04        29.00        16.01        13.15        21.07        11.74 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC 
        7.30        16.70         9.34        12.72        14.79        12.43 
TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       12.72        15.91        43.59        54.67         2.83        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF 
       41.16        42.02        44.65        62.27        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       21.86        16.11        13.94        20.75        22.36        32.65 
TCGA-WA-A7GZ 
       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        57.44         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        94.62 
TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-8596 
        4.60        18.35        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        24.92        41.69        55.27 
TCGA-CN-5369 TCGA-CN-5374 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y 
       12.49        56.94        17.59        21.21        15.91         5.75 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
        2.70        10.09         7.33         7.69         6.18        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5333 TCGA-CQ-6227 TCGA-CQ-7068 
       39.68        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 
       28.83        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        31.10        30.58        48.39        94.88 
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-A6ES TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 
       15.88        12.79        35.54        25.48        20.45        12.13 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-A50J TCGA-F7-A622 TCGA-H7-7774 TCGA-H7-A76A 
       12.10        11.18        19.23        11.80        13.38         6.77 
TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       25.74        22.03         0.36         4.27         6.90        34.75 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61I TCGA-KU-A66S TCGA-KU-A6H7 TCGA-MT-A51X 
       12.76        14.50         0.07        13.35        12.43         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 
       30.05         1.84        12.62         3.68         7.13        16.08 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T6 TCGA-QK-A6IF TCGA-QK-A6V9 
       51.25        10.85        36.82        12.99        17.65        18.64 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ 
       16.96         6.87         7.10        32.45        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A7JC TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
       13.68        17.95         2.96        17.03        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 
         18.54          18.67 
[1] "0.1 - 180.2 (18.5)" "0.1 - 211.0 (18.7)"
[1] "hr=" "1.6"
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  TP53 MUTATED        17       51        55       188         9
  TP53 WILD-TYPE       8       25        22        60         2
D1V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I             17              8
  STAGE II            51             25
  STAGE III           55             22
  STAGE IVA          188             60
  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  87  77 131
  TP53 WILD-TYPE    18  44  21  37
D1V4, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T0+T1           30             18
  T2              87             44
  T3              77             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   124  48 124   5
  TP53 WILD-TYPE  50  17  37   2
D1V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0          124             50
  N1           48             17
  N2          124             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    99 257
  TP53 WILD-TYPE  40 110
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     99  257
  TP53 WILD-TYPE   40  110
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           99             40
  MALE            257            110
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  TP53 MUTATED                                     354
  TP53 WILD-TYPE                                   144
                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
D1V7, multiclass
                                                             clus
vv                                                            TP53 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                354
  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                                  144
  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"
D1V8, binary
                cls
clus               0   1
  TP53 MUTATED    62 294
  TP53 WILD-TYPE  21 129
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     62  294
  TP53 WILD-TYPE   21  129
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            62             21
  YES          294            129
[1] 2 2
[1] FALSE
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                          28   302
  TP53 WILD-TYPE                         8   139
D1V12, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            2              0
  ASIAN                                       8              3
  BLACK OR AFRICAN AMERICAN                  28              8
  WHITE                                     302            139
[1] 4 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    21 307
  TP53 WILD-TYPE   4 138
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     21  307
  TP53 WILD-TYPE    4  138
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO               21              4
  NOT HISPANIC OR LATINO          307            138
[1] 2 2
[1] FALSE

Clustering(2) Variable = CDKN2A MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2                0   1
  CDKN2A MUTATED    62  48
  CDKN2A WILD-TYPE 241 153
  CDKN2A MUTATED CDKN2A WILD-TYPE 
             110              394 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              48              153 
$`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        53.79        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DG 
        4.01         7.76        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        23.70        32.65        12.99 
TCGA-CN-4738 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 
       14.33        12.39        35.54         8.52        22.45        20.68 
TCGA-CN-6013 TCGA-CN-6021 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A640 
       20.65         9.07        17.42        14.10        11.74         4.41 
TCGA-CN-A6V3 TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-6220 TCGA-CQ-6224 
        9.80         2.93        45.80        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        32.81        11.77        11.51 
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        29.52 
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       126.08        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        24.99 
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-A74Q 
        6.38        13.25        25.41        16.14         7.63        11.11 
TCGA-DQ-5629 TCGA-DQ-7595 TCGA-F7-A50I TCGA-F7-A61S TCGA-H7-8501 TCGA-H7-A6C4 
       30.94        10.65         3.02        18.94        15.16        13.61 
TCGA-HD-8224 TCGA-HD-A633 TCGA-MT-A67A TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T3 
       14.66        13.84        30.05        56.75        47.01        18.97 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-RS-A6TO 
       21.07        11.74         7.30         9.34        12.72        12.72 
TCGA-UF-A7J9 TCGA-UF-A7JO 
       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        57.44        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 
       94.62         9.14         4.60         4.41        18.35        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        40.44        37.84        12.89        26.86 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 
       21.11        24.92        41.10        20.55        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5361 
       41.69        13.05        33.11        34.36         8.58        55.27 
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        20.71        30.67        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
       14.20         6.74         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A498 
       20.09        12.95        24.16         3.68        35.01        14.56 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       17.59        12.85        29.72        21.21         7.40        17.29 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       15.91        11.44         5.75        12.07         2.70        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        7.33         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       54.58        46.75        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        34.75        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
       14.99        51.29        33.11        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE 
       28.83        64.11        11.61        23.24        29.36        25.81 
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        31.10        29.85 
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        94.88        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        22.03         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-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
        9.60        23.05         2.53        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP 
       25.32        17.72        12.36        15.88        14.30        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.10        12.79        58.45        35.54        33.86        18.02 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       14.04        18.90        25.48        20.45         9.83        12.13 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J 
       12.10        11.18        37.18        21.63        20.25        19.23 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       12.62         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.38        21.11         6.77         0.07         0.16        25.74 
TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 
        1.22        22.03        12.66        22.85         0.36         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        12.76        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       19.33        11.84        13.55         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       11.54        11.84        13.35        18.15        12.43        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         3.68        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A5QF 
        7.13        16.08        17.98        15.78        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       36.82        19.00        75.55         2.04        29.00        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A6VB 
       16.01        13.15        17.65        16.70        18.64        14.79 
TCGA-QK-A6VC TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.43        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        13.68        43.59        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       43.36        41.16        42.02        62.27        17.95        24.16 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT 
       49.22        21.86        16.11        13.94        22.36        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        17.03        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 
          19.855           18.380 
[1] "0.5 - 180.2 (19.9)" "0.1 - 211.0 (18.4)"
[1] "hr=" "1.1"
D2V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  CDKN2A MUTATED         7       13        22        51         1
  CDKN2A WILD-TYPE      18       63        55       197        10
D2V3, multiclass
           clus
vv          CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE I                7               18
  STAGE II              13               63
  STAGE III             22               55
  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  24  24  37
  CDKN2A WILD-TYPE    37 107  74 131
D2V4, multiclass
       clus
vv      CDKN2A MUTATED CDKN2A WILD-TYPE
  T0+T1             11               37
  T2                24              107
  T3                24               74
  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  15  32   0
  CDKN2A WILD-TYPE 138  50 129   7
D2V5, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  N0             36              138
  N1             15               50
  N2             32              129
  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  79
  CDKN2A WILD-TYPE 108 288
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     31   79
  CDKN2A WILD-TYPE  108  288
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE             31              108
  MALE               79              288
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  CDKN2A MUTATED                                     110
  CDKN2A WILD-TYPE                                   388
                  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
D2V7, multiclass
                                                             clus
vv                                                            CDKN2A MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  110
  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                                    388
  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"
D2V8, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    23  87
  CDKN2A WILD-TYPE  60 336
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     23   87
  CDKN2A WILD-TYPE   60  336
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO              23               60
  YES             87              336
[1] 2 2
[1] FALSE
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                           5    99
  CDKN2A WILD-TYPE                        31   342
D2V12, multiclass
                                  clus
vv                                 CDKN2A MUTATED CDKN2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     5               31
  WHITE                                        99              342
[1] 4 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  99
  CDKN2A WILD-TYPE  18 346
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      7   99
  CDKN2A WILD-TYPE   18  346
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  7               18
  NOT HISPANIC OR LATINO             99              346
[1] 2 2
[1] FALSE

Clustering(3) Variable = PIK3CA MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    53  40
  PIK3CA WILD-TYPE 250 161
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              93              411 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              40              161 
$`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        94.62 
TCGA-BB-7863 TCGA-CN-4723 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5360 TCGA-CN-5365 
       33.70        23.70        43.73        41.69        35.54        11.54 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6994 
       22.45        20.71        20.65         9.07        11.08        24.16 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A6V1 TCGA-CQ-5331 TCGA-CQ-6218 
       11.74        14.56        12.85         7.33        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 
       29.52        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        18.90        21.63        19.23        18.94        13.38 
TCGA-HD-7754 TCGA-HD-8634 TCGA-HL-7533 TCGA-IQ-A61E TCGA-MZ-A6I9 TCGA-P3-A5QF 
       25.74        12.66        34.75        19.33        16.08        10.85 
TCGA-P3-A6T0 TCGA-T2-A6WZ TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A71B TCGA-UF-A7J9 
       19.00        15.91        13.55        13.68        43.36        44.65 
TCGA-UF-A7JF TCGA-UF-A7JO TCGA-UF-A7JV 
       49.22        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        53.79        57.44        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         7.76 
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        18.35        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        40.44        37.84 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.65        21.11        24.92        41.10 
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        33.11 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 
       34.36         8.58        12.39        55.27         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 
       20.68        19.53        20.68        19.07        14.20         6.74 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 
        9.24        36.49        10.45        20.09        12.95         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C 
       17.42        14.10        35.01        17.59        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        17.29        15.91        11.44         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
       12.07         2.70        10.09         9.80         7.69         6.18 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        39.68        21.50         2.93        54.58        46.75 
TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-6221 
       45.80        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 
       34.75        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        51.29        33.11        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       28.83        64.11        11.61        23.24        29.36        32.81 
TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5250 
       25.81        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        11.51 
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        31.10        29.85         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        94.88        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-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       126.08        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        24.99       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 
       22.03         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 
       10.42        10.55        18.84        34.36        25.41        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-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       12.36        15.88         7.63        14.30        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 
       12.79        11.11        58.45        35.54        30.94        18.02 
TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       14.04        25.48        20.45         9.83        12.13        12.10 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V 
       10.65        11.18        37.18        20.25         3.02        12.62 
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-7917 
       13.61        21.11         6.77         0.07         0.16         1.22 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       14.66        22.03        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-A61G 
        3.65         6.90        15.95        12.76        14.50        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       13.55         0.07        14.47         5.29        11.54        11.84 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        12.43        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         3.68        15.42         7.13 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
       17.98        15.78        56.75        51.25        36.82        47.01 
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        11.74        17.65         7.30        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO 
        9.34        12.72        18.64        14.79        12.43        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HJ TCGA-UF-A718 
       16.96         6.87         7.10        32.45        13.25        43.59 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC 
       54.67         2.83        41.16        42.02        62.27        17.95 
TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT 
       24.16        21.86        16.11        13.94        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        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 
           21.80            17.85 
[1] "1.0 - 211.0 (21.8)" "0.1 - 169.4 (17.9)"
[1] "hr=" "1.1"
D3V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  PIK3CA MUTATED         5        9        13        49         3
  PIK3CA WILD-TYPE      20       67        64       199         8
D3V3, multiclass
           clus
vv          PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                5               20
  STAGE II               9               67
  STAGE III             13               64
  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    41 113  77 133
D3V4, multiclass
       clus
vv      PIK3CA MUTATED PIK3CA WILD-TYPE
  T0+T1              7               41
  T2                18              113
  T3                21               77
  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 135  57 134   5
D3V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             39              135
  N1              8               57
  N2             27              134
  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"
D3V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    34  60
  PIK3CA WILD-TYPE 105 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     34   60
  PIK3CA WILD-TYPE  105  307
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             34              105
  MALE               60              307
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  PIK3CA MUTATED                                      94
  PIK3CA WILD-TYPE                                   404
                  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
D3V7, 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                                    404
  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"
D3V8, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    17  77
  PIK3CA WILD-TYPE  66 346
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     17   77
  PIK3CA WILD-TYPE   66  346
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              17               66
  YES             77              346
[1] 2 2
[1] FALSE
D3V9, continuous
D3V10, continuous
D3V11, 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    89
  PIK3CA WILD-TYPE                        35   352
D3V12, multiclass
                                  clus
vv                                 PIK3CA MUTATED PIK3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               35
  WHITE                                        89              352
[1] 4 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
  PIK3CA MUTATED     4  83
  PIK3CA WILD-TYPE  21 362
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      4   83
  PIK3CA WILD-TYPE   21  362
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  4               21
  NOT HISPANIC OR LATINO             83              362
[1] 2 2
[1] FALSE

Clustering(4) Variable = NSD1 MUTATION ANALYSIS
D4V1, survival
                sevent
clus2              0   1
  NSD1 MUTATED    46  17
  NSD1 WILD-TYPE 257 184
  NSD1 MUTATED NSD1 WILD-TYPE 
            63            441 
  NSD1 MUTATED NSD1 WILD-TYPE 
            17            184 
$`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        40.44        26.86        43.73        34.36        35.54 
TCGA-CN-A497 TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V3 
       35.01         7.40        17.29        11.44        12.07         9.80 
TCGA-CQ-7072 TCGA-CR-5247 TCGA-CR-6481 TCGA-CR-7364 TCGA-CR-7385 TCGA-CR-7395 
       64.11        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        94.88         9.60        11.24       126.08 
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        14.30        11.11 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A623 TCGA-H7-A6C5 TCGA-HD-7917 TCGA-KU-A66S 
       10.65        37.18        20.25        21.11         1.22        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        14.79        13.68        54.67 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JF 
       43.36        41.16        49.22 

$`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        53.79 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
       57.44        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 
        7.76        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        94.62         9.14         4.60         4.41        18.35 
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        23.70        38.04         4.67        37.84 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
       12.89        32.65        21.11        24.92        41.10        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        41.69        13.05        33.11 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
        8.58        12.39        55.27         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        22.45        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       20.71        30.67        20.68        20.65        19.53        20.68 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        14.20         6.74         9.07         9.24        36.49 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       11.08        10.45        20.09        12.95        24.16         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       17.42        14.10        11.74        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 
       29.72        21.21        15.91         5.75         4.41         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       10.09         7.33         7.69         6.18        48.20        39.68 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        46.75        45.80        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        34.75        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        51.29        33.11        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       43.04        41.88        28.83        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        32.81        25.81        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        11.51 
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        31.10        29.85 
TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 
       29.52         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 
       24.99       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 
       22.03        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-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EP 
       24.95        17.72        12.36        15.88         7.63        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
       12.10        12.79        58.45        35.54        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        18.90        25.48        20.45         9.83 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       12.13        12.10        11.18        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       19.23        18.94        12.62         0.46        17.85        11.80 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 
       12.43        13.38        15.16        13.61         6.77         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
        0.16        25.74        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        12.76        14.50        19.33        11.84        13.55 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66T 
        0.07        14.47         5.29        11.54        11.84        18.15 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       12.43        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         3.68        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        56.75        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 
       11.74        17.65         7.30        16.70         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       18.64        12.43        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        43.59         2.83 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
       42.02        44.65        62.27        17.95        24.16        21.86 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       16.11        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 
          1.22           0.07 
  NSD1 MUTATED NSD1 WILD-TYPE 
        156.49         210.97 
  NSD1 MUTATED NSD1 WILD-TYPE 
         21.17          18.35 
[1] "1.2 - 156.5 (21.2)" "0.1 - 211.0 (18.4)"
[1] "hr=" "1.7"
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       62        68       218         9
D4V3, multiclass
           clus
vv          NSD1 MUTATED NSD1 WILD-TYPE
  STAGE I              0             25
  STAGE II            14             62
  STAGE III            9             68
  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    42 118  86 142
D4V4, multiclass
       clus
vv      NSD1 MUTATED NSD1 WILD-TYPE
  T0+T1            6             42
  T2              13            118
  T3              12             86
  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 143  59 148   6
D4V5, multiclass
    clus
vv   NSD1 MUTATED NSD1 WILD-TYPE
  N0           31            143
  N1            6             59
  N2           13            148
  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 128 315
[1] "tbl2"
                cls
clus             [,1] [,2]
  NSD1 MUTATED     11   52
  NSD1 WILD-TYPE  128  315
        clus
vv       NSD1 MUTATED NSD1 WILD-TYPE
  FEMALE           11            128
  MALE             52            315
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  NSD1 MUTATED                                      62
  NSD1 WILD-TYPE                                   436
                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
D4V7, 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                                  436
  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"
D4V8, binary
                cls
clus               0   1
  NSD1 MUTATED     6  57
  NSD1 WILD-TYPE  77 366
[1] "tbl2"
                cls
clus             [,1] [,2]
  NSD1 MUTATED      6   57
  NSD1 WILD-TYPE   77  366
     clus
vv    NSD1 MUTATED NSD1 WILD-TYPE
  NO             6             77
  YES           57            366
[1] 2 2
[1] FALSE
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    53
  NSD1 WILD-TYPE                        31   388
D4V12, multiclass
                                  clus
vv                                 NSD1 MUTATED NSD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   5             31
  WHITE                                      53            388
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, binary
                cls
clus               0   1
  NSD1 MUTATED     5  53
  NSD1 WILD-TYPE  20 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  NSD1 MUTATED      5   53
  NSD1 WILD-TYPE   20  392
                        clus
vv                       NSD1 MUTATED NSD1 WILD-TYPE
  HISPANIC OR LATINO                5             20
  NOT HISPANIC OR LATINO           53            392
[1] 2 2
[1] FALSE

Clustering(5) Variable = CASP8 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED    28  26
  CASP8 WILD-TYPE 275 175
  CASP8 MUTATED CASP8 WILD-TYPE 
             54             450 
  CASP8 MUTATED CASP8 WILD-TYPE 
             26             175 
$`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        24.92        12.49         2.70 
TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6220 
       39.68        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        28.83        34.06        26.17        29.52        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 
       24.99         1.05         0.76        15.25         5.98         6.38 
TCGA-CV-A6JO TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-A6EK TCGA-F7-A624 TCGA-H7-7774 
        6.48        10.42        10.55        15.88        12.43        13.38 
TCGA-H7-8501 TCGA-HD-A4C1 TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A6T2 TCGA-QK-A64Z 
       15.16         0.36         1.84        12.62        75.55        21.07 
TCGA-QK-A6IG TCGA-QK-A6VB TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-UF-A7JO 
        7.30        14.79        12.72         6.87        32.45        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        53.79        57.44 
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         7.76 
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        94.62         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.41        18.35        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 
       23.70        38.04         4.67        40.44        37.84        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       26.86        32.65        21.11        41.10        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        43.73        27.58        41.69        13.05        33.11 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       34.36         8.58        12.39        35.54        55.27         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        22.45 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       56.94        20.71        30.67        20.68        20.65        19.53 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       20.68        19.07        14.20         6.74         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
       36.49        11.08        10.45        20.09        12.95        24.16 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        3.68        17.42        14.10        11.74        35.01        14.56 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       17.59        12.85        29.72        21.21         7.40        17.29 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A6UY 
       15.91        11.44         5.75         4.41        12.07        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5325 
        7.33         9.80         7.69         6.18        48.20        21.50 
TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6219 
        2.93        46.75        45.80        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        34.75        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        51.29        33.11        16.73 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        64.11        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 
       32.81        25.81        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 
       11.51        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        31.10 
TCGA-CR-7393 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 
       29.85         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        94.88        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 
      126.08        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        22.03         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 
       22.52        10.42        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-A6EM TCGA-D6-A6EO 
       24.95        25.32        17.72        12.36         7.63        14.30 
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        35.54 
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        18.90        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45         9.83        12.13        12.10        10.65        11.18 
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        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-A6C4 
       12.62         0.46        17.85        11.80        20.25        13.61 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
       21.11         6.77         0.07         0.16        25.74         1.22 
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        12.76        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       19.33        11.84        13.55         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       11.54        11.84        13.35        18.15        12.43        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       14.37         7.96        30.05         3.68        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        56.75        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       36.82        47.01        19.00        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH 
       12.99        16.01        13.15        11.74        17.65        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-RS-A6TP TCGA-T2-A6WZ 
        9.34        12.72        18.64        12.43        16.96        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        13.68        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        43.36        41.16        42.02        44.65        62.27 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.16        49.22        21.86        16.11        13.94 
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 

  CASP8 MUTATED CASP8 WILD-TYPE 
           0.36            0.07 
  CASP8 MUTATED CASP8 WILD-TYPE 
          75.55          210.97 
  CASP8 MUTATED CASP8 WILD-TYPE 
         15.565          18.870 
[1] "0.4 - 75.5 (15.6)"  "0.1 - 211.0 (18.9)"
[1] "hr=" "1.6"
D5V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  CASP8 MUTATED         2       11         8        26         1
  CASP8 WILD-TYPE      23       65        69       222        10
D5V3, multiclass
           clus
vv          CASP8 MUTATED CASP8 WILD-TYPE
  STAGE I               2              23
  STAGE II             11              65
  STAGE III             8              69
  STAGE IVA            26             222
  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  16  10  21
  CASP8 WILD-TYPE    46 115  88 147
D5V4, multiclass
       clus
vv      CASP8 MUTATED CASP8 WILD-TYPE
  T0+T1             2              46
  T2               16             115
  T3               10              88
  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   5  10   1
  CASP8 WILD-TYPE 149  60 151   6
D5V5, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  N0            25             149
  N1             5              60
  N2            10             151
  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
  CASP8 MUTATED    27  27
  CASP8 WILD-TYPE 112 340
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     27   27
  CASP8 WILD-TYPE  112  340
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  FEMALE            27             112
  MALE              27             340
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  CASP8 MUTATED                                      54
  CASP8 WILD-TYPE                                   444
                 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
D5V7, multiclass
                                                             clus
vv                                                            CASP8 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  54
  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                                   444
  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"
D5V8, binary
                 cls
clus                0   1
  CASP8 MUTATED     5  49
  CASP8 WILD-TYPE  78 374
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      5   49
  CASP8 WILD-TYPE   78  374
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO              5              78
  YES            49             374
[1] 2 2
[1] FALSE
D5V9, continuous
D5V10, continuous
D5V11, 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    49
  CASP8 WILD-TYPE                        34   392
D5V12, multiclass
                                  clus
vv                                 CASP8 MUTATED CASP8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              34
  WHITE                                       49             392
[1] 4 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
  CASP8 MUTATED     4  48
  CASP8 WILD-TYPE  21 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      4   48
  CASP8 WILD-TYPE   21  397
                        clus
vv                       CASP8 MUTATED CASP8 WILD-TYPE
  HISPANIC OR LATINO                 4              21
  NOT HISPANIC OR LATINO            48             397
[1] 2 2
[1] FALSE

Clustering(6) Variable = HRAS MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  HRAS MUTATED    18  10
  HRAS WILD-TYPE 285 191
  HRAS MUTATED HRAS WILD-TYPE 
            28            476 
  HRAS MUTATED HRAS WILD-TYPE 
            10            191 
$`HRAS MUTATED`
TCGA-BA-5556 TCGA-BA-A6DJ TCGA-CN-A63V TCGA-CN-A642 TCGA-CQ-5324 TCGA-CQ-5333 
       23.84        13.38        15.91         2.70        39.68        11.21 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CG TCGA-CR-7382 TCGA-CR-7394 
       70.13        43.04        28.83        14.14        26.17        29.52 
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-H7-8501 TCGA-HD-A4C1 
       24.99         5.98         6.48        25.32        15.16         0.36 
TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-P3-A6T2 TCGA-T2-A6WX 
        6.90        19.33        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        53.79 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       57.44        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         7.76        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        94.62         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.35        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        23.70        38.04         4.67        40.44        37.84 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.65        21.11        24.92        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        33.11        34.36         8.58        12.39        35.54 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       55.27         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        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        14.56        17.59        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
       21.21         7.40        17.29        11.44         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
       12.07        10.09         7.33         9.80         7.69         6.18 
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        46.75        45.80 
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        34.75        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        51.29        33.11        16.73        41.88 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       64.11        44.48        11.61        23.24        29.36        32.81 
TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       25.81        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        11.51        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        31.10        29.85 
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        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-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       126.08        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        22.03 
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-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
       24.95        17.72        12.36        15.88         7.63        14.30 
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        35.54 
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        18.90        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45         9.83        12.13        12.10        10.65        11.18 
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        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       12.62         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       13.38        13.61        21.11         6.77         0.07         0.16 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       25.74         1.22        14.66        22.03        12.66        22.85 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         3.65        34.75        15.95        12.76 
TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       14.50        11.84        13.55         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       11.54        11.84        13.35        18.15        12.43        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         3.68 
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        56.75 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 
       51.25        10.85        36.82        47.01        19.00        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-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 
       11.74        17.65         7.30        16.70         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WZ 
       18.64        14.79        12.43        12.72        16.96        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        13.68        43.59 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        43.36        41.16        42.02        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       62.27        17.95        24.16        49.22        21.86        16.11 
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 

  HRAS MUTATED HRAS WILD-TYPE 
          0.36           0.07 
  HRAS MUTATED HRAS WILD-TYPE 
        130.88         210.97 
  HRAS MUTATED HRAS WILD-TYPE 
        24.415         18.475 
[1] "0.4 - 130.9 (24.4)" "0.1 - 211.0 (18.5)"
[1] "hr=" "1.2"
D6V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  HRAS MUTATED         2        7         4        12         1
  HRAS WILD-TYPE      23       69        73       236        10
D6V3, multiclass
           clus
vv          HRAS MUTATED HRAS WILD-TYPE
  STAGE I              2             23
  STAGE II             7             69
  STAGE III            4             73
  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   9   5  10
  HRAS WILD-TYPE    46 122  93 158
D6V4, multiclass
       clus
vv      HRAS MUTATED HRAS WILD-TYPE
  T0+T1            2             46
  T2               9            122
  T3               5             93
  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   3   5   1
  HRAS WILD-TYPE 160  62 156   6
D6V5, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  N0           14            160
  N1            3             62
  N2            5            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"
D6V6, binary
                cls
clus               0   1
  HRAS MUTATED    12  16
  HRAS WILD-TYPE 127 351
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED     12   16
  HRAS WILD-TYPE  127  351
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  FEMALE           12            127
  MALE             16            351
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  HRAS MUTATED                                      28
  HRAS WILD-TYPE                                   470
                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
D6V7, multiclass
                                                             clus
vv                                                            HRAS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                 28
  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                                  470
  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"
D6V8, binary
                cls
clus               0   1
  HRAS MUTATED     1  27
  HRAS WILD-TYPE  82 396
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      1   27
  HRAS WILD-TYPE   82  396
     clus
vv    HRAS MUTATED HRAS WILD-TYPE
  NO             1             82
  YES           27            396
[1] 2 2
[1] FALSE
D6V9, continuous
D6V10, continuous
D6V11, 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    26
  HRAS WILD-TYPE                        35   415
D6V12, multiclass
                                  clus
vv                                 HRAS MUTATED HRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             35
  WHITE                                      26            415
[1] 4 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
  HRAS MUTATED     0  28
  HRAS WILD-TYPE  25 417
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0   28
  HRAS WILD-TYPE   25  417
                        clus
vv                       HRAS MUTATED HRAS WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO           28            417
[1] 2 2
[1] FALSE

Clustering(7) Variable = TGFBR2 MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2                0   1
  TGFBR2 MUTATED    13  10
  TGFBR2 WILD-TYPE 290 191
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              23              481 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              10              191 
$`TGFBR2 MUTATED`
TCGA-CN-4731 TCGA-CQ-7071 TCGA-CR-7376 TCGA-CR-7402 TCGA-CV-5444 TCGA-CV-6943 
       32.65        28.83        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 
       24.99        10.42        11.18        21.63        11.80        13.55 
TCGA-IQ-A61J TCGA-P3-A5QF TCGA-QK-A6II TCGA-QK-A6VB TCGA-T2-A6X2 
       14.47        10.85         9.34        14.79        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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4734 
       40.44        37.84        12.89        26.86        21.11        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       35.54        55.27         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        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        20.68        20.65        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       14.20         6.74         9.07         9.24        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        46.75        45.80        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        34.75        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        51.29        33.11        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        64.11        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 
       32.81        25.81        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 
       11.51        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 
       31.10        29.85        29.52        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        94.88 
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       126.08 
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        22.03         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 
       22.52        10.42        10.55        18.84        34.36        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        15.88 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        14.30        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        35.54        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 
       18.90        25.48        20.45         9.83        12.13        12.10 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       10.65        37.18        20.25         3.02        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
       12.62         0.46        17.85        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         6.77         0.07         0.16 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       25.74         1.22        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-A61I 
       15.95        12.76        14.50        19.33        11.84         0.07 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
        5.29        11.54        11.84        13.35        18.15        12.43 
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 
        3.68        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 
       56.75        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        11.74        17.65         7.30        16.70        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       18.64        12.43        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        13.68        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        43.36        41.16        42.02        44.65        62.27 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.16        49.22        21.86        16.11        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 
           19.79            18.64 
[1] "2.5 - 89.3 (19.8)"  "0.1 - 211.0 (18.6)"
[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       72        72       238        11
D7V3, multiclass
           clus
vv          TGFBR2 MUTATED TGFBR2 WILD-TYPE
  STAGE I                1               24
  STAGE II               4               72
  STAGE III              5               72
  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    47 124  95 159
D7V4, multiclass
       clus
vv      TGFBR2 MUTATED TGFBR2 WILD-TYPE
  T0+T1              1               47
  T2                 7              124
  T3                 3               95
  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 165  62 157   7
D7V5, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  N0              9              165
  N1              3               62
  N2              4              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"
D7V6, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     6  17
  TGFBR2 WILD-TYPE 133 350
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      6   17
  TGFBR2 WILD-TYPE  133  350
        clus
vv       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  FEMALE              6              133
  MALE               17              350
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  TGFBR2 MUTATED                                      23
  TGFBR2 WILD-TYPE                                   475
                  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
D7V7, 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                                    475
  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"
D7V8, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     0  23
  TGFBR2 WILD-TYPE  83 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      0   23
  TGFBR2 WILD-TYPE   83  400
     clus
vv    TGFBR2 MUTATED TGFBR2 WILD-TYPE
  NO               0               83
  YES             23              400
[1] 2 2
[1] FALSE
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                        33   421
D7V12, multiclass
                                  clus
vv                                 TGFBR2 MUTATED TGFBR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     3               33
  WHITE                                        20              421
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     1  21
  TGFBR2 WILD-TYPE  24 424
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      1   21
  TGFBR2 WILD-TYPE   24  424
                        clus
vv                       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  HISPANIC OR LATINO                  1               24
  NOT HISPANIC OR LATINO             21              424
[1] 2 2
[1] FALSE

Clustering(8) Variable = FAT1 MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  FAT1 MUTATED    62  51
  FAT1 WILD-TYPE 241 150
  FAT1 MUTATED FAT1 WILD-TYPE 
           113            391 
  FAT1 MUTATED FAT1 WILD-TYPE 
            51            150 
$`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         7.76        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        32.65        11.84        12.49         8.52 
TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-A49A 
       20.68        19.53        19.07        11.08        20.09        12.85 
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        34.75        51.29 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-6477 TCGA-CR-6492 
       32.81        25.81        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 
       29.52        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       126.08        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-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7592 
       17.72        12.36        15.88        30.94        18.02         9.83 
TCGA-DQ-7595 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A622 TCGA-F7-A624 
       10.65        21.63         3.02        18.94        11.80        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-HL-7533 
       13.38        15.16         0.36        13.84         6.90        34.75 
TCGA-IQ-A61E TCGA-MT-A67A TCGA-P3-A6T0 TCGA-QK-A64Z TCGA-QK-A6II TCGA-UF-A71D 
       19.33        30.05        19.00        21.07         9.34        41.16 
TCGA-UF-A7J9 TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JT TCGA-WA-A7GZ 
       44.65        16.11        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        53.79        57.44 
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        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44        37.84 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
       12.89        26.86        21.11        24.92        41.10        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        43.73        27.58        41.69        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 
       33.11        34.36         8.58        12.39        35.54        55.27 
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        22.45        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 
       20.71        30.67        20.65        20.68        14.20         6.74 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 
        9.07         9.24        36.49        10.45        12.95        24.16 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        3.68        17.42        14.10        11.74        35.01        14.56 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       17.59        29.72        21.21         7.40        17.29        15.91 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
       11.44         5.75        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        2.93        46.75        45.80        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        33.11        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       43.04        41.88        28.83        64.11        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        11.51         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        31.10        29.85         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        94.88        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 
       24.99       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        22.03        21.24        19.92        18.84 
TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       34.36        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-A6EM 
       16.14        11.44        18.67        24.95        25.32         7.63 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       14.30        13.94        12.10        12.79        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
       35.54        33.86        14.04        18.90        25.48        20.45 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A50J 
       12.13        12.10        11.18        37.18        20.25        19.23 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-A6C4 TCGA-H7-A6C5 
       12.62         0.46        17.85        20.25        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
        6.77         0.07         0.16        25.74         1.22        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-7630 
       22.03        12.66        22.85         4.27         3.65        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       12.76        14.50        11.84        13.55         0.07        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
        5.29        11.54        11.84        13.35        18.15        12.43 
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         3.68 
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        56.75 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 
       51.25        10.85        36.82        47.01        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A652 
        2.04        29.00        12.99        16.01        13.15        11.74 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
       17.65         7.30        16.70        12.72        18.64        14.79 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       12.43        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        13.68        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
        2.83        43.36        42.02        62.27        17.95        24.16 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JV TCGA-UP-A6WW 
       49.22        21.86        13.94        22.36         2.96        17.03 
TCGA-WA-A7H4 
       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 
         18.81          18.64 
[1] "0.4 - 180.2 (18.8)" "0.1 - 211.0 (18.6)"
[1] "hr=" "1.1"
D8V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  FAT1 MUTATED         4       20        16        53         3
  FAT1 WILD-TYPE      21       56        61       195         8
D8V3, multiclass
           clus
vv          FAT1 MUTATED FAT1 WILD-TYPE
  STAGE I              4             21
  STAGE II            20             56
  STAGE III           16             61
  STAGE IVA           53            195
  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  32  18  43
  FAT1 WILD-TYPE    44  99  80 125
D8V4, multiclass
       clus
vv      FAT1 MUTATED FAT1 WILD-TYPE
  T0+T1            4             44
  T2              32             99
  T3              18             80
  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  13  27   1
  FAT1 WILD-TYPE 131  52 134   6
D8V5, multiclass
    clus
vv   FAT1 MUTATED FAT1 WILD-TYPE
  N0           43            131
  N1           13             52
  N2           27            134
  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  71
  FAT1 WILD-TYPE  97 296
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED     42   71
  FAT1 WILD-TYPE   97  296
        clus
vv       FAT1 MUTATED FAT1 WILD-TYPE
  FEMALE           42             97
  MALE             71            296
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  FAT1 MUTATED                                     112
  FAT1 WILD-TYPE                                   386
                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
D8V7, multiclass
                                                             clus
vv                                                            FAT1 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                    1
                                                             clus
vv                                                            FAT1 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  386
  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"
D8V8, binary
                cls
clus               0   1
  FAT1 MUTATED    18  95
  FAT1 WILD-TYPE  65 328
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED     18   95
  FAT1 WILD-TYPE   65  328
     clus
vv    FAT1 MUTATED FAT1 WILD-TYPE
  NO            18             65
  YES           95            328
[1] 2 2
[1] FALSE
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    96
  FAT1 WILD-TYPE                        29   345
D8V12, multiclass
                                  clus
vv                                 FAT1 MUTATED FAT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   7             29
  WHITE                                      96            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"
D8V13, binary
                cls
clus               0   1
  FAT1 MUTATED     7  95
  FAT1 WILD-TYPE  18 350
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED      7   95
  FAT1 WILD-TYPE   18  350
                        clus
vv                       FAT1 MUTATED FAT1 WILD-TYPE
  HISPANIC OR LATINO                7             18
  NOT HISPANIC OR LATINO           95            350
[1] 2 2
[1] FALSE

Clustering(9) Variable = NOTCH1 MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2                0   1
  NOTCH1 MUTATED    48  38
  NOTCH1 WILD-TYPE 255 163
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              86              418 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              38              163 
$`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        23.70        12.89        12.99        13.05 
TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-5369 TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6021 
       33.11         8.32        12.49        30.67        19.53         9.07 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-A63W TCGA-CQ-5329 TCGA-CQ-5333 TCGA-CQ-5334 
       20.09        24.16        11.44        46.75        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        28.83        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 
       29.52        30.58        19.20        17.95        94.88        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       126.08        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        15.88 
TCGA-DQ-5625 TCGA-DQ-5631 TCGA-F7-A50I TCGA-F7-A622 TCGA-HD-8635 TCGA-HD-A6I0 
       35.54        18.02         3.02        11.80        22.85         6.90 
TCGA-IQ-A61E TCGA-MT-A67A TCGA-MT-A67D TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6II 
       19.33        30.05         1.84        13.15        11.74         9.34 
TCGA-T2-A6X2 TCGA-TN-A7HL 
       32.45        13.68 

$`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        53.79        57.44        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         7.76        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        94.62         9.14         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8601 
       18.35        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        40.44        37.84        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 
       32.65        21.11        24.92        41.10        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       43.73        27.58        41.69        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       35.54        55.27        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        22.45        56.94        20.71        20.68        20.65 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 
       20.68        19.07        14.20         6.74         9.24        36.49 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       11.08        10.45        12.95         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        14.56        17.59        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       21.21         7.40        17.29        15.91         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        10.09         7.33         9.80         7.69 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
        6.18        48.20        39.68        21.50         2.93        54.58 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6222 
       45.80        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 
       34.75        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        51.29        33.11        16.73        43.04        41.88 
TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       64.11        11.61        23.24        29.36        32.81        25.81 
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        11.51         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        31.10        29.85         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        24.99       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 
       22.03         3.62        23.47        19.92        10.42        10.42 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        34.36        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-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       17.72        12.36         7.63        14.30        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 
       12.79        11.11        58.45        30.94        33.86        14.04 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       18.90        25.48        20.45         9.83        12.13        12.10 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J 
       10.65        11.18        37.18        21.63        20.25        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 
       18.94        12.62         0.46        17.85        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         6.77         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
        0.16        25.74         1.22        14.66        22.03        12.66 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 
        0.36        13.84         4.27         3.65        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       12.76        14.50        11.84        13.55         0.07        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
        5.29        11.54        11.84        13.35        18.15        12.43 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
       10.75        14.37         7.96        12.62         3.68        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        56.75        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-QK-A64Z TCGA-QK-A6IF 
        2.04        29.00        12.99        16.01        21.07        17.65 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
        7.30        16.70        12.72        18.64        14.79        12.43 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-TN-A7HI 
       12.72        16.96         6.87        15.91         7.10        13.55 
TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D 
       13.25        43.59        54.67         2.83        43.36        41.16 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       42.02        44.65        62.27        17.95        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       21.86        16.11        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 

  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
            0.76             0.07 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
          156.49           210.97 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
          18.610           18.655 
[1] "0.8 - 156.5 (18.6)" "0.1 - 211.0 (18.7)"
[1] "hr=" "1.2"
D9V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  NOTCH1 MUTATED         3       13        15        43         2
  NOTCH1 WILD-TYPE      22       63        62       205         9
D9V3, multiclass
           clus
vv          NOTCH1 MUTATED NOTCH1 WILD-TYPE
  STAGE I                3               22
  STAGE II              13               63
  STAGE III             15               62
  STAGE IVA             43              205
  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  19  17  35
  NOTCH1 WILD-TYPE    42 112  81 133
D9V4, multiclass
       clus
vv      NOTCH1 MUTATED NOTCH1 WILD-TYPE
  T0+T1              6               42
  T2                19              112
  T3                17               81
  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  11  21   1
  NOTCH1 WILD-TYPE 141  54 140   6
D9V5, multiclass
    clus
vv   NOTCH1 MUTATED NOTCH1 WILD-TYPE
  N0             33              141
  N1             11               54
  N2             21              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"
D9V6, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED    31  55
  NOTCH1 WILD-TYPE 108 312
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED     31   55
  NOTCH1 WILD-TYPE  108  312
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  FEMALE             31              108
  MALE               55              312
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  NOTCH1 MUTATED                                      86
  NOTCH1 WILD-TYPE                                   412
                  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
D9V7, multiclass
                                                             clus
vv                                                            NOTCH1 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   86
  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                                    412
  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"
D9V8, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED    13  73
  NOTCH1 WILD-TYPE  70 350
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED     13   73
  NOTCH1 WILD-TYPE   70  350
     clus
vv    NOTCH1 MUTATED NOTCH1 WILD-TYPE
  NO              13               70
  YES             73              350
[1] 2 2
[1] FALSE
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    77
  NOTCH1 WILD-TYPE                        31   364
D9V12, multiclass
                                  clus
vv                                 NOTCH1 MUTATED NOTCH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     5               31
  WHITE                                        77              364
[1] 4 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  76
  NOTCH1 WILD-TYPE  18 369
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      7   76
  NOTCH1 WILD-TYPE   18  369
                        clus
vv                       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  HISPANIC OR LATINO                  7               18
  NOT HISPANIC OR LATINO             76              369
[1] 2 2
[1] FALSE

Clustering(10) Variable = EPHA2 MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2               0   1
  EPHA2 MUTATED    12  11
  EPHA2 WILD-TYPE 291 190
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             23             481 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             11             190 
$`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        24.92        33.11 
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-F7-A624 
       56.48         6.38        22.19        45.96        10.42        12.43 
TCGA-IQ-A61E TCGA-P3-A5QF TCGA-RS-A6TP TCGA-T2-A6X2 TCGA-UF-A7JD 
       19.33        10.85        16.96        32.45        24.16 

$`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        53.79        57.44 
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         7.76 
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        94.62         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.41        18.35        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 
       23.70        38.04        40.44        37.84        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       32.65        21.11        41.10        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 
       43.73        27.58        41.69        13.05        34.36         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       12.39        35.54        55.27         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        22.45        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       20.71        30.67        20.68        20.65        19.53        20.68 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        14.20         6.74         9.07         9.24        36.49 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       11.08        10.45        20.09        12.95        24.16         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        14.10        11.74        35.01        14.56        17.59 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       12.85        29.72        21.21        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        2.93        46.75        45.80        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        34.75 
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 
       51.29        33.11        16.73        43.04        28.83        64.11 
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        32.81        25.81 
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        11.51        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        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       29.85        29.52        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        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      126.08        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        24.99       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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        34.36        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-A6EO TCGA-D6-A6EP 
       17.72        12.36        15.88         7.63        14.30        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        35.54        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        18.90        25.48        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
        9.83        12.13        12.10        10.65        11.18        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        19.23        18.94        12.62 
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         6.77         0.07         0.16        25.74 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
        1.22        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-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       12.76        14.50        11.84        13.55         0.07        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
        5.29        11.54        11.84        13.35        18.15        12.43 
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 
        3.68        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 
       56.75        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-A6II 
       21.07        11.74        17.65         7.30        16.70         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-T2-A6WX 
       12.72        18.64        14.79        12.43        12.72         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       15.91         7.10        13.55        13.25        13.68        43.59 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        43.36        41.16        42.02        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       62.27        17.95        49.22        21.86        16.11        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 

  EPHA2 MUTATED EPHA2 WILD-TYPE 
           4.01            0.07 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
          56.48          210.97 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
          19.33           18.64 
[1] "4.0 - 56.5 (19.3)"  "0.1 - 211.0 (18.6)"
[1] "hr=" "1.4"
D10V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  EPHA2 MUTATED         1        6         3        13         0
  EPHA2 WILD-TYPE      24       70        74       235        11
D10V3, multiclass
           clus
vv          EPHA2 MUTATED EPHA2 WILD-TYPE
  STAGE I               1              24
  STAGE II              6              70
  STAGE III             3              74
  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   7   7   8
  EPHA2 WILD-TYPE    47 124  91 160
D10V4, multiclass
       clus
vv      EPHA2 MUTATED EPHA2 WILD-TYPE
  T0+T1             1              47
  T2                7             124
  T3                7              91
  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   0   8   0
  EPHA2 WILD-TYPE 163  65 153   7
D10V5, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  N0            11             163
  N1             0              65
  N2             8             153
  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
  EPHA2 MUTATED     8  15
  EPHA2 WILD-TYPE 131 352
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      8   15
  EPHA2 WILD-TYPE  131  352
        clus
vv       EPHA2 MUTATED EPHA2 WILD-TYPE
  FEMALE             8             131
  MALE              15             352
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  EPHA2 MUTATED                                      23
  EPHA2 WILD-TYPE                                   475
                 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
D10V7, multiclass
                                                             clus
vv                                                            EPHA2 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                                                            EPHA2 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   475
  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"
D10V8, binary
                 cls
clus                0   1
  EPHA2 MUTATED     3  20
  EPHA2 WILD-TYPE  80 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      3   20
  EPHA2 WILD-TYPE   80  403
     clus
vv    EPHA2 MUTATED EPHA2 WILD-TYPE
  NO              3              80
  YES            20             403
[1] 2 2
[1] FALSE
D10V9, continuous
D10V10, continuous
D10V11, 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    19
  EPHA2 WILD-TYPE                        34   422
D10V12, multiclass
                                  clus
vv                                 EPHA2 MUTATED EPHA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              34
  WHITE                                       19             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"
D10V13, binary
                 cls
clus                0   1
  EPHA2 MUTATED     1  21
  EPHA2 WILD-TYPE  24 424
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      1   21
  EPHA2 WILD-TYPE   24  424
                        clus
vv                       EPHA2 MUTATED EPHA2 WILD-TYPE
  HISPANIC OR LATINO                 1              24
  NOT HISPANIC OR LATINO            21             424
[1] 2 2
[1] FALSE

Clustering(11) Variable = HLA-B MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2               0   1
  HLA-B MUTATED    16   8
  HLA-B WILD-TYPE 287 193
  HLA-B MUTATED HLA-B WILD-TYPE 
             24             480 
  HLA-B MUTATED HLA-B WILD-TYPE 
              8             193 
$`HLA-B MUTATED`
TCGA-BA-5559 TCGA-BA-A6D8 TCGA-BA-A6DJ TCGA-CN-4723 TCGA-CN-A63Y TCGA-CN-A642 
       57.44        27.95        13.38        23.70         5.75         2.70 
TCGA-CQ-5324 TCGA-CQ-7071 TCGA-CR-6481 TCGA-CR-7395 TCGA-CV-5973 TCGA-CV-7099 
       39.68        28.83        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        41.16        42.02        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 
       53.79        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         7.76        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        94.62         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.41        18.35        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        40.44        37.84        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       32.65        21.11        24.92        41.10        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        43.73        27.58        41.69        13.05        33.11 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       34.36         8.58        12.39        35.54        55.27         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 
       22.45        56.94        20.71        30.67        20.68        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
       19.53        20.68        19.07        14.20         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        9.24        36.49        11.08        10.45        20.09        12.95 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 
       24.16         3.68        17.42        14.10        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       14.56        17.59        12.85        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A6UY 
       17.29        15.91        11.44         4.41        12.07        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5325 
        7.33         9.80         7.69         6.18        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        46.75        45.80        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        34.75        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        51.29        33.11        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        64.11        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 
       32.81        25.81        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        11.51 
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 
       31.10        29.85        29.52         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        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-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       126.08 
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        24.99       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 
       22.03         3.62        21.24        23.47        19.92        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 
       10.55        18.84        34.36        13.25         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-A6EO TCGA-D6-A6EP 
       17.72        12.36        15.88         7.63        14.30        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        35.54        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        18.90        25.48        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
        9.83        12.13        12.10        10.65        11.18        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        19.23        18.94        12.62 
TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
        0.46        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.61        21.11         6.77         0.07         0.16        25.74 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A633 
        1.22        14.66        22.03        12.66        22.85        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        12.76 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        19.33        11.84        13.55         0.07        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
        5.29        11.54        11.84        13.35        18.15        12.43 
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 
        3.68        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 
       56.75        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        11.74        17.65         7.30        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO 
        9.34        12.72        18.64        14.79        12.43        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 
       13.68        43.59        54.67         2.83        43.36        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       62.27        17.95        24.16        49.22        21.86        16.11 
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 
         23.110          18.475 
[1] "0.4 - 86.8 (23.1)"  "0.1 - 211.0 (18.5)"
[1] "hr=" "1.1"
D11V2, 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       73        72       237        10
D11V3, multiclass
           clus
vv          HLA-B MUTATED HLA-B WILD-TYPE
  STAGE I               1              24
  STAGE II              3              73
  STAGE III             5              72
  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    47 127  94 156
D11V4, multiclass
       clus
vv      HLA-B MUTATED HLA-B WILD-TYPE
  T0+T1             1              47
  T2                4             127
  T3                4              94
  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 161  62 158   6
D11V5, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  N0            13             161
  N1             3              62
  N2             3             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"
D11V6, binary
                 cls
clus                0   1
  HLA-B MUTATED    10  14
  HLA-B WILD-TYPE 129 353
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED     10   14
  HLA-B WILD-TYPE  129  353
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  FEMALE            10             129
  MALE              14             353
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  HLA-B MUTATED                                      23
  HLA-B WILD-TYPE                                   475
                 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
D11V7, 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                                   475
  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"
D11V8, binary
                 cls
clus                0   1
  HLA-B MUTATED     0  24
  HLA-B WILD-TYPE  83 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      0   24
  HLA-B WILD-TYPE   83  399
     clus
vv    HLA-B MUTATED HLA-B WILD-TYPE
  NO              0              83
  YES            24             399
[1] 2 2
[1] FALSE
D11V9, continuous
D11V10, continuous
D11V11, 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                        34   420
D11V12, 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              34
  WHITE                                       21             420
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, binary
                 cls
clus                0   1
  HLA-B MUTATED     0  18
  HLA-B WILD-TYPE  25 427
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      0   18
  HLA-B WILD-TYPE   25  427
                        clus
vv                       HLA-B MUTATED HLA-B WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO            18             427
[1] 2 2
[1] FALSE

Clustering(12) Variable = RAC1 MUTATION ANALYSIS
D12V1, survival
                sevent
clus2              0   1
  RAC1 MUTATED     7   8
  RAC1 WILD-TYPE 296 193
  RAC1 MUTATED RAC1 WILD-TYPE 
            15            489 
  RAC1 MUTATED RAC1 WILD-TYPE 
             8            193 
$`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        34.75        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        24.99         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        53.79 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       57.44        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         7.76        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        94.62         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.35        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        23.70        38.04         4.67        40.44        37.84 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.65        21.11        24.92        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        33.11        34.36         8.58        12.39        35.54 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       55.27         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        22.45        56.94        20.71        30.67        20.68 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       20.65        19.53        20.68        19.07        14.20         6.74 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        9.07         9.24        36.49        11.08        10.45        20.09 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       12.95        24.16         3.68        17.42        14.10        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        14.56        17.59        12.85        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 
        7.40        17.29        15.91        11.44         5.75        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
        2.70        10.09         7.33         9.80         7.69         6.18 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        39.68        21.50         2.93        54.58        46.75 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       45.80        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        51.29        33.11 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       16.73        43.04        41.88        28.83        64.11        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        32.81        25.81        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        11.51        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        31.10        29.85        29.52        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        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       126.08        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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       15.88         7.63        14.30        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        35.54        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        18.90        25.48        20.45         9.83        12.13 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       12.10        10.65        11.18        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        19.23        18.94        12.62         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 
       11.80        20.25        12.43        15.16        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
        6.77         0.07         0.16        25.74         1.22        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        12.76        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       19.33        11.84        13.55         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       11.54        11.84        13.35        18.15        12.43        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         3.68 
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        56.75 
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        11.74        17.65         7.30        16.70         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP 
       12.72        18.64        14.79        12.43        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 
       13.68        43.59        54.67         2.83        43.36        41.16 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       42.02        44.65        62.27        17.95        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JV 
       21.86        16.11        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 
         22.52          18.64 
[1] "4.4 - 156.5 (22.5)" "0.1 - 211.0 (18.6)"
[1] "hr=" "1.3"
D12V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  RAC1 MUTATED         2        2         0         7         0
  RAC1 WILD-TYPE      23       74        77       241        11
D12V3, multiclass
           clus
vv          RAC1 MUTATED RAC1 WILD-TYPE
  STAGE I              2             23
  STAGE II             2             74
  STAGE III            0             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
  RAC1 MUTATED       2   3   0   6
  RAC1 WILD-TYPE    46 128  98 162
D12V4, multiclass
       clus
vv      RAC1 MUTATED RAC1 WILD-TYPE
  T0+T1            2             46
  T2               3            128
  T3               0             98
  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 167  64 159   7
D12V5, multiclass
    clus
vv   RAC1 MUTATED RAC1 WILD-TYPE
  N0            7            167
  N1            1             64
  N2            2            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"
D12V6, binary
                cls
clus               0   1
  RAC1 MUTATED     9   6
  RAC1 WILD-TYPE 130 361
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      9    6
  RAC1 WILD-TYPE  130  361
        clus
vv       RAC1 MUTATED RAC1 WILD-TYPE
  FEMALE            9            130
  MALE              6            361
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  RAC1 MUTATED                                      15
  RAC1 WILD-TYPE                                   483
                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
D12V7, 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                                  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"
D12V8, binary
                cls
clus               0   1
  RAC1 MUTATED     2  13
  RAC1 WILD-TYPE  81 410
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      2   13
  RAC1 WILD-TYPE   81  410
     clus
vv    RAC1 MUTATED RAC1 WILD-TYPE
  NO             2             81
  YES           13            410
[1] 2 2
[1] FALSE
D12V9, continuous
D12V10, continuous
D12V11, 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                        36   427
D12V12, multiclass
                                  clus
vv                                 RAC1 MUTATED RAC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             36
  WHITE                                      14            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"
D12V13, binary
                cls
clus               0   1
  RAC1 MUTATED     0  14
  RAC1 WILD-TYPE  25 431
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      0   14
  RAC1 WILD-TYPE   25  431
                        clus
vv                       RAC1 MUTATED RAC1 WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO           14            431
[1] 2 2
[1] FALSE

Clustering(13) Variable = NFE2L2 MUTATION ANALYSIS
D13V1, survival
                  sevent
clus2                0   1
  NFE2L2 MUTATED    13  13
  NFE2L2 WILD-TYPE 290 188
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              26              478 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              13              188 
$`NFE2L2 MUTATED`
TCGA-BA-7269 TCGA-CN-4723 TCGA-CN-6019 TCGA-CQ-5324 TCGA-CQ-A4CG TCGA-CR-7383 
        7.76        23.70        14.20        39.68        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       126.08        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        15.88        13.38 
TCGA-HD-A6HZ TCGA-IQ-A61H TCGA-MT-A67A TCGA-P3-A5QF TCGA-P3-A6T4 TCGA-TN-A7HL 
        3.65        13.55        30.05        10.85         2.04        13.68 
TCGA-UF-A71B TCGA-UF-A71D 
       43.36        41.16 

$`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 
       53.79        57.44        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        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.35        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        40.44        37.84 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.65        21.11        24.92        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        33.11        34.36         8.58        12.39        35.54 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       55.27         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        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6020 
       20.68        20.65        19.53        20.68        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        36.49        11.08        10.45        20.09 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       12.95        24.16         3.68        17.42        14.10        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        14.56        17.59        12.85        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        17.29        15.91        11.44         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        10.09         7.33         9.80         7.69 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
        6.18        48.20        21.50         2.93        54.58        46.75 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       45.80        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        34.75        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        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       33.11        16.73        43.04        41.88        28.83        64.11 
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        32.81        25.81 
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        11.51        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        31.10        29.85        29.52 
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        94.88        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       60.49         7.07        43.23        54.74        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-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        24.99       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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        34.36        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        14.30        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        35.54        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        18.90        25.48        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
        9.83        12.13        12.10        10.65        11.18        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        19.23        18.94        12.62 
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         6.77         0.07         0.16        25.74 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
        1.22        14.66        22.03        12.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         6.90        34.75        15.95        12.76 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       14.50        19.33        11.84         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       11.54        11.84        13.35        18.15        12.43        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         3.68        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        56.75        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        11.74        17.65 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        16.70         9.34        12.72        18.64        14.79 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       12.43        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        43.59        54.67         2.83 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       42.02        44.65        62.27        17.95        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       21.86        16.11        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 
          126.08           210.97 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
          14.545           18.920 
[1] "2.0 - 126.1 (14.5)" "0.1 - 211.0 (18.9)"
[1] "hr=" "1.5"
D13V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  NFE2L2 MUTATED         2        6         5        13         0
  NFE2L2 WILD-TYPE      23       70        72       235        11
D13V3, multiclass
           clus
vv          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE I                2               23
  STAGE II               6               70
  STAGE III              5               72
  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
  NFE2L2 MUTATED       2  10   5   9
  NFE2L2 WILD-TYPE    46 121  93 159
D13V4, multiclass
       clus
vv      NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T0+T1              2               46
  T2                10              121
  T3                 5               93
  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 164  60 155   7
D13V5, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0             10              164
  N1              5               60
  N2              6              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"
D13V6, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED    11  15
  NFE2L2 WILD-TYPE 128 352
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     11   15
  NFE2L2 WILD-TYPE  128  352
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE             11              128
  MALE               15              352
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  NFE2L2 MUTATED                                      26
  NFE2L2 WILD-TYPE                                   472
                  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
D13V7, 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                                    472
  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"
D13V8, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     2  24
  NFE2L2 WILD-TYPE  81 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      2   24
  NFE2L2 WILD-TYPE   81  399
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  NO               2               81
  YES             24              399
[1] 2 2
[1] FALSE
D13V9, continuous
D13V10, continuous
D13V11, 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    23
  NFE2L2 WILD-TYPE                        36   418
D13V12, multiclass
                                  clus
vv                                 NFE2L2 MUTATED NFE2L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               36
  WHITE                                        23              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"
D13V13, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     2  20
  NFE2L2 WILD-TYPE  23 425
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      2   20
  NFE2L2 WILD-TYPE   23  425
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  2               23
  NOT HISPANIC OR LATINO             20              425
[1] 2 2
[1] FALSE

Clustering(14) Variable = ZNF750 MUTATION ANALYSIS
D14V1, survival
                  sevent
clus2                0   1
  ZNF750 MUTATED    11   8
  ZNF750 WILD-TYPE 292 193
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              19              485 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               8              193 
$`ZNF750 MUTATED`
TCGA-BB-7870 TCGA-CN-A63Y TCGA-CR-6481 TCGA-CR-7368 TCGA-CR-7404 TCGA-CV-5434 
       66.28         5.75        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        12.43         3.68        17.98        10.85         6.87 
TCGA-TN-A7HL 
       13.68 

$`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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       37.84        12.89        26.86        32.65        21.11        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       35.54        55.27         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        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        20.68        20.65        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       14.20         6.74         9.07         9.24        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.69         6.18        48.20        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        46.75        45.80        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 
       34.75        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        51.29        33.11        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       28.83        64.11        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 
       32.81        25.81        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        11.51 
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        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       29.85        29.52        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        94.88        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       126.08        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        24.99       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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        34.36        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-A6EO TCGA-D6-A6EP 
       17.72        12.36        15.88         7.63        14.30        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       12.10        12.79        11.11        58.45        35.54        33.86 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       18.02        14.04        18.90        25.48        20.45         9.83 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
       12.13        12.10        10.65        11.18        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        19.23        18.94        12.62         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         6.77         0.07         0.16        25.74 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
        1.22        14.66        22.03        12.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         3.65         6.90        15.95        12.76 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        19.33        11.84        13.55         0.07        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H8 
        5.29        11.54        11.84        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        56.75        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        11.74        17.65 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        16.70         9.34        12.72        18.64        14.79 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.43        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        43.59        54.67         2.83        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       41.16        42.02        44.65        62.27        17.95        24.16 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       49.22        21.86        16.11        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 
           17.98            18.67 
[1] "0.5 - 109.0 (18.0)" "0.1 - 211.0 (18.7)"
[1] "hr=" "1"  
D14V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  ZNF750 MUTATED         0        3         0        11         0
  ZNF750 WILD-TYPE      25       73        77       237        11
D14V3, multiclass
           clus
vv          ZNF750 MUTATED ZNF750 WILD-TYPE
  STAGE I                0               25
  STAGE II               3               73
  STAGE III              0               77
  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    46 128  96 161
D14V4, multiclass
       clus
vv      ZNF750 MUTATED ZNF750 WILD-TYPE
  T0+T1              2               46
  T2                 3              128
  T3                 2               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
  ZNF750 MUTATED     4   2   8   0
  ZNF750 WILD-TYPE 170  63 153   7
D14V5, multiclass
    clus
vv   ZNF750 MUTATED ZNF750 WILD-TYPE
  N0              4              170
  N1              2               63
  N2              8              153
  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
  ZNF750 MUTATED     3  16
  ZNF750 WILD-TYPE 136 351
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      3   16
  ZNF750 WILD-TYPE  136  351
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  FEMALE              3              136
  MALE               16              351
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  ZNF750 MUTATED                                      19
  ZNF750 WILD-TYPE                                   479
                  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
D14V7, 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                                    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"
D14V8, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     2  17
  ZNF750 WILD-TYPE  81 406
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      2   17
  ZNF750 WILD-TYPE   81  406
     clus
vv    ZNF750 MUTATED ZNF750 WILD-TYPE
  NO               2               81
  YES             17              406
[1] 2 2
[1] FALSE
D14V9, continuous
D14V10, continuous
D14V11, 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                        33   425
D14V12, multiclass
                                  clus
vv                                 ZNF750 MUTATED ZNF750 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     3               33
  WHITE                                        16              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"
D14V13, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     0  19
  ZNF750 WILD-TYPE  25 426
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      0   19
  ZNF750 WILD-TYPE   25  426
                        clus
vv                       ZNF750 MUTATED ZNF750 WILD-TYPE
  HISPANIC OR LATINO                  0               25
  NOT HISPANIC OR LATINO             19              426
[1] 2 2
[1] FALSE

Clustering(15) Variable = PTEN MUTATION ANALYSIS
D15V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    12   2
  PTEN WILD-TYPE 291 199
  PTEN MUTATED PTEN WILD-TYPE 
            14            490 
  PTEN MUTATED PTEN WILD-TYPE 
             2            199 
$`PTEN MUTATED`
TCGA-BA-4074 TCGA-BA-5559 TCGA-BB-A6UM TCGA-CN-4723 TCGA-CN-A499 TCGA-CR-7369 
       15.19        57.44        12.92        23.70        17.59        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        14.79 
TCGA-T2-A6X0 TCGA-UF-A7JF 
        7.10        49.22 

$`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        53.79 
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 
        7.76        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        94.62         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.35        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        40.44        37.84        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       32.65        21.11        24.92        41.10        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        43.73        27.58        41.69        13.05        33.11 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       34.36         8.58        12.39        35.54        55.27         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 
       22.45        56.94        20.71        30.67        20.68        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
       19.53        20.68        19.07        14.20         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        9.24        36.49        11.08        10.45        20.09        12.95 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 
       24.16         3.68        17.42        14.10        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       14.56        12.85        29.72        21.21         7.40        17.29 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       15.91        11.44         5.75         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       10.09         7.33         9.80         7.69         6.18        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       39.68        21.50         2.93        54.58        46.75        45.80 
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        34.75        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        51.29        33.11 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       16.73        43.04        41.88        28.83        64.11        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        32.81        25.81        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        11.51        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        31.10        29.85        29.52        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        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        7.07        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-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       126.08        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        24.99       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 
       22.03         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-D6-6515 
       10.42        10.42        10.55        18.84        34.36        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        15.88 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 
        7.63        14.30        13.94        12.10        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       35.54        30.94        33.86        18.02        14.04        18.90 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       25.48        20.45         9.83        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       11.18        37.18        21.63        20.25         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        12.62         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         6.77 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        0.07         0.16        25.74         1.22        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        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        13.55         0.07        14.47         5.29        11.54 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       11.84        13.35        18.15        12.43        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         3.68         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        56.75        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        11.74        17.65 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC 
        7.30        16.70         9.34        12.72        18.64        12.43 
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        13.68        43.59        54.67         2.83        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       41.16        42.02        44.65        62.27        17.95        24.16 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       21.86        16.11        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 
         57.44         210.97 
  PTEN MUTATED PTEN WILD-TYPE 
        15.305         18.825 
[1] "1.0 - 57.4 (15.3)"  "0.1 - 211.0 (18.8)"
[1] "hr=" "2.5"
D15V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  PTEN MUTATED         0        2         1         8         0
  PTEN WILD-TYPE      25       74        76       240        11
D15V3, multiclass
           clus
vv          PTEN MUTATED PTEN WILD-TYPE
  STAGE I              0             25
  STAGE II             2             74
  STAGE III            1             76
  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    47 128  98 162
D15V4, multiclass
       clus
vv      PTEN MUTATED PTEN WILD-TYPE
  T0+T1            1             47
  T2               3            128
  T3               0             98
  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 168  65 157   7
D15V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0            6            168
  N1            0             65
  N2            4            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"
D15V6, binary
                cls
clus               0   1
  PTEN MUTATED     4  10
  PTEN WILD-TYPE 135 357
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4   10
  PTEN WILD-TYPE  135  357
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            4            135
  MALE             10            357
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  PTEN MUTATED                                      14
  PTEN WILD-TYPE                                   484
                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
D15V7, 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                                  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"
D15V8, binary
                cls
clus               0   1
  PTEN MUTATED     1  13
  PTEN WILD-TYPE  82 410
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1   13
  PTEN WILD-TYPE   82  410
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             1             82
  YES           13            410
[1] 2 2
[1] FALSE
D15V9, continuous
D15V10, continuous
D15V11, 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                        36   427
D15V12, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             36
  WHITE                                      14            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"
D15V13, binary
                cls
clus               0   1
  PTEN MUTATED     0  12
  PTEN WILD-TYPE  25 433
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0   12
  PTEN WILD-TYPE   25  433
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO           12            433
[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 289 193
  HLA-A MUTATED HLA-A WILD-TYPE 
             22             482 
  HLA-A MUTATED HLA-A WILD-TYPE 
              8             193 
$`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         7.33        28.83        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        15.88        12.10        12.43        15.16         0.36 
TCGA-QK-A6IF TCGA-RS-A6TO TCGA-UF-A7JJ TCGA-UF-A7JT 
       17.65        12.72        16.11        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        53.79 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
       57.44        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 
        7.76        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        94.62         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.35        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        23.70        38.04         4.67        40.44        37.84 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.65        21.11        24.92        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        33.11        34.36         8.58        12.39        35.54 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       55.27         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        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        14.56        17.59        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        17.29        15.91        11.44         5.75 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V3 TCGA-CN-A6V6 
        4.41        12.07         2.70        10.09         9.80         7.69 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
        6.18        48.20        39.68        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       46.75        45.80        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        34.75 
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 
       51.29        33.11        16.73        43.04        41.88        64.11 
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        32.81        25.81 
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        11.51        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        31.10        29.85        29.52 
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        94.88        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       126.08        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 
       24.99       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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        14.30        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        35.54        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-7595 
       18.90        25.48        20.45         9.83        12.13        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       11.18        37.18        21.63        20.25         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        12.62         0.46        17.85        11.80        20.25 
TCGA-H7-7774 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       13.38        13.61        21.11         6.77         0.07         0.16 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       25.74         1.22        14.66        22.03        12.66        22.85 
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 
       12.76        14.50        19.33        11.84        13.55         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
       14.47         5.29        11.54        11.84        13.35        18.15 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       12.43        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         3.68        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        56.75        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        11.74         7.30        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TP 
        9.34        12.72        18.64        14.79        12.43        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 
       13.68        43.59        54.67         2.83        43.36        41.16 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       42.02        44.65        62.27        17.95        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JV TCGA-UP-A6WW 
       21.86        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 
          16.88           18.74 
[1] "0.4 - 67.9 (16.9)"  "0.1 - 211.0 (18.7)"
[1] "hr=" "1"  
D16V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  HLA-A MUTATED         0        4         3        11         0
  HLA-A WILD-TYPE      25       72        74       237        11
D16V3, multiclass
           clus
vv          HLA-A MUTATED HLA-A WILD-TYPE
  STAGE I               0              25
  STAGE II              4              72
  STAGE III             3              74
  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
  HLA-A MUTATED       0   8   1   9
  HLA-A WILD-TYPE    48 123  97 159
D16V4, multiclass
       clus
vv      HLA-A MUTATED HLA-A WILD-TYPE
  T0+T1             0              48
  T2                8             123
  T3                1              97
  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 168  60 157   7
D16V5, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  N0             6             168
  N1             5              60
  N2             4             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"
D16V6, binary
                 cls
clus                0   1
  HLA-A MUTATED     6  16
  HLA-A WILD-TYPE 133 351
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      6   16
  HLA-A WILD-TYPE  133  351
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  FEMALE             6             133
  MALE              16             351
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  HLA-A MUTATED                                      22
  HLA-A WILD-TYPE                                   476
                 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
D16V7, 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                                   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"
D16V8, binary
                 cls
clus                0   1
  HLA-A MUTATED     4  18
  HLA-A WILD-TYPE  79 405
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      4   18
  HLA-A WILD-TYPE   79  405
     clus
vv    HLA-A MUTATED HLA-A WILD-TYPE
  NO              4              79
  YES            18             405
[1] 2 2
[1] FALSE
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                        34   422
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              34
  WHITE                                       19             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"
D16V13, binary
                 cls
clus                0   1
  HLA-A MUTATED     0  18
  HLA-A WILD-TYPE  25 427
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      0   18
  HLA-A WILD-TYPE   25  427
                        clus
vv                       HLA-A MUTATED HLA-A WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO            18             427
[1] 2 2
[1] FALSE

Clustering(17) Variable = RB1 MUTATION ANALYSIS
D17V1, survival
               sevent
clus2             0   1
  RB1 MUTATED    15   2
  RB1 WILD-TYPE 288 199
  RB1 MUTATED RB1 WILD-TYPE 
           17           487 
  RB1 MUTATED RB1 WILD-TYPE 
            2           199 
$`RB1 MUTATED`
TCGA-CN-5360 TCGA-CN-A499 TCGA-CQ-5327 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CR-6487 
       35.54        17.59        54.58        41.88        28.83         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-KU-A6H7 TCGA-QK-A6V9 TCGA-T2-A6WZ 
       12.10        19.23        12.43        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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       40.44        37.84        12.89        26.86        32.65        21.11 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       24.92        41.10        12.99        20.55        14.33        43.73 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        41.69        13.05        33.11        34.36         8.58 
TCGA-CN-5359 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       12.39        55.27         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        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        20.68        20.65        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       14.20         6.74         9.07         9.24        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B 
       14.10        11.74        35.01        14.56        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        17.29        15.91        11.44         5.75 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.69         6.18        48.20        39.68        21.50         2.93 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       46.75        45.80        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        34.75 
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 
       51.29        33.11        16.73        43.04        64.11        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        32.81        25.81        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        11.51        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        31.10        29.85        29.52        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        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
        5.46        20.52         4.73        26.43        11.24       126.08 
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 
       24.99       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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       34.36        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       16.14        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       12.36        15.88         7.63        14.30        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        35.54        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        18.90        25.48        20.45         9.83 
TCGA-DQ-7593 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       12.13        10.65        11.18        37.18        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
        3.02        18.94        12.62         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-7917 TCGA-HD-8224 
        6.77         0.07         0.16        25.74         1.22        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        12.76        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       19.33        11.84        13.55         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H8 TCGA-MT-A51W 
       11.54        11.84        13.35        18.15        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         3.68        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        56.75        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 
       11.74        17.65         7.30        16.70         9.34        12.72 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
       14.79        12.43        12.72        16.96         6.87         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        13.68        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        43.36        41.16        42.02        44.65        62.27 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.16        49.22        21.86        16.11        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 

  RB1 MUTATED RB1 WILD-TYPE 
         0.99          0.07 
  RB1 MUTATED RB1 WILD-TYPE 
        54.58        210.97 
  RB1 MUTATED RB1 WILD-TYPE 
        17.59         18.81 
[1] "1.0 - 54.6 (17.6)"  "0.1 - 211.0 (18.8)"
[1] "hr=" "2.7"
D17V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  RB1 MUTATED         2        4         2         4         0
  RB1 WILD-TYPE      23       72        75       244        11
D17V3, multiclass
           clus
vv          RB1 MUTATED RB1 WILD-TYPE
  STAGE I             2            23
  STAGE II            4            72
  STAGE III           2            75
  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   3   2
  RB1 WILD-TYPE    46 125  95 166
D17V4, multiclass
       clus
vv      RB1 MUTATED RB1 WILD-TYPE
  T0+T1           2            46
  T2              6           125
  T3              3            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     7   1   4   0
  RB1 WILD-TYPE 167  64 157   7
D17V5, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  N0           7           167
  N1           1            64
  N2           4           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"
D17V6, binary
               cls
clus              0   1
  RB1 MUTATED    10   7
  RB1 WILD-TYPE 129 360
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     10    7
  RB1 WILD-TYPE  129  360
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE          10           129
  MALE             7           360
[1] 2 2
[1] FALSE
               vv
clus            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  RB1 MUTATED                                      17
  RB1 WILD-TYPE                                   481
               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
D17V7, multiclass
                                                             clus
vv                                                            RB1 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                                                            RB1 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                     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"
D17V8, binary
               cls
clus              0   1
  RB1 MUTATED     2  15
  RB1 WILD-TYPE  81 408
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      2   15
  RB1 WILD-TYPE   81  408
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO            2            81
  YES          15           408
[1] 2 2
[1] FALSE
D17V9, continuous
D17V10, continuous
D17V11, 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    16
  RB1 WILD-TYPE                        36   425
D17V12, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  0            36
  WHITE                                     16           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"
D17V13, binary
               cls
clus              0   1
  RB1 MUTATED     0  16
  RB1 WILD-TYPE  25 429
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0   16
  RB1 WILD-TYPE   25  429
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               0            25
  NOT HISPANIC OR LATINO          16           429
[1] 2 2
[1] FALSE

Clustering(18) Variable = MAPK1 MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2               0   1
  MAPK1 MUTATED     8   1
  MAPK1 WILD-TYPE 295 200
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              9             495 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              1             200 
$`MAPK1 MUTATED`
TCGA-C9-A480 TCGA-CN-A63Y TCGA-CQ-5334 TCGA-CV-5442 TCGA-CV-5971 TCGA-CV-7261 
       12.69         5.75         4.24        76.50        23.05        36.13 
TCGA-D6-A74Q TCGA-MT-A67F TCGA-TN-A7HL 
       11.11        12.62        13.68 

$`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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       37.84        12.89        26.86        32.65        21.11        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       35.54        55.27         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        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        20.68        20.65        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       14.20         6.74         9.07         9.24        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.69         6.18        48.20        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        46.75        45.80        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        34.75 
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 
       51.29        33.11        16.73        43.04        41.88        28.83 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       64.11        44.48        11.61        23.24        29.36        32.81 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       25.81        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        11.51 
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 
       31.10        29.85        29.52        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 
       94.88        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       126.08 
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        24.99 
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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       34.36        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       16.14        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       12.36        15.88         7.63        14.30        13.94        12.10 
TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        58.45        35.54        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        18.90        25.48        20.45         9.83        12.13 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       12.10        10.65        11.18        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        19.23        18.94        12.62         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-7917 
       21.11         6.77         0.07         0.16        25.74         1.22 
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        12.76 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        19.33        11.84        13.55         0.07        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
        5.29        11.54        11.84        13.35        18.15        12.43 
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         3.68 
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        56.75 
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        11.74        17.65         7.30        16.70         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP 
       12.72        18.64        14.79        12.43        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 
       43.59        54.67         2.83        43.36        41.16        42.02 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        62.27        17.95        24.16        49.22        21.86 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       16.11        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 
          12.69           18.81 
[1] "4.2 - 76.5 (12.7)"  "0.1 - 211.0 (18.8)"
[1] "hr=" "2.9"
D18V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  MAPK1 MUTATED         0        1         1         7         0
  MAPK1 WILD-TYPE      25       75        76       241        11
D18V3, multiclass
           clus
vv          MAPK1 MUTATED MAPK1 WILD-TYPE
  STAGE I               0              25
  STAGE II              1              75
  STAGE III             1              76
  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    48 130  95 163
D18V4, multiclass
       clus
vv      MAPK1 MUTATED MAPK1 WILD-TYPE
  T0+T1             0              48
  T2                1             130
  T3                3              95
  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 169  65 157   7
D18V5, multiclass
    clus
vv   MAPK1 MUTATED MAPK1 WILD-TYPE
  N0             5             169
  N1             0              65
  N2             4             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"
D18V6, binary
                 cls
clus                0   1
  MAPK1 MUTATED     3   6
  MAPK1 WILD-TYPE 136 361
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      3    6
  MAPK1 WILD-TYPE  136  361
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  FEMALE             3             136
  MALE               6             361
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  MAPK1 MUTATED                                       9
  MAPK1 WILD-TYPE                                   489
                 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
D18V7, 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                                   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"
D18V8, binary
                 cls
clus                0   1
  MAPK1 MUTATED     0   9
  MAPK1 WILD-TYPE  83 414
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      0    9
  MAPK1 WILD-TYPE   83  414
     clus
vv    MAPK1 MUTATED MAPK1 WILD-TYPE
  NO              0              83
  YES             9             414
[1] 2 2
[1] FALSE
D18V9, continuous
[1] "Remove cluster labels:" "MAPK1 MUTATED"         
clus
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              2             280 
     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-5250      TCGA-CR-6467 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-6471      TCGA-CR-6473      TCGA-CR-6474      TCGA-CR-6482 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-6487      TCGA-CR-6491      TCGA-CR-6492      TCGA-CR-6493 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-7364      TCGA-CR-7367      TCGA-CR-7368      TCGA-CR-7369 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-7370      TCGA-CR-7371      TCGA-CR-7373      TCGA-CR-7374 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-7376      TCGA-CR-7377      TCGA-CR-7379      TCGA-CR-7383 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-7385      TCGA-CR-7386      TCGA-CR-7388      TCGA-CR-7389 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-7390      TCGA-CR-7392      TCGA-CR-7394      TCGA-CR-7395 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CR-7398      TCGA-CR-7399      TCGA-CR-7401      TCGA-CR-7402 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-6436      TCGA-CV-6933      TCGA-CV-6934      TCGA-CV-6936 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-6941      TCGA-CV-6945      TCGA-CV-6952      TCGA-CV-6961 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-7095      TCGA-CV-7097      TCGA-CV-7235      TCGA-CV-7242 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-7245      TCGA-CV-7248      TCGA-CV-7250      TCGA-CV-7254 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-7263      TCGA-CV-7406      TCGA-CV-7410      TCGA-CV-7418 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-7422      TCGA-CV-7424      TCGA-CV-7427      TCGA-CV-7430 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-7432      TCGA-CV-7433      TCGA-CV-7434      TCGA-CV-7440 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-7446      TCGA-CV-7568      TCGA-CV-A45Y      TCGA-CV-A45Z 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-A460      TCGA-CV-A464      TCGA-CV-A468      TCGA-CV-A6JD 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-A6JN      TCGA-CV-A6JO      TCGA-CV-A6JU      TCGA-CV-A6JZ 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CV-A6K1      TCGA-CV-A6K2      TCGA-CX-7082      TCGA-CX-7085 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-CX-7086      TCGA-CX-7219      TCGA-D6-6516      TCGA-D6-6517 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-D6-6823      TCGA-D6-6824      TCGA-D6-6825      TCGA-D6-6827 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-D6-8568      TCGA-D6-8569      TCGA-D6-A4Z9      TCGA-D6-A4ZB 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-D6-A6EK      TCGA-D6-A6EP      TCGA-DQ-5625      TCGA-DQ-5629 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-DQ-5630      TCGA-DQ-5631      TCGA-DQ-7588      TCGA-DQ-7589 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-DQ-7590      TCGA-DQ-7591      TCGA-DQ-7592      TCGA-DQ-7593 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-DQ-7595      TCGA-F7-7848      TCGA-F7-8489      TCGA-F7-A50G 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-F7-A50I      TCGA-F7-A50J      TCGA-F7-A61S      TCGA-F7-A61V 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-F7-A61W      TCGA-F7-A620      TCGA-F7-A623      TCGA-H7-7774 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-H7-A6C4      TCGA-H7-A6C5      TCGA-HD-7753      TCGA-HD-7754 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-HD-7832      TCGA-HD-8634      TCGA-HD-8635      TCGA-HD-A634 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-HD-A6I0      TCGA-HL-7533      TCGA-IQ-7631      TCGA-IQ-7632 
"MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" "MAPK1 WILD-TYPE" 
     TCGA-IQ-A61E      TCGA-IQ-A61G      TCGA-IQ-A61H      TCGA-IQ-A61K 
"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" 
D18V10, continuous
D18V11, 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                        36   433
D18V12, multiclass
                                  clus
vv                                 MAPK1 MUTATED MAPK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              36
  WHITE                                        8             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"
D18V13, binary
                 cls
clus                0   1
  MAPK1 MUTATED     0   9
  MAPK1 WILD-TYPE  25 436
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      0    9
  MAPK1 WILD-TYPE   25  436
                        clus
vv                       MAPK1 MUTATED MAPK1 WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO             9             436
[1] 2 2
[1] FALSE

Clustering(19) Variable = KDM6A MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED    11   6
  KDM6A WILD-TYPE 292 195
  KDM6A MUTATED KDM6A WILD-TYPE 
             17             487 
  KDM6A MUTATED KDM6A WILD-TYPE 
              6             195 
$`KDM6A MUTATED`
TCGA-BA-A6DE TCGA-CN-5355 TCGA-CR-7368 TCGA-CV-5441 TCGA-CV-6935 TCGA-CV-7177 
       14.47        33.11        40.93        94.88         9.70        21.80 
TCGA-CV-7253 TCGA-CV-A45Q TCGA-CV-A45W TCGA-CV-A6JE TCGA-D6-8568 TCGA-F7-A623 
       11.87       169.38        45.96        35.34        24.95        20.25 
TCGA-F7-A624 TCGA-HD-7229 TCGA-HD-7753 TCGA-MT-A67G TCGA-P3-A6SX 
       12.43         0.07         0.16         3.68        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 
       53.79        57.44        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         7.76        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        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       37.84        12.89        26.86        32.65        21.11        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       41.69        13.05        34.36         8.58        12.39        35.54 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       55.27         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        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        14.56        17.59        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        17.29        15.91        11.44         5.75 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.69         6.18        48.20        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        46.75        45.80        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 
       34.75        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        51.29        33.11        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       28.83        64.11        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 
       32.81        25.81        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 
       11.51        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 
       31.10        29.85        29.52        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       126.08 
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        24.99       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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        34.36        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 
       23.05         2.53        16.14        11.44        18.67        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP 
       17.72        12.36        15.88         7.63        14.30        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        35.54        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        18.90        25.48        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
        9.83        12.13        12.10        10.65        11.18        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        19.23        18.94        12.62 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 
        0.46        17.85        11.80        13.38        15.16        13.61 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       21.11         6.77        25.74         1.22        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        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        13.55         0.07        14.47         5.29        11.54 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       11.84        13.35        18.15        12.43        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        56.75        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        11.74        17.65 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        16.70         9.34        12.72        18.64        14.79 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       12.43        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        13.68        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        43.36        41.16        42.02        44.65        62.27 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.16        49.22        21.86        16.11        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 
          21.80           18.54 
[1] "0.1 - 169.4 (21.8)" "0.1 - 211.0 (18.5)"
[1] "hr=" "1.4"
D19V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  KDM6A MUTATED         1        5         1         8         0
  KDM6A WILD-TYPE      24       71        76       240        11
D19V3, multiclass
           clus
vv          KDM6A MUTATED KDM6A WILD-TYPE
  STAGE I               1              24
  STAGE II              5              71
  STAGE III             1              76
  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    45 125  97 163
D19V4, multiclass
       clus
vv      KDM6A MUTATED KDM6A WILD-TYPE
  T0+T1             3              45
  T2                6             125
  T3                1              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
  KDM6A MUTATED     7   2   4   0
  KDM6A WILD-TYPE 167  63 157   7
D19V5, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  N0             7             167
  N1             2              63
  N2             4             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"
D19V6, binary
                 cls
clus                0   1
  KDM6A MUTATED     4  13
  KDM6A WILD-TYPE 135 354
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      4   13
  KDM6A WILD-TYPE  135  354
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE             4             135
  MALE              13             354
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  KDM6A MUTATED                                      17
  KDM6A WILD-TYPE                                   481
                 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
D19V7, 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                                   481
  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"
D19V8, binary
                 cls
clus                0   1
  KDM6A MUTATED     1  16
  KDM6A WILD-TYPE  82 407
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      1   16
  KDM6A WILD-TYPE   82  407
     clus
vv    KDM6A MUTATED KDM6A WILD-TYPE
  NO              1              82
  YES            16             407
[1] 2 2
[1] FALSE
D19V9, continuous
D19V10, continuous
D19V11, 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                        33   427
D19V12, multiclass
                                  clus
vv                                 KDM6A MUTATED KDM6A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    3              33
  WHITE                                       14             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"
D19V13, binary
                 cls
clus                0   1
  KDM6A MUTATED     0  17
  KDM6A WILD-TYPE  25 428
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      0   17
  KDM6A WILD-TYPE   25  428
                        clus
vv                       KDM6A MUTATED KDM6A WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO            17             428
[1] 2 2
[1] FALSE

Clustering(20) Variable = EP300 MUTATION ANALYSIS
D20V1, survival
                 sevent
clus2               0   1
  EP300 MUTATED    21  18
  EP300 WILD-TYPE 282 183
  EP300 MUTATED EP300 WILD-TYPE 
             39             465 
  EP300 MUTATED EP300 WILD-TYPE 
             18             183 
$`EP300 MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5559 TCGA-BA-A6DA TCGA-BB-7863 TCGA-BB-7870 
        9.30        13.64        57.44        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        11.44         2.70         7.69         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        29.52 
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        12.13        10.65        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        53.79        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         7.76 
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        94.62         9.14         4.60         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-7872 
       18.35        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        23.70        38.04         4.67        40.44        37.84 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.65        21.11        24.92        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        33.11        34.36         8.58        12.39        35.54 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       55.27         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        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        14.56        17.59        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       21.21         7.40        17.29        15.91         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 
       12.07        10.09         7.33         9.80         6.18        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 
       39.68        21.50        46.75        45.80        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 
       34.75        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        51.29        33.11        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       28.83        64.11        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 
       32.81        25.81        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        11.51        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        31.10        29.85 
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        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6940 
        2.14         9.70         5.46        20.52        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
       11.24       126.08        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        24.99       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        22.03         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-D6-6515 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       18.84        13.25         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       15.88         7.63        14.30        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        35.54        30.94        33.86        18.02 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       14.04        18.90        25.48        20.45         9.83        12.10 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       11.18        37.18        21.63        20.25         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 
       18.94        12.62         0.46        17.85        11.80        12.43 
TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       15.16        13.61        21.11         6.77         0.07         0.16 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       25.74         1.22        14.66        22.03        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
        0.36        13.84         4.27         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       12.76        14.50        19.33        11.84        13.55         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
       14.47         5.29        11.54        11.84        13.35        18.15 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       12.43        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         3.68        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 
       56.75        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        11.74        17.65        16.70         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       18.64        14.79        12.43        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        13.68 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       43.59        54.67         2.83        43.36        41.16        42.02 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        62.27        17.95        24.16        49.22        21.86 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       16.11        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 
          13.64           18.90 
[1] "2.0 - 156.5 (13.6)" "0.1 - 211.0 (18.9)"
[1] "hr=" "1.2"
D20V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  EP300 MUTATED         2        5         7        18         1
  EP300 WILD-TYPE      23       71        70       230        10
D20V3, multiclass
           clus
vv          EP300 MUTATED EP300 WILD-TYPE
  STAGE I               2              23
  STAGE II              5              71
  STAGE III             7              70
  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    44 121  93 153
D20V4, multiclass
       clus
vv      EP300 MUTATED EP300 WILD-TYPE
  T0+T1             4              44
  T2               10             121
  T3                5              93
  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 164  60 148   6
D20V5, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  N0            10             164
  N1             5              60
  N2            13             148
  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"
D20V6, binary
                 cls
clus                0   1
  EP300 MUTATED    13  26
  EP300 WILD-TYPE 126 341
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     13   26
  EP300 WILD-TYPE  126  341
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  FEMALE            13             126
  MALE              26             341
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  EP300 MUTATED                                      39
  EP300 WILD-TYPE                                   459
                 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
D20V7, 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                                   459
  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"
D20V8, binary
                 cls
clus                0   1
  EP300 MUTATED     5  34
  EP300 WILD-TYPE  78 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      5   34
  EP300 WILD-TYPE   78  389
     clus
vv    EP300 MUTATED EP300 WILD-TYPE
  NO              5              78
  YES            34             389
[1] 2 2
[1] FALSE
D20V9, continuous
D20V10, continuous
D20V11, 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                        33   408
D20V12, multiclass
                                  clus
vv                                 EP300 MUTATED EP300 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    3              33
  WHITE                                       33             408
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, binary
                 cls
clus                0   1
  EP300 MUTATED     3  34
  EP300 WILD-TYPE  22 411
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      3   34
  EP300 WILD-TYPE   22  411
                        clus
vv                       EP300 MUTATED EP300 WILD-TYPE
  HISPANIC OR LATINO                 3              22
  NOT HISPANIC OR LATINO            34             411
[1] 2 2
[1] FALSE

Clustering(21) Variable = RASA1 MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2               0   1
  RASA1 MUTATED    10   6
  RASA1 WILD-TYPE 293 195
  RASA1 MUTATED RASA1 WILD-TYPE 
             16             488 
  RASA1 MUTATED RASA1 WILD-TYPE 
              6             195 
$`RASA1 MUTATED`
TCGA-BB-7863 TCGA-BB-8601 TCGA-CN-4723 TCGA-CN-5366 TCGA-CN-6023 TCGA-CQ-6219 
       33.70        20.52        23.70        11.84        36.49        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-IQ-7630 
        0.46        22.52        30.94        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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        40.44        37.84        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
       26.86        32.65        21.11        24.92        41.10        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        43.73        27.58        41.69        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 
       33.11        34.36         8.58        12.39        35.54        55.27 
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 
       22.45        56.94        20.71        30.67        20.68        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
       19.53        20.68        19.07        14.20         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        20.09        12.95        24.16 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        3.68        17.42        14.10        11.74        35.01        14.56 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       17.59        12.85        29.72        21.21         7.40        17.29 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       15.91        11.44         5.75         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       10.09         7.33         9.80         7.69         6.18        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       39.68        21.50         2.93        54.58        46.75        45.80 
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        34.75        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        51.29        33.11        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        28.83        64.11        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        32.81        25.81        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        11.51         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 
       31.10        29.85        29.52        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 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       54.74        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        9.70         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       126.08        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        24.99       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        22.03         3.62        21.24        23.47        19.92 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 
       10.42        10.42        10.55        18.84        34.36        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        15.88 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        14.30        13.94        12.10        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       58.45        35.54        33.86        18.02        14.04        18.90 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       25.48        20.45         9.83        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       11.18        37.18        21.63        20.25         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        12.62         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         6.77 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        0.07         0.16        25.74         1.22        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-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        6.90        34.75        12.76        14.50        19.33        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       13.55         0.07        14.47         5.29        11.54        11.84 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        12.43        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         3.68        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        56.75        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        11.74 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       17.65         7.30        16.70         9.34        12.72        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       14.79        12.43        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        13.68        43.59 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        43.36        41.16        42.02        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       62.27        17.95        24.16        49.22        21.86        16.11 
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 

  RASA1 MUTATED RASA1 WILD-TYPE 
           0.46            0.07 
  RASA1 MUTATED RASA1 WILD-TYPE 
          56.58          210.97 
  RASA1 MUTATED RASA1 WILD-TYPE 
          21.52           18.59 
[1] "0.5 - 56.6 (21.5)"  "0.1 - 211.0 (18.6)"
[1] "hr=" "1"  
D21V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  RASA1 MUTATED         0        2         5         9         0
  RASA1 WILD-TYPE      25       74        72       239        11
D21V3, multiclass
           clus
vv          RASA1 MUTATED RASA1 WILD-TYPE
  STAGE I               0              25
  STAGE II              2              74
  STAGE III             5              72
  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    48 125  93 163
D21V4, multiclass
       clus
vv      RASA1 MUTATED RASA1 WILD-TYPE
  T0+T1             0              48
  T2                6             125
  T3                5              93
  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 167  62 155   7
D21V5, multiclass
    clus
vv   RASA1 MUTATED RASA1 WILD-TYPE
  N0             7             167
  N1             3              62
  N2             6             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"
D21V6, binary
                 cls
clus                0   1
  RASA1 MUTATED     3  14
  RASA1 WILD-TYPE 136 353
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      3   14
  RASA1 WILD-TYPE  136  353
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  FEMALE             3             136
  MALE              14             353
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  RASA1 MUTATED                                      17
  RASA1 WILD-TYPE                                   481
                 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
D21V7, 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                                   481
  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"
D21V8, binary
                 cls
clus                0   1
  RASA1 MUTATED     6  11
  RASA1 WILD-TYPE  77 412
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      6   11
  RASA1 WILD-TYPE   77  412
     clus
vv    RASA1 MUTATED RASA1 WILD-TYPE
  NO              6              77
  YES            11             412
[1] 2 2
[1] FALSE
D21V9, continuous
D21V10, continuous
D21V11, 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                        35   425
D21V12, multiclass
                                  clus
vv                                 RASA1 MUTATED RASA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              35
  WHITE                                       16             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"
D21V13, binary
                 cls
clus                0   1
  RASA1 MUTATED     2  15
  RASA1 WILD-TYPE  23 430
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      2   15
  RASA1 WILD-TYPE   23  430
                        clus
vv                       RASA1 MUTATED RASA1 WILD-TYPE
  HISPANIC OR LATINO                 2              23
  NOT HISPANIC OR LATINO            15             430
[1] 2 2
[1] FALSE

Clustering(22) Variable = NAP1L2 MUTATION ANALYSIS
D22V1, survival
                  sevent
clus2                0   1
  NAP1L2 MUTATED     4   3
  NAP1L2 WILD-TYPE 299 198
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               7              497 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               3              198 
$`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        11.54 
TCGA-UF-A71E 
       42.02 

$`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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       40.44        37.84        12.89        26.86        32.65        21.11 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       24.92        41.10        12.99        20.55        14.33        43.73 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        41.69        13.05        33.11        34.36         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       12.39        35.54        55.27         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        22.45        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       20.71        30.67        20.68        20.65        19.53        20.68 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        14.20         6.74         9.07         9.24        36.49 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       11.08        10.45        20.09        12.95        24.16         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        14.10        11.74        35.01        14.56        17.59 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       12.85        29.72        21.21         7.40        17.29        15.91 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       11.44         5.75         4.41        12.07         2.70        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
        7.33         9.80         7.69         6.18        48.20        39.68 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        46.75        45.80        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        34.75        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        51.29        33.11        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        28.83        64.11        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        32.81        25.81        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        11.51        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        31.10        29.85        29.52        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        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       126.08        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        24.99       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        22.03 
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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        34.36        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        15.88         7.63        14.30 
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        35.54 
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        18.90        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45         9.83        12.13        12.10        10.65        11.18 
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        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       12.62         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         6.77         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
        0.16        25.74         1.22        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-A61H 
       34.75        15.95        12.76        14.50        19.33        13.55 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
        0.07        14.47         5.29        11.84        13.35        18.15 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       12.43        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         3.68        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        56.75        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        11.74        17.65         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       16.70         9.34        12.72        18.64        14.79        12.43 
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        13.68        43.59        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       43.36        41.16        44.65        62.27        17.95        24.16 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       49.22        21.86        16.11        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 
           42.02           210.97 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
           17.85            18.67 
[1] "10.4 - 42.0 (17.9)" "0.1 - 211.0 (18.7)"
[1] "hr=" "1.3"
D22V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  NAP1L2 MUTATED         0        1         0         5         1
  NAP1L2 WILD-TYPE      25       75        77       243        10
D22V3, multiclass
           clus
vv          NAP1L2 MUTATED NAP1L2 WILD-TYPE
  STAGE I                0               25
  STAGE II               1               75
  STAGE III              0               77
  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    48 130  96 164
D22V4, multiclass
       clus
vv      NAP1L2 MUTATED NAP1L2 WILD-TYPE
  T0+T1              0               48
  T2                 1              130
  T3                 2               96
  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 171  65 158   6
D22V5, multiclass
    clus
vv   NAP1L2 MUTATED NAP1L2 WILD-TYPE
  N0              3              171
  N1              0               65
  N2              3              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"
D22V6, binary
                  cls
clus                 0   1
  NAP1L2 MUTATED     2   5
  NAP1L2 WILD-TYPE 137 362
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      2    5
  NAP1L2 WILD-TYPE  137  362
        clus
vv       NAP1L2 MUTATED NAP1L2 WILD-TYPE
  FEMALE              2              137
  MALE                5              362
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  NAP1L2 MUTATED                                       6
  NAP1L2 WILD-TYPE                                   492
                  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
D22V7, 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                                    492
  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"
D22V8, binary
                  cls
clus                 0   1
  NAP1L2 MUTATED     1   6
  NAP1L2 WILD-TYPE  82 417
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      1    6
  NAP1L2 WILD-TYPE   82  417
     clus
vv    NAP1L2 MUTATED NAP1L2 WILD-TYPE
  NO               1               82
  YES              6              417
[1] 2 2
[1] FALSE
D22V9, continuous
D22V10, continuous
D22V11, 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                        35   436
D22V12, multiclass
                                  clus
vv                                 NAP1L2 MUTATED NAP1L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               35
  WHITE                                         5              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"
D22V13, binary
                  cls
clus                 0   1
  NAP1L2 MUTATED     3   3
  NAP1L2 WILD-TYPE  22 442
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      3    3
  NAP1L2 WILD-TYPE   22  442
                        clus
vv                       NAP1L2 MUTATED NAP1L2 WILD-TYPE
  HISPANIC OR LATINO                  3               22
  NOT HISPANIC OR LATINO              3              442
[1] 2 2
[1] FALSE

Clustering(23) Variable = CREBBP MUTATION ANALYSIS
D23V1, survival
                  sevent
clus2                0   1
  CREBBP MUTATED    20  15
  CREBBP WILD-TYPE 283 186
  CREBBP MUTATED CREBBP WILD-TYPE 
              35              469 
  CREBBP MUTATED CREBBP WILD-TYPE 
              15              186 
$`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         9.80        11.21        28.83        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         9.83        12.10        12.43 
TCGA-H7-7774 TCGA-IQ-7631 TCGA-P3-A5QF TCGA-QK-A6IJ TCGA-RS-A6TO TCGA-T2-A6WX 
       13.38        12.76        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        13.68        41.16        62.27        16.11 

$`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        53.79 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
       57.44        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 
        7.76        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        94.62         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.41        18.35        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        23.70 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       38.04         4.67        40.44        37.84        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 
       32.65        21.11        24.92        41.10        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       43.73        27.58        41.69        13.05        33.11        34.36 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 
        8.58        12.39        35.54        55.27         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        22.45        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       20.71        30.67        20.68        20.65        19.53        20.68 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        14.20         6.74         9.07         9.24        36.49 
TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       11.08        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.69         6.18        48.20        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 
       54.58        46.75        45.80        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        34.75 
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 
       51.29        33.11        16.73        43.04        41.88        64.11 
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        32.81        25.81 
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        11.51        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        31.10        29.85        29.52        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        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       126.08        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        24.99       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        22.03 
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        15.88         7.63 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       14.30        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 
       35.54        30.94        33.86        18.02        14.04        18.90 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       25.48        20.45        12.13        10.65        11.18        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        19.23        18.94        12.62 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-A6C4 
        0.46        17.85        11.80        20.25        15.16        13.61 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
       21.11         6.77         0.07         0.16        25.74         1.22 
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-7632 
        4.27         3.65         6.90        34.75        15.95        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       19.33        11.84        13.55         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       11.54        11.84        13.35        18.15        12.43        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         3.68 
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        56.75 
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 
       11.74        17.65         7.30        16.70         9.34        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-TN-A7HI 
       14.79        12.43        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        43.59        54.67         2.83        43.36        42.02 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK 
       44.65        17.95        24.16        49.22        21.86        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 
           12.76            18.97 
[1] "3.5 - 129.2 (12.8)" "0.1 - 211.0 (19.0)"
[1] "hr=" "1.4"
D23V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  CREBBP MUTATED         0        4         6        18         0
  CREBBP WILD-TYPE      25       72        71       230        11
D23V3, multiclass
           clus
vv          CREBBP MUTATED CREBBP WILD-TYPE
  STAGE I                0               25
  STAGE II               4               72
  STAGE III              6               71
  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    46 124  92 154
D23V4, multiclass
       clus
vv      CREBBP MUTATED CREBBP WILD-TYPE
  T0+T1              2               46
  T2                 7              124
  T3                 6               92
  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 164  60 151   7
D23V5, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  N0             10              164
  N1              5               60
  N2             10              151
  N3              0                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                  cls
clus                 0   1
  CREBBP MUTATED    11  24
  CREBBP WILD-TYPE 128 343
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     11   24
  CREBBP WILD-TYPE  128  343
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  FEMALE             11              128
  MALE               24              343
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  CREBBP MUTATED                                      34
  CREBBP WILD-TYPE                                   464
                  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
D23V7, 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                                    464
  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"
D23V8, binary
                  cls
clus                 0   1
  CREBBP MUTATED     3  32
  CREBBP WILD-TYPE  80 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED      3   32
  CREBBP WILD-TYPE   80  391
     clus
vv    CREBBP MUTATED CREBBP WILD-TYPE
  NO               3               80
  YES             32              391
[1] 2 2
[1] FALSE
D23V9, continuous
D23V10, continuous
D23V11, 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                        35   409
D23V12, multiclass
                                  clus
vv                                 CREBBP MUTATED CREBBP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               35
  WHITE                                        32              409
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, binary
                  cls
clus                 0   1
  CREBBP MUTATED     1  30
  CREBBP WILD-TYPE  24 415
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED      1   30
  CREBBP WILD-TYPE   24  415
                        clus
vv                       CREBBP MUTATED CREBBP WILD-TYPE
  HISPANIC OR LATINO                  1               24
  NOT HISPANIC OR LATINO             30              415
[1] 2 2
[1] FALSE

Clustering(24) Variable = CTCF MUTATION ANALYSIS
D24V1, survival
                sevent
clus2              0   1
  CTCF MUTATED     8   8
  CTCF WILD-TYPE 295 193
  CTCF MUTATED CTCF WILD-TYPE 
            16            488 
  CTCF MUTATED CTCF WILD-TYPE 
             8            193 
$`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        16.70 

$`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        53.79 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       57.44        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         7.76        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        94.62         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.35        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        23.70        38.04         4.67        40.44        37.84 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.65        21.11        24.92        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        33.11        34.36         8.58        12.39        35.54 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       55.27         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        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        14.56        17.59        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        17.29        15.91        11.44         5.75 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.69         6.18        48.20        39.68        21.50         2.93 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6219 
       46.75        45.80        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        34.75        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        51.29        33.11        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       43.04        41.88        28.83        64.11        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        32.81        25.81        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        11.51        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        31.10        29.85        29.52        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        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        7.07        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-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       126.08        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 
       24.99       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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       34.36        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       16.14        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       12.36        15.88         7.63        14.30        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        35.54        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        18.90        25.48        20.45         9.83 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
       12.13        12.10        10.65        11.18        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        19.23        18.94        12.62         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 
       17.85        11.80        20.25        15.16        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
        6.77         0.07         0.16        25.74         1.22        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        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        13.55         0.07        14.47         5.29        11.54 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       11.84        13.35        18.15        12.43        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         3.68        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        56.75        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 
       11.74        17.65         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 
       14.79        12.43        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        13.68        43.59 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        43.36        41.16        42.02        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       62.27        17.95        24.16        49.22        21.86        16.11 
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         18.870 
[1] "1.1 - 54.6 (12.9)"  "0.1 - 211.0 (18.9)"
[1] "hr=" "1.9"
D24V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  CTCF MUTATED         0        4         0        10         1
  CTCF WILD-TYPE      25       72        77       238        10
D24V3, multiclass
           clus
vv          CTCF MUTATED CTCF WILD-TYPE
  STAGE I              0             25
  STAGE II             4             72
  STAGE III            0             77
  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    47 126  95 162
D24V4, multiclass
       clus
vv      CTCF MUTATED CTCF WILD-TYPE
  T0+T1            1             47
  T2               5            126
  T3               3             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
  CTCF MUTATED     7   0   6   0
  CTCF WILD-TYPE 167  65 155   7
D24V5, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  N0            7            167
  N1            0             65
  N2            6            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"
D24V6, binary
                cls
clus               0   1
  CTCF MUTATED     8   8
  CTCF WILD-TYPE 131 359
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED      8    8
  CTCF WILD-TYPE  131  359
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  FEMALE            8            131
  MALE              8            359
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  CTCF MUTATED                                      16
  CTCF WILD-TYPE                                   482
                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
D24V7, 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                                  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"
D24V8, binary
                cls
clus               0   1
  CTCF MUTATED     4  12
  CTCF WILD-TYPE  79 411
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED      4   12
  CTCF WILD-TYPE   79  411
     clus
vv    CTCF MUTATED CTCF WILD-TYPE
  NO             4             79
  YES           12            411
[1] 2 2
[1] FALSE
D24V9, continuous
D24V10, continuous
D24V11, 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                        35   427
D24V12, multiclass
                                  clus
vv                                 CTCF MUTATED CTCF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             35
  WHITE                                      14            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"
D24V13, binary
                cls
clus               0   1
  CTCF MUTATED     0  16
  CTCF WILD-TYPE  25 429
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED      0   16
  CTCF WILD-TYPE   25  429
                        clus
vv                       CTCF MUTATED CTCF WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO           16            429
[1] 2 2
[1] FALSE

Clustering(25) Variable = KEAP1 MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2               0   1
  KEAP1 MUTATED    13   9
  KEAP1 WILD-TYPE 290 192
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             482 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
              9             192 
$`KEAP1 MUTATED`
TCGA-BA-7269 TCGA-BB-7870 TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-5359 TCGA-CN-6010 
        7.76        66.28        23.70        40.44        12.39        20.71 
TCGA-CN-6012 TCGA-CR-6492 TCGA-CV-5434 TCGA-CV-5978 TCGA-CV-7238 TCGA-CV-7248 
       20.68        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 
       42.02        49.22        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 
       53.79        57.44        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        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.35        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        37.84        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       32.65        21.11        24.92        41.10        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        43.73        27.58        41.69        13.05        33.11 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 
       34.36         8.58        35.54        55.27         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        22.45 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       56.94        30.67        20.65        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       14.20         6.74         9.07         9.24        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        46.75        45.80        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        34.75        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        51.29        33.11        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        28.83        64.11        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        32.81        25.81        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        11.51         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        31.10        29.85        29.52        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 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-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 
      126.08        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        24.99 
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        22.03        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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       15.88         7.63        14.30        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        35.54        30.94        33.86        18.02 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       18.90        25.48        20.45         9.83        12.13        12.10 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       10.65        11.18        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 
       19.23        18.94        12.62         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-7917 TCGA-HD-8224 
        6.77         0.07         0.16        25.74         1.22        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6HZ 
       22.03        12.66        22.85         0.36         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        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        13.55         0.07        14.47         5.29        11.54 
TCGA-IQ-A61O TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       11.84        18.15        12.43        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         3.68        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        56.75        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        11.74        17.65 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        16.70         9.34        12.72        18.64        14.79 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.43        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        13.68        43.59        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       43.36        41.16        44.65        62.27        17.95        24.16 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JV TCGA-UP-A6WW 
       21.86        16.11        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 
          19.84           18.59 
[1] "3.6 - 109.0 (19.8)" "0.1 - 211.0 (18.6)"
[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       75        74       234         9
D25V3, multiclass
           clus
vv          KEAP1 MUTATED KEAP1 WILD-TYPE
  STAGE I               0              25
  STAGE II              1              75
  STAGE III             3              74
  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    47 128  97 153
D25V4, multiclass
       clus
vv      KEAP1 MUTATED KEAP1 WILD-TYPE
  T0+T1             1              47
  T2                3             128
  T3                1              97
  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 164  62 155   6
D25V5, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  N0            10             164
  N1             3              62
  N2             6             155
  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 130 354
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      9   13
  KEAP1 WILD-TYPE  130  354
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  FEMALE             9             130
  MALE              13             354
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  KEAP1 MUTATED                                      20
  KEAP1 WILD-TYPE                                   478
                 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
D25V7, 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                                   478
  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"
D25V8, binary
                 cls
clus                0   1
  KEAP1 MUTATED     7  15
  KEAP1 WILD-TYPE  76 408
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      7   15
  KEAP1 WILD-TYPE   76  408
     clus
vv    KEAP1 MUTATED KEAP1 WILD-TYPE
  NO              7              76
  YES            15             408
[1] 2 2
[1] FALSE
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                        33   422
D25V12, multiclass
                                  clus
vv                                 KEAP1 MUTATED KEAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    3              33
  WHITE                                       19             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"
D25V13, binary
                 cls
clus                0   1
  KEAP1 MUTATED     0  18
  KEAP1 WILD-TYPE  25 427
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      0   18
  KEAP1 WILD-TYPE   25  427
                        clus
vv                       KEAP1 MUTATED KEAP1 WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO            18             427
[1] 2 2
[1] FALSE

Clustering(26) Variable = RHOA MUTATION ANALYSIS
D26V1, survival
                sevent
clus2              0   1
  RHOA MUTATED     6   4
  RHOA WILD-TYPE 297 197
  RHOA MUTATED RHOA WILD-TYPE 
            10            494 
  RHOA MUTATED RHOA WILD-TYPE 
             4            197 
$`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         9.80         1.84       210.97 
TCGA-DQ-5625 TCGA-F7-A624 TCGA-KU-A66S TCGA-TN-A7HL 
       35.54        12.43        13.35        13.68 

$`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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44        37.84 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.65        21.11        24.92        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        33.11        34.36         8.58        12.39        35.54 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       55.27         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        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        14.56        17.59        12.85        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        17.29        15.91        11.44         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 
       12.07         2.70        10.09         7.33         7.69         6.18 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        39.68        21.50         2.93        54.58        46.75 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       45.80        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        34.75        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        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       33.11        16.73        43.04        41.88        28.83        64.11 
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        32.81        25.81 
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        11.51        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        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       29.85        29.52        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        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      126.08        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        24.99 
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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       34.36        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       16.14        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       12.36        15.88         7.63        14.30        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        11.11        58.45        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        18.90        25.48        20.45         9.83        12.13 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       12.10        10.65        11.18        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        19.23        18.94        12.62         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 
       11.80        20.25        13.38        15.16        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
        6.77         0.07         0.16        25.74         1.22        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        12.76        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       19.33        11.84        13.55         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       11.54        11.84        18.15        12.43        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         3.68        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        56.75        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 
       11.74        17.65         7.30        16.70         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       18.64        14.79        12.43        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        43.59 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        43.36        41.16        42.02        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       62.27        17.95        24.16        49.22        21.86        16.11 
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 
        13.515         18.740 
[1] "1.8 - 211.0 (13.5)" "0.1 - 180.2 (18.7)"
[1] "hr=" "1.8"
D26V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  RHOA MUTATED         0        1         2         6         0
  RHOA WILD-TYPE      25       75        75       242        11
D26V3, multiclass
           clus
vv          RHOA MUTATED RHOA WILD-TYPE
  STAGE I              0             25
  STAGE II             1             75
  STAGE III            2             75
  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    47 129  94 166
D26V4, multiclass
       clus
vv      RHOA MUTATED RHOA WILD-TYPE
  T0+T1            1             47
  T2               2            129
  T3               4             94
  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 174  62 157   7
D26V5, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  N0            0            174
  N1            3             62
  N2            4            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"
D26V6, binary
                cls
clus               0   1
  RHOA MUTATED     4   6
  RHOA WILD-TYPE 135 361
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      4    6
  RHOA WILD-TYPE  135  361
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  FEMALE            4            135
  MALE              6            361
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  RHOA MUTATED                                       9
  RHOA WILD-TYPE                                   489
                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
D26V7, 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                                  489
  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"
D26V8, binary
                cls
clus               0   1
  RHOA MUTATED     0  10
  RHOA WILD-TYPE  83 413
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      0   10
  RHOA WILD-TYPE   83  413
     clus
vv    RHOA MUTATED RHOA WILD-TYPE
  NO             0             83
  YES           10            413
[1] 2 2
[1] FALSE
D26V9, continuous
D26V10, continuous
D26V11, 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                        36   431
D26V12, multiclass
                                  clus
vv                                 RHOA MUTATED RHOA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             36
  WHITE                                      10            431
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, binary
                cls
clus               0   1
  RHOA MUTATED     0  10
  RHOA WILD-TYPE  25 435
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      0   10
  RHOA WILD-TYPE   25  435
                        clus
vv                       RHOA MUTATED RHOA WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO           10            435
[1] 2 2
[1] FALSE

Clustering(27) Variable = FBXW7 MUTATION ANALYSIS
D27V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED    16  17
  FBXW7 WILD-TYPE 287 184
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             33             471 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             17             184 
$`FBXW7 MUTATED`
TCGA-BA-6868 TCGA-BA-A6DF TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-8601 TCGA-BB-A6UO 
       15.52         7.82        18.35        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        12.95        14.56         6.18        10.42 
TCGA-CQ-6221 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-7379 TCGA-CR-7398 TCGA-CV-6436 
       32.88        25.81        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 
       53.79        57.44        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         7.76        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        94.62         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        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       40.44        37.84        12.89        32.65        21.11        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 
       35.54        55.27         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        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       20.09        24.16         3.68        17.42        14.10        11.74 
TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       35.01        17.59        12.85        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       17.29        15.91        11.44         5.75         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5323 
        2.70        10.09         7.33         9.80         7.69        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       39.68        21.50         2.93        54.58        46.75        45.80 
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        34.75        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        51.29        33.11        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        28.83        64.11        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        32.81        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        11.51 
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        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 
       29.85        29.52        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        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-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       126.08        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        24.99       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        22.03         3.62        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 
       10.42        10.42        10.55        18.84        34.36        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        15.88 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        14.30        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        35.54        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 
       18.90        25.48        20.45         9.83        12.13        12.10 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       10.65        11.18        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 
       19.23        18.94        12.62         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         6.77 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        0.07         0.16        25.74         1.22        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        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        13.55         0.07        14.47         5.29        11.54 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       11.84        13.35        18.15        12.43        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         3.68        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        56.75        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        11.74        17.65         7.30 
TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO 
       16.70        12.72        18.64        14.79        12.43        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        13.68        43.59        54.67         2.83        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       41.16        42.02        62.27        17.95        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       21.86        16.11        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 
          18.41           18.67 
[1] "1.1 - 180.2 (18.4)" "0.1 - 211.0 (18.7)"
[1] "hr=" "1.3"
D27V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  FBXW7 MUTATED         1        5         8        16         1
  FBXW7 WILD-TYPE      24       71        69       232        10
D27V3, multiclass
           clus
vv          FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I               1              24
  STAGE II              5              71
  STAGE III             8              69
  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    47 123  89 154
D27V4, multiclass
       clus
vv      FBXW7 MUTATED FBXW7 WILD-TYPE
  T0+T1             1              47
  T2                8             123
  T3                9              89
  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 160  62 153   6
D27V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0            14             160
  N1             3              62
  N2             8             153
  N3             1               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                 cls
clus                0   1
  FBXW7 MUTATED    13  20
  FBXW7 WILD-TYPE 126 347
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     13   20
  FBXW7 WILD-TYPE  126  347
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE            13             126
  MALE              20             347
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  FBXW7 MUTATED                                      33
  FBXW7 WILD-TYPE                                   465
                 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
D27V7, 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                                   465
  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"
D27V8, binary
                 cls
clus                0   1
  FBXW7 MUTATED     4  29
  FBXW7 WILD-TYPE  79 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      4   29
  FBXW7 WILD-TYPE   79  394
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO              4              79
  YES            29             394
[1] 2 2
[1] FALSE
D27V9, continuous
D27V10, continuous
D27V11, 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                        33   413
D27V12, multiclass
                                  clus
vv                                 FBXW7 MUTATED FBXW7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    3              33
  WHITE                                       28             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"
D27V13, binary
                 cls
clus                0   1
  FBXW7 MUTATED     2  27
  FBXW7 WILD-TYPE  23 418
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      2   27
  FBXW7 WILD-TYPE   23  418
                        clus
vv                       FBXW7 MUTATED FBXW7 WILD-TYPE
  HISPANIC OR LATINO                 2              23
  NOT HISPANIC OR LATINO            27             418
[1] 2 2
[1] FALSE

Clustering(28) Variable = TIGD4 MUTATION ANALYSIS
D28V1, survival
                 sevent
clus2               0   1
  TIGD4 MUTATED     4   3
  TIGD4 WILD-TYPE 299 198
  TIGD4 MUTATED TIGD4 WILD-TYPE 
              7             497 
  TIGD4 MUTATED TIGD4 WILD-TYPE 
              3             198 
$`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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       40.44        37.84        12.89        26.86        32.65        21.11 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       24.92        41.10        12.99        20.55        14.33        43.73 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        41.69        13.05        33.11        34.36         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       12.39        35.54        55.27         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        22.45        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       20.71        30.67        20.68        20.65        19.53        20.68 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        14.20         6.74         9.07         9.24        36.49 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       11.08        10.45        20.09        12.95        24.16         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        14.10        11.74        35.01        14.56        17.59 
TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       12.85        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        46.75        45.80        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        34.75        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        51.29        33.11        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        28.83        64.11        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        32.81        25.81        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        11.51        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        31.10        29.85        29.52        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        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        7.07        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-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       126.08        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        24.99       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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       10.55        34.36        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-A6EO TCGA-D6-A6EP 
       17.72        12.36        15.88         7.63        14.30        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        35.54        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        18.90        25.48        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
        9.83        12.13        12.10        10.65        11.18        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        19.23        18.94        12.62 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-A6C4 
        0.46        17.85        11.80        20.25        15.16        13.61 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
       21.11         6.77         0.07         0.16        25.74         1.22 
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        12.76 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        19.33        11.84        13.55         0.07        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
        5.29        11.54        11.84        13.35        18.15        12.43 
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 
        3.68        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 
       56.75        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        11.74        17.65         7.30        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO 
        9.34        12.72        18.64        14.79        12.43        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        13.68        43.59        54.67         2.83        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       41.16        42.02        44.65        62.27        17.95        24.16 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       49.22        21.86        16.11        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           18.81 
[1] "2.5 - 29.7 (13.4)"  "0.1 - 211.0 (18.8)"
[1] "hr=" "1.8"
D28V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  TIGD4 MUTATED         0        3         2         2         0
  TIGD4 WILD-TYPE      25       73        75       246        11
D28V3, multiclass
           clus
vv          TIGD4 MUTATED TIGD4 WILD-TYPE
  STAGE I               0              25
  STAGE II              3              73
  STAGE III             2              75
  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    48 128  96 166
D28V4, multiclass
       clus
vv      TIGD4 MUTATED TIGD4 WILD-TYPE
  T0+T1             0              48
  T2                3             128
  T3                2              96
  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 171  63 161   7
D28V5, multiclass
    clus
vv   TIGD4 MUTATED TIGD4 WILD-TYPE
  N0             3             171
  N1             2              63
  N2             0             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"
D28V6, binary
                 cls
clus                0   1
  TIGD4 MUTATED     1   6
  TIGD4 WILD-TYPE 138 361
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD4 MUTATED      1    6
  TIGD4 WILD-TYPE  138  361
        clus
vv       TIGD4 MUTATED TIGD4 WILD-TYPE
  FEMALE             1             138
  MALE               6             361
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  TIGD4 MUTATED                                       7
  TIGD4 WILD-TYPE                                   491
                 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
D28V7, 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                                   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"
D28V8, binary
                 cls
clus                0   1
  TIGD4 MUTATED     0   7
  TIGD4 WILD-TYPE  83 416
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD4 MUTATED      0    7
  TIGD4 WILD-TYPE   83  416
     clus
vv    TIGD4 MUTATED TIGD4 WILD-TYPE
  NO              0              83
  YES             7             416
[1] 2 2
[1] FALSE
D28V9, continuous
D28V10, continuous
D28V11, 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                        35   435
D28V12, multiclass
                                  clus
vv                                 TIGD4 MUTATED TIGD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              35
  WHITE                                        6             435
[1] 4 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
  TIGD4 MUTATED     0   7
  TIGD4 WILD-TYPE  25 438
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD4 MUTATED      0    7
  TIGD4 WILD-TYPE   25  438
                        clus
vv                       TIGD4 MUTATED TIGD4 WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO             7             438
[1] 2 2
[1] FALSE

Clustering(29) Variable = KRT5 MUTATION ANALYSIS
D29V1, survival
                sevent
clus2              0   1
  KRT5 MUTATED     7   4
  KRT5 WILD-TYPE 296 197
  KRT5 MUTATED KRT5 WILD-TYPE 
            11            493 
  KRT5 MUTATED KRT5 WILD-TYPE 
             4            197 
$`KRT5 MUTATED`
TCGA-BB-7862 TCGA-CN-4731 TCGA-CN-5373 TCGA-CQ-5323 TCGA-CQ-7065 TCGA-CV-6940 
       36.72        32.65        22.45        48.20        33.11        26.43 
TCGA-CV-6961 TCGA-CV-7432 TCGA-H7-7774 TCGA-P3-A5QA TCGA-UF-A71A 
        2.50        84.49        13.38        56.75         2.83 

$`KRT5 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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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-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        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       37.84        12.89        26.86        21.11        24.92        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        33.11        34.36         8.58        12.39        35.54 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       55.27         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
       12.49         8.52        56.94        20.71        30.67        20.68 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       20.65        19.53        20.68        19.07        14.20         6.74 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        9.07         9.24        36.49        11.08        10.45        20.09 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       12.95        24.16         3.68        17.42        14.10        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        14.56        17.59        12.85        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        17.29        15.91        11.44         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        10.09         7.33         9.80         7.69 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
        6.18        39.68        21.50         2.93        54.58        46.75 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       45.80        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        34.75        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        51.29 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       16.73        43.04        41.88        28.83        64.11        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        32.81        25.81        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        11.51        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        31.10        29.85 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       29.52        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        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
       20.52         4.73        21.90        11.24       126.08        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-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-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-7427 TCGA-CV-7429 TCGA-CV-7430 
      100.57        14.89        56.48       156.49         3.52        16.27 
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        24.99       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 
       22.03         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-D6-6515 
       10.42        10.42        10.55        18.84        34.36        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        15.88 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        14.30        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        35.54        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 
       18.90        25.48        20.45         9.83        12.13        12.10 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       10.65        11.18        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 
       19.23        18.94        12.62         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       20.25        12.43        15.16        13.61        21.11         6.77 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        0.07         0.16        25.74         1.22        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        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        13.55         0.07        14.47         5.29        11.54 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       11.84        13.35        18.15        12.43        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         3.68        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A5QF 
        7.13        16.08        17.98        15.78        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        11.74 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       17.65         7.30        16.70         9.34        12.72        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       14.79        12.43        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        13.68        43.59 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67        43.36        41.16        42.02        44.65        62.27 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.16        49.22        21.86        16.11        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 

  KRT5 MUTATED KRT5 WILD-TYPE 
          2.50           0.07 
  KRT5 MUTATED KRT5 WILD-TYPE 
         84.49         210.97 
  KRT5 MUTATED KRT5 WILD-TYPE 
         32.65          18.41 
[1] "2.5 - 84.5 (32.6)"  "0.1 - 211.0 (18.4)"
[1] "hr=" "1.3"
D29V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  KRT5 MUTATED         3        3         1         4         0
  KRT5 WILD-TYPE      22       73        76       244        11
D29V3, multiclass
           clus
vv          KRT5 MUTATED KRT5 WILD-TYPE
  STAGE I              3             22
  STAGE II             3             73
  STAGE III            1             76
  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
  KRT5 MUTATED       3   4   1   3
  KRT5 WILD-TYPE    45 127  97 165
D29V4, multiclass
       clus
vv      KRT5 MUTATED KRT5 WILD-TYPE
  T0+T1            3             45
  T2               4            127
  T3               1             97
  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
  KRT5 MUTATED     6   1   3   0
  KRT5 WILD-TYPE 168  64 158   7
D29V5, multiclass
    clus
vv   KRT5 MUTATED KRT5 WILD-TYPE
  N0            6            168
  N1            1             64
  N2            3            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"
D29V6, binary
                cls
clus               0   1
  KRT5 MUTATED     4   7
  KRT5 WILD-TYPE 135 360
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT5 MUTATED      4    7
  KRT5 WILD-TYPE  135  360
        clus
vv       KRT5 MUTATED KRT5 WILD-TYPE
  FEMALE            4            135
  MALE              7            360
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  KRT5 MUTATED                                      11
  KRT5 WILD-TYPE                                   487
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  KRT5 MUTATED                                                             0
  KRT5 WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  KRT5 MUTATED                                                     0
  KRT5 WILD-TYPE                                                   7
D29V7, multiclass
                                                             clus
vv                                                            KRT5 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                                                            KRT5 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"
D29V8, binary
                cls
clus               0   1
  KRT5 MUTATED     2   9
  KRT5 WILD-TYPE  81 414
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT5 MUTATED      2    9
  KRT5 WILD-TYPE   81  414
     clus
vv    KRT5 MUTATED KRT5 WILD-TYPE
  NO             2             81
  YES            9            414
[1] 2 2
[1] FALSE
D29V9, continuous
D29V10, continuous
D29V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT5 MUTATED                                  0     1
  KRT5 WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KRT5 MUTATED                           0     9
  KRT5 WILD-TYPE                        36   432
D29V12, multiclass
                                  clus
vv                                 KRT5 MUTATED KRT5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             36
  WHITE                                       9            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"
D29V13, binary
                cls
clus               0   1
  KRT5 MUTATED     0   9
  KRT5 WILD-TYPE  25 436
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT5 MUTATED      0    9
  KRT5 WILD-TYPE   25  436
                        clus
vv                       KRT5 MUTATED KRT5 WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO            9            436
[1] 2 2
[1] FALSE

Clustering(30) Variable = SMAD4 MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2               0   1
  SMAD4 MUTATED     7   7
  SMAD4 WILD-TYPE 296 194
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             14             490 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              7             194 
$`SMAD4 MUTATED`
TCGA-BA-5555 TCGA-BB-A6UO TCGA-CN-4723 TCGA-CN-5364 TCGA-CN-A6V1 TCGA-CQ-6222 
       17.10         8.81        23.70        16.21         7.33        66.28 
TCGA-CR-7365 TCGA-CV-7097 TCGA-CV-7406 TCGA-D6-A74Q TCGA-HD-8635 TCGA-P3-A6T5 
       39.16        12.66        57.47        11.11        22.85        29.00 
TCGA-P3-A6T7 TCGA-UF-A7JC 
       16.01        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        53.79 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       57.44        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         7.76        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        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.35        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        40.44        37.84        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
       26.86        32.65        21.11        24.92        41.10        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        43.73        27.58        41.69        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 
       33.11        34.36         8.58        12.39        35.54        55.27 
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 
       22.45        56.94        20.71        30.67        20.68        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
       19.53        20.68        19.07        14.20         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        9.24        36.49        11.08        10.45        20.09        12.95 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 
       24.16         3.68        17.42        14.10        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       14.56        17.59        12.85        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       17.29        15.91        11.44         5.75         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
        2.70        10.09         9.80         7.69         6.18        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       39.68        21.50         2.93        54.58        46.75        45.80 
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        34.75        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        51.29        33.11        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       43.04        41.88        28.83        64.11        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        32.81        25.81        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        11.51        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        31.10        29.85        29.52        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        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        7.07        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-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       126.08        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        24.99       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        22.03 
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        15.88         7.63 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 
       14.30        13.94        12.10        12.79        58.45        35.54 
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        18.90        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45         9.83        12.13        12.10        10.65        11.18 
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        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       12.62         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         6.77         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
        0.16        25.74         1.22        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-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        12.76        14.50        19.33        11.84        13.55 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
        0.07        14.47         5.29        11.54        11.84        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        12.43        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         3.68        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        56.75        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 
       47.01        19.00        75.55        18.97         2.04        12.99 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        11.74        17.65         7.30        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO 
        9.34        12.72        18.64        14.79        12.43        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        13.68        43.59        54.67         2.83        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF 
       41.16        42.02        44.65        62.27        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       21.86        16.11        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 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
           7.33            0.07 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          66.28          210.97 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
         17.525          18.740 
[1] "7.3 - 66.3 (17.5)"  "0.1 - 211.0 (18.7)"
[1] "hr=" "1.3"
D30V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  SMAD4 MUTATED         0        2         1        11         0
  SMAD4 WILD-TYPE      25       74        76       237        11
D30V3, multiclass
           clus
vv          SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE I               0              25
  STAGE II              2              74
  STAGE III             1              76
  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
  SMAD4 MUTATED       1   4   3   6
  SMAD4 WILD-TYPE    47 127  95 162
D30V4, multiclass
       clus
vv      SMAD4 MUTATED SMAD4 WILD-TYPE
  T0+T1             1              47
  T2                4             127
  T3                3              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
  SMAD4 MUTATED     5   1   7   0
  SMAD4 WILD-TYPE 169  64 154   7
D30V5, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  N0             5             169
  N1             1              64
  N2             7             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"
D30V6, binary
                 cls
clus                0   1
  SMAD4 MUTATED     3  11
  SMAD4 WILD-TYPE 136 356
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      3   11
  SMAD4 WILD-TYPE  136  356
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  FEMALE             3             136
  MALE              11             356
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  SMAD4 MUTATED                                      14
  SMAD4 WILD-TYPE                                   484
                 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
D30V7, multiclass
                                                             clus
vv                                                            SMAD4 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                                                            SMAD4 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"
D30V8, binary
                 cls
clus                0   1
  SMAD4 MUTATED     3  11
  SMAD4 WILD-TYPE  80 412
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      3   11
  SMAD4 WILD-TYPE   80  412
     clus
vv    SMAD4 MUTATED SMAD4 WILD-TYPE
  NO              3              80
  YES            11             412
[1] 2 2
[1] FALSE
D30V9, continuous
D30V10, continuous
D30V11, 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    13
  SMAD4 WILD-TYPE                        35   428
D30V12, multiclass
                                  clus
vv                                 SMAD4 MUTATED SMAD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              35
  WHITE                                       13             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"
D30V13, binary
                 cls
clus                0   1
  SMAD4 MUTATED     0  12
  SMAD4 WILD-TYPE  25 433
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      0   12
  SMAD4 WILD-TYPE   25  433
                        clus
vv                       SMAD4 MUTATED SMAD4 WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO            12             433
[1] 2 2
[1] FALSE

Clustering(31) Variable = ASXL1 MUTATION ANALYSIS
D31V1, survival
                 sevent
clus2               0   1
  ASXL1 MUTATED     6   9
  ASXL1 WILD-TYPE 297 192
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             15             489 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
              9             192 
$`ASXL1 MUTATED`
TCGA-BA-A6D8 TCGA-CN-A498 TCGA-CR-7388 TCGA-CV-5439 TCGA-CV-5978 TCGA-CV-7089 
       27.95        14.56        27.06        17.95         7.07        64.83 
TCGA-CV-7177 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-A45U TCGA-CV-A6JY TCGA-D6-A6ES 
       21.80        84.49        19.76        35.47        21.24        12.79 
TCGA-DQ-5631 TCGA-DQ-7596 TCGA-MT-A67F 
       18.02        11.18        12.62 

$`ASXL1 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 
       53.79        57.44        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         7.76        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       30.18        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        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       37.84        12.89        26.86        32.65        21.11        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       35.54        55.27         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        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        20.68        20.65        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       14.20         6.74         9.07         9.24        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       14.10        11.74        35.01        17.59        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        17.29        15.91        11.44         5.75 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.69         6.18        48.20        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        46.75        45.80        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 
       34.75        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        51.29        33.11        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       28.83        64.11        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 
       32.81        25.81        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 
       11.51        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-7398 
       31.10        29.85        29.52        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-5440 TCGA-CV-5441 
      129.21       108.95        76.24        19.20       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       86.83        48.59        60.49        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       126.08 
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-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        2.50         4.14       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-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-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-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        24.99       169.38       180.16       159.65 
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        22.03         3.62 
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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        34.36        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-A6EO TCGA-D6-A6EP 
       17.72        12.36        15.88         7.63        14.30        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        35.54        30.94        33.86 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       14.04        18.90        25.48        20.45         9.83        12.13 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       12.10        10.65        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 
       19.23        18.94        12.62         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-7917 TCGA-HD-8224 
        6.77         0.07         0.16        25.74         1.22        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        12.76        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       19.33        11.84        13.55         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       11.54        11.84        13.35        18.15        12.43        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         3.68        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        56.75        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 
       11.74        17.65         7.30        16.70         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       18.64        14.79        12.43        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        13.68 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       43.59        54.67         2.83        43.36        41.16        42.02 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        62.27        17.95        24.16        49.22        21.86 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       16.11        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 

  ASXL1 MUTATED ASXL1 WILD-TYPE 
           7.07            0.07 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
          84.49          210.97 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
          19.76           18.64 
[1] "7.1 - 84.5 (19.8)"  "0.1 - 211.0 (18.6)"
[1] "hr=" "1.5"
D31V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  ASXL1 MUTATED         0        2         1         9         1
  ASXL1 WILD-TYPE      25       74        76       239        10
D31V3, multiclass
           clus
vv          ASXL1 MUTATED ASXL1 WILD-TYPE
  STAGE I               0              25
  STAGE II              2              74
  STAGE III             1              76
  STAGE IVA             9             239
  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
  ASXL1 MUTATED       0   2   2   9
  ASXL1 WILD-TYPE    48 129  96 159
D31V4, multiclass
       clus
vv      ASXL1 MUTATED ASXL1 WILD-TYPE
  T0+T1             0              48
  T2                2             129
  T3                2              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
  ASXL1 MUTATED     6   0   5   1
  ASXL1 WILD-TYPE 168  65 156   6
D31V5, multiclass
    clus
vv   ASXL1 MUTATED ASXL1 WILD-TYPE
  N0             6             168
  N1             0              65
  N2             5             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"
D31V6, binary
                 cls
clus                0   1
  ASXL1 MUTATED     5  11
  ASXL1 WILD-TYPE 134 356
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED      5   11
  ASXL1 WILD-TYPE  134  356
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  FEMALE             5             134
  MALE              11             356
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  ASXL1 MUTATED                                      16
  ASXL1 WILD-TYPE                                   482
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  ASXL1 MUTATED                                                             0
  ASXL1 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  ASXL1 MUTATED                                                     0
  ASXL1 WILD-TYPE                                                   7
D31V7, multiclass
                                                             clus
vv                                                            ASXL1 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                                                            ASXL1 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"
D31V8, binary
                 cls
clus                0   1
  ASXL1 MUTATED     2  14
  ASXL1 WILD-TYPE  81 409
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED      2   14
  ASXL1 WILD-TYPE   81  409
     clus
vv    ASXL1 MUTATED ASXL1 WILD-TYPE
  NO              2              81
  YES            14             409
[1] 2 2
[1] FALSE
D31V9, continuous
D31V10, continuous
D31V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASXL1 MUTATED                                  0     0
  ASXL1 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ASXL1 MUTATED                           2    14
  ASXL1 WILD-TYPE                        34   427
D31V12, multiclass
                                  clus
vv                                 ASXL1 MUTATED ASXL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              34
  WHITE                                       14             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"
D31V13, binary
                 cls
clus                0   1
  ASXL1 MUTATED     0  15
  ASXL1 WILD-TYPE  25 430
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED      0   15
  ASXL1 WILD-TYPE   25  430
                        clus
vv                       ASXL1 MUTATED ASXL1 WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO            15             430
[1] 2 2
[1] FALSE

Clustering(32) Variable = CES2 MUTATION ANALYSIS
D32V1, survival
                sevent
clus2              0   1
  CES2 MUTATED     6   5
  CES2 WILD-TYPE 297 196
  CES2 MUTATED CES2 WILD-TYPE 
            11            493 
  CES2 MUTATED CES2 WILD-TYPE 
             5            196 
$`CES2 MUTATED`
TCGA-BA-A6DA TCGA-CQ-5334 TCGA-CR-6477 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7418 
       11.54         4.24        16.90        95.34        47.97        25.94 
TCGA-CV-A45Z TCGA-D6-8568 TCGA-DQ-5625 TCGA-DQ-7592 TCGA-HD-8635 
       48.20        24.95        35.54         9.83        22.85 

$`CES2 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 
       53.79        57.44        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         7.76        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       30.18        27.95         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        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       37.84        12.89        26.86        32.65        21.11        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       35.54        55.27         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        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        20.68        20.65        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       14.20         6.74         9.07         9.24        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        46.75        45.80        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6222 
       11.21        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 
       34.75        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        51.29        33.11        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       28.83        64.11        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 
       32.81        25.81        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-6478 TCGA-CR-6480 
       39.52        34.52        36.99        18.54         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        11.51 
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 
       31.10        29.85        29.52        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 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       54.74        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        9.70         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       126.08        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-7252 TCGA-CV-7253 TCGA-CV-7255 
       26.20        18.97        17.13         4.96        11.87         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        24.99 
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-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
        6.51        88.87        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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       11.44        18.67        25.32        17.72        12.36        15.88 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        14.30        13.94        12.10        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       58.45        30.94        33.86        18.02        14.04        18.90 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       25.48        20.45        12.13        12.10        10.65        11.18 
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        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       12.62         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         6.77         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
        0.16        25.74         1.22        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-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        12.76        14.50        19.33        11.84        13.55 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
        0.07        14.47         5.29        11.54        11.84        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        12.43        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         3.68        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        56.75        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        11.74        17.65 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        16.70         9.34        12.72        18.64        14.79 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       12.43        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        13.68        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        43.36        41.16        42.02        44.65        62.27 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.16        49.22        21.86        16.11        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 

  CES2 MUTATED CES2 WILD-TYPE 
          4.24           0.07 
  CES2 MUTATED CES2 WILD-TYPE 
         95.34         210.97 
  CES2 MUTATED CES2 WILD-TYPE 
         24.95          18.54 
[1] "4.2 - 95.3 (24.9)"  "0.1 - 211.0 (18.5)"
[1] "hr=" "1"  
D32V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  CES2 MUTATED         0        3         1         4         0
  CES2 WILD-TYPE      25       73        76       244        11
D32V3, multiclass
           clus
vv          CES2 MUTATED CES2 WILD-TYPE
  STAGE I              0             25
  STAGE II             3             73
  STAGE III            1             76
  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
  CES2 MUTATED       2   2   1   3
  CES2 WILD-TYPE    46 129  97 165
D32V4, multiclass
       clus
vv      CES2 MUTATED CES2 WILD-TYPE
  T0+T1            2             46
  T2               2            129
  T3               1             97
  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
  CES2 MUTATED     3   1   3   0
  CES2 WILD-TYPE 171  64 158   7
D32V5, multiclass
    clus
vv   CES2 MUTATED CES2 WILD-TYPE
  N0            3            171
  N1            1             64
  N2            3            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"
D32V6, binary
                cls
clus               0   1
  CES2 MUTATED     4   7
  CES2 WILD-TYPE 135 360
[1] "tbl2"
                cls
clus             [,1] [,2]
  CES2 MUTATED      4    7
  CES2 WILD-TYPE  135  360
        clus
vv       CES2 MUTATED CES2 WILD-TYPE
  FEMALE            4            135
  MALE              7            360
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  CES2 MUTATED                                      11
  CES2 WILD-TYPE                                   487
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  CES2 MUTATED                                                             0
  CES2 WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  CES2 MUTATED                                                     0
  CES2 WILD-TYPE                                                   7
D32V7, multiclass
                                                             clus
vv                                                            CES2 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                                                            CES2 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"
D32V8, binary
                cls
clus               0   1
  CES2 MUTATED     1  10
  CES2 WILD-TYPE  82 413
[1] "tbl2"
                cls
clus             [,1] [,2]
  CES2 MUTATED      1   10
  CES2 WILD-TYPE   82  413
     clus
vv    CES2 MUTATED CES2 WILD-TYPE
  NO             1             82
  YES           10            413
[1] 2 2
[1] FALSE
D32V9, continuous
D32V10, continuous
D32V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CES2 MUTATED                                  1     0
  CES2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CES2 MUTATED                           1     9
  CES2 WILD-TYPE                        35   432
D32V12, multiclass
                                  clus
vv                                 CES2 MUTATED CES2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             35
  WHITE                                       9            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"
D32V13, binary
                cls
clus               0   1
  CES2 MUTATED     0  11
  CES2 WILD-TYPE  25 434
[1] "tbl2"
                cls
clus             [,1] [,2]
  CES2 MUTATED      0   11
  CES2 WILD-TYPE   25  434
                        clus
vv                       CES2 MUTATED CES2 WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO           11            434
[1] 2 2
[1] FALSE

Clustering(33) Variable = IRS4 MUTATION ANALYSIS
D33V1, survival
                sevent
clus2              0   1
  IRS4 MUTATED     9   8
  IRS4 WILD-TYPE 294 193
  IRS4 MUTATED IRS4 WILD-TYPE 
            17            487 
  IRS4 MUTATED IRS4 WILD-TYPE 
             8            193 
$`IRS4 MUTATED`
TCGA-BA-6868 TCGA-CN-4741 TCGA-CR-7388 TCGA-CR-7398 TCGA-CV-6953 TCGA-CV-7245 
       15.52        41.69        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        12.13 
TCGA-F7-A50J TCGA-QK-A6IF TCGA-QK-A6V9 TCGA-TN-A7HL TCGA-UF-A7JJ 
       19.23        17.65        18.64        13.68        16.11 

$`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 
       53.79        57.44        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         7.76        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        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       37.84        12.89        26.86        32.65        21.11        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        33.11        34.36         8.58        12.39        35.54 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       55.27         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        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        14.56        17.59        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        17.29        15.91        11.44         5.75 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.69         6.18        48.20        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        46.75        45.80        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 
       34.75        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        51.29        33.11        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       28.83        64.11        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 
       32.81        25.81        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 
       11.51        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 
       31.10        29.85        29.52        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        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      126.08        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        24.99       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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        34.36        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-A6EO TCGA-D6-A6EP 
       17.72        12.36        15.88         7.63        14.30        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        35.54        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        18.90        25.48        20.45 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
        9.83        12.10        10.65        11.18        37.18        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
       20.25         3.02        18.94        12.62         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-7917 
       21.11         6.77         0.07         0.16        25.74         1.22 
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        12.76 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        19.33        11.84        13.55         0.07        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
        5.29        11.54        11.84        13.35        18.15        12.43 
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 
        3.68        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 
       56.75        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        11.74         7.30        16.70         9.34 
TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       12.72        14.79        12.43        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        43.59 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        43.36        41.16        42.02        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK 
       62.27        17.95        24.16        49.22        21.86        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 
         18.64          18.67 
[1] "5.1 - 156.5 (18.6)" "0.1 - 211.0 (18.7)"
[1] "hr=" "1"  
D33V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  IRS4 MUTATED         0        4         2         7         0
  IRS4 WILD-TYPE      25       72        75       241        11
D33V3, multiclass
           clus
vv          IRS4 MUTATED IRS4 WILD-TYPE
  STAGE I              0             25
  STAGE II             4             72
  STAGE III            2             75
  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    48 127  95 162
D33V4, multiclass
       clus
vv      IRS4 MUTATED IRS4 WILD-TYPE
  T0+T1            0             48
  T2               4            127
  T3               3             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
  IRS4 MUTATED     6   0   3   0
  IRS4 WILD-TYPE 168  65 158   7
D33V5, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  N0            6            168
  N1            0             65
  N2            3            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"
D33V6, binary
                cls
clus               0   1
  IRS4 MUTATED     7  10
  IRS4 WILD-TYPE 132 357
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      7   10
  IRS4 WILD-TYPE  132  357
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  FEMALE            7            132
  MALE             10            357
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  IRS4 MUTATED                                      17
  IRS4 WILD-TYPE                                   481
                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
D33V7, 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                                  481
  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"
D33V8, binary
                cls
clus               0   1
  IRS4 MUTATED     2  15
  IRS4 WILD-TYPE  81 408
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      2   15
  IRS4 WILD-TYPE   81  408
     clus
vv    IRS4 MUTATED IRS4 WILD-TYPE
  NO             2             81
  YES           15            408
[1] 2 2
[1] FALSE
D33V9, continuous
D33V10, continuous
D33V11, 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                        34   428
D33V12, multiclass
                                  clus
vv                                 IRS4 MUTATED IRS4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   2             34
  WHITE                                      13            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"
D33V13, binary
                cls
clus               0   1
  IRS4 MUTATED     2  13
  IRS4 WILD-TYPE  23 432
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      2   13
  IRS4 WILD-TYPE   23  432
                        clus
vv                       IRS4 MUTATED IRS4 WILD-TYPE
  HISPANIC OR LATINO                2             23
  NOT HISPANIC OR LATINO           13            432
[1] 2 2
[1] FALSE

Clustering(34) Variable = ARID2 MUTATION ANALYSIS
D34V1, survival
                 sevent
clus2               0   1
  ARID2 MUTATED    15   5
  ARID2 WILD-TYPE 288 196
  ARID2 MUTATED ARID2 WILD-TYPE 
             20             484 
  ARID2 MUTATED ARID2 WILD-TYPE 
              5             196 
$`ARID2 MUTATED`
TCGA-BA-A6DA TCGA-BB-7863 TCGA-C9-A47Z TCGA-CN-5355 TCGA-CR-7394 TCGA-CR-7395 
       11.54        33.70         6.28        33.11        29.52        30.58 
TCGA-CV-5430 TCGA-CV-5976 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7252 TCGA-CV-A6JN 
      139.43        48.59        28.34         2.50         4.96        29.79 
TCGA-D6-6826 TCGA-D6-A6EQ TCGA-DQ-7589 TCGA-F7-A624 TCGA-MT-A67F TCGA-P3-A6T2 
       11.44        12.10        18.90        12.43        12.62        75.55 
TCGA-QK-A6V9 TCGA-T2-A6X2 
       18.64        32.45 

$`ARID2 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 
       53.79        57.44        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         7.76        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       30.18        27.95         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        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.35        22.42        36.72 
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-A480 
       25.71        10.55        27.19        12.92         8.81        12.69 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       23.70        38.04         4.67        40.44        37.84        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
       26.86        32.65        21.11        24.92        41.10        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        43.73        27.58        41.69        13.05 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       34.36         8.58        12.39        35.54        55.27         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 
       22.45        56.94        20.71        30.67        20.68        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
       19.53        20.68        19.07        14.20         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        9.24        36.49        11.08        10.45        20.09        12.95 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 
       24.16         3.68        17.42        14.10        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       14.56        17.59        12.85        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       17.29        15.91        11.44         5.75         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
        2.70        10.09         7.33         9.80         7.69         6.18 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        39.68        21.50         2.93        54.58        46.75 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       45.80        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        34.75        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        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       33.11        16.73        43.04        41.88        28.83        64.11 
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        32.81        25.81 
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        11.51        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        31.10 
TCGA-CR-7393 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       29.85         7.10         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
       48.39        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        94.88        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-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       126.08        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-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
        7.13         8.42         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-7253 TCGA-CV-7254 TCGA-CV-7255 
       18.97        17.13        95.34        11.87        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-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 
       24.99       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-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
        6.38         6.48        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       34.36        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       16.14        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q 
       15.88         7.63        14.30        13.94        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       58.45        35.54        30.94        33.86        18.02        14.04 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       25.48        20.45         9.83        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       11.18        37.18        21.63        20.25         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        12.62         0.46        17.85        11.80        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         6.77         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
        0.16        25.74         1.22        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        12.76        14.50        19.33        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       13.55         0.07        14.47         5.29        11.54        11.84 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        12.43        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
       30.05         1.84         3.68        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        56.75        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-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       16.01        13.15        21.07        11.74        17.65         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO 
       16.70         9.34        12.72        14.79        12.43        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-A71D 
       13.68        43.59        54.67         2.83        43.36        41.16 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       42.02        44.65        62.27        17.95        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       21.86        16.11        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 

  ARID2 MUTATED ARID2 WILD-TYPE 
           2.50            0.07 
  ARID2 MUTATED ARID2 WILD-TYPE 
         139.43          210.97 
  ARID2 MUTATED ARID2 WILD-TYPE 
         23.620          18.475 
[1] "2.5 - 139.4 (23.6)" "0.1 - 211.0 (18.5)"
[1] "hr=" "1.7"
D34V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  ARID2 MUTATED         0        4         4        10         0
  ARID2 WILD-TYPE      25       72        73       238        11
D34V3, multiclass
           clus
vv          ARID2 MUTATED ARID2 WILD-TYPE
  STAGE I               0              25
  STAGE II              4              72
  STAGE III             4              73
  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
  ARID2 MUTATED       0   5   4   9
  ARID2 WILD-TYPE    48 126  94 159
D34V4, multiclass
       clus
vv      ARID2 MUTATED ARID2 WILD-TYPE
  T0+T1             0              48
  T2                5             126
  T3                4              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
  ARID2 MUTATED     9   2   5   0
  ARID2 WILD-TYPE 165  63 156   7
D34V5, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  N0             9             165
  N1             2              63
  N2             5             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
  ARID2 MUTATED     7  13
  ARID2 WILD-TYPE 132 354
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      7   13
  ARID2 WILD-TYPE  132  354
        clus
vv       ARID2 MUTATED ARID2 WILD-TYPE
  FEMALE             7             132
  MALE              13             354
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  ARID2 MUTATED                                      20
  ARID2 WILD-TYPE                                   478
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  ARID2 MUTATED                                                             0
  ARID2 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  ARID2 MUTATED                                                     0
  ARID2 WILD-TYPE                                                   7
D34V7, multiclass
                                                             clus
vv                                                            ARID2 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                                                            ARID2 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"
D34V8, binary
                 cls
clus                0   1
  ARID2 MUTATED     1  19
  ARID2 WILD-TYPE  82 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      1   19
  ARID2 WILD-TYPE   82  404
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  NO              1              82
  YES            19             404
[1] 2 2
[1] FALSE
D34V9, continuous
D34V10, continuous
D34V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID2 MUTATED                                  0     1
  ARID2 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ARID2 MUTATED                           3    16
  ARID2 WILD-TYPE                        33   425
D34V12, multiclass
                                  clus
vv                                 ARID2 MUTATED ARID2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    3              33
  WHITE                                       16             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"
D34V13, binary
                 cls
clus                0   1
  ARID2 MUTATED     2  17
  ARID2 WILD-TYPE  23 428
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      2   17
  ARID2 WILD-TYPE   23  428
                        clus
vv                       ARID2 MUTATED ARID2 WILD-TYPE
  HISPANIC OR LATINO                 2              23
  NOT HISPANIC OR LATINO            17             428
[1] 2 2
[1] FALSE

Clustering(35) Variable = CBWD1 MUTATION ANALYSIS
D35V1, survival
                 sevent
clus2               0   1
  CBWD1 MUTATED     2   3
  CBWD1 WILD-TYPE 301 198
  CBWD1 MUTATED CBWD1 WILD-TYPE 
              5             499 
  CBWD1 MUTATED CBWD1 WILD-TYPE 
              3             198 
$`CBWD1 MUTATED`
TCGA-CN-5370 TCGA-CQ-5326 TCGA-F7-A624 TCGA-QK-A6II TCGA-QK-A6VB 
        8.52         2.93        12.43         9.34        14.79 

$`CBWD1 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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       40.44        37.84        12.89        26.86        32.65        21.11 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       24.92        41.10        12.99        20.55        14.33        43.73 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        41.69        13.05        33.11        34.36         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       12.39        35.54        55.27         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.84        11.57        12.49        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        20.68        20.65        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       14.20         6.74         9.07         9.24        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        46.75        45.80        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 
       34.75        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        51.29        33.11        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       28.83        64.11        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 
       32.81        25.81        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 
       11.51        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        31.10        29.85        29.52        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        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       126.08        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-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        24.99       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 
       22.03         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-D6-6515 
       10.42        10.42        10.55        18.84        34.36        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        15.88 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        14.30        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        35.54        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 
       18.90        25.48        20.45         9.83        12.13        12.10 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       10.65        11.18        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 
       19.23        18.94        12.62         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         6.77 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        0.07         0.16        25.74         1.22        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        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        13.55         0.07        14.47         5.29        11.54 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       11.84        13.35        18.15        12.43        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         3.68        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        56.75        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-A6IJ TCGA-QK-A6V9 
       11.74        17.65         7.30        16.70        12.72        18.64 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       12.43        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        13.68        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        43.36        41.16        42.02        44.65        62.27 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.16        49.22        21.86        16.11        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 

  CBWD1 MUTATED CBWD1 WILD-TYPE 
           2.93            0.07 
  CBWD1 MUTATED CBWD1 WILD-TYPE 
          14.79          210.97 
  CBWD1 MUTATED CBWD1 WILD-TYPE 
           9.34           18.84 
[1] "2.9 - 14.8 (9.3)"   "0.1 - 211.0 (18.8)"
[1] "hr=" "4.1"
D35V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  CBWD1 MUTATED         0        1         1         3         0
  CBWD1 WILD-TYPE      25       75        76       245        11
D35V3, multiclass
           clus
vv          CBWD1 MUTATED CBWD1 WILD-TYPE
  STAGE I               0              25
  STAGE II              1              75
  STAGE III             1              76
  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
  CBWD1 MUTATED       0   1   1   3
  CBWD1 WILD-TYPE    48 130  97 165
D35V4, multiclass
       clus
vv      CBWD1 MUTATED CBWD1 WILD-TYPE
  T0+T1             0              48
  T2                1             130
  T3                1              97
  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
  CBWD1 MUTATED     1   1   2   0
  CBWD1 WILD-TYPE 173  64 159   7
D35V5, multiclass
    clus
vv   CBWD1 MUTATED CBWD1 WILD-TYPE
  N0             1             173
  N1             1              64
  N2             2             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
  CBWD1 MUTATED     0   5
  CBWD1 WILD-TYPE 139 362
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD1 MUTATED      0    5
  CBWD1 WILD-TYPE  139  362
        clus
vv       CBWD1 MUTATED CBWD1 WILD-TYPE
  FEMALE             0             139
  MALE               5             362
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  CBWD1 MUTATED                                       5
  CBWD1 WILD-TYPE                                   493
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  CBWD1 MUTATED                                                             0
  CBWD1 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  CBWD1 MUTATED                                                     0
  CBWD1 WILD-TYPE                                                   7
D35V7, multiclass
                                                             clus
vv                                                            CBWD1 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                                                            CBWD1 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"
D35V8, binary
                 cls
clus                0   1
  CBWD1 MUTATED     1   4
  CBWD1 WILD-TYPE  82 419
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD1 MUTATED      1    4
  CBWD1 WILD-TYPE   82  419
     clus
vv    CBWD1 MUTATED CBWD1 WILD-TYPE
  NO              1              82
  YES             4             419
[1] 2 2
[1] FALSE
D35V9, continuous
[1] "Remove cluster labels:" "CBWD1 MUTATED"         
clus
  CBWD1 MUTATED CBWD1 WILD-TYPE 
              2             280 
     TCGA-BA-4074      TCGA-BA-4075      TCGA-BA-4076      TCGA-BA-4077 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-BA-4078      TCGA-BA-5149      TCGA-BA-5151      TCGA-BA-5555 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-BA-5556      TCGA-BA-6868      TCGA-BA-6869      TCGA-BA-6870 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-BA-6871      TCGA-BA-6872      TCGA-BA-6873      TCGA-BA-7269 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-BA-A4IF      TCGA-BA-A4IH      TCGA-BA-A4II      TCGA-BA-A6D8 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-BA-A6DA      TCGA-BA-A6DD      TCGA-BA-A6DE      TCGA-BA-A6DG 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-BA-A6DI      TCGA-BA-A6DJ      TCGA-BA-A6DL      TCGA-BB-4217 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-BB-4225      TCGA-BB-4227      TCGA-BB-4228      TCGA-BB-7862 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-BB-7864      TCGA-BB-7870      TCGA-BB-7871      TCGA-BB-8596 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-BB-A5HY      TCGA-BB-A6UM      TCGA-BB-A6UO      TCGA-CN-4726 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-4727      TCGA-CN-4728      TCGA-CN-4729      TCGA-CN-4730 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-4731      TCGA-CN-4735      TCGA-CN-4736      TCGA-CN-4738 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-4739      TCGA-CN-4740      TCGA-CN-4741      TCGA-CN-4742 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-5355      TCGA-CN-5358      TCGA-CN-5359      TCGA-CN-5360 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-5361      TCGA-CN-5363      TCGA-CN-5365      TCGA-CN-5366 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-5367      TCGA-CN-5373      TCGA-CN-5374      TCGA-CN-6010 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-6011      TCGA-CN-6012      TCGA-CN-6016      TCGA-CN-6017 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-6019      TCGA-CN-6021      TCGA-CN-6023      TCGA-CN-6024 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-6988      TCGA-CN-6989      TCGA-CN-6992      TCGA-CN-6994 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-6997      TCGA-CN-6998      TCGA-CN-A498      TCGA-CN-A49B 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-A49C      TCGA-CN-A63T      TCGA-CN-A63U      TCGA-CN-A63V 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-A641      TCGA-CN-A642      TCGA-CN-A6UY      TCGA-CN-A6V3 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-A6V6      TCGA-CQ-5323      TCGA-CQ-5324      TCGA-CQ-5325 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CQ-5330      TCGA-CQ-5331      TCGA-CQ-5332      TCGA-CQ-5333 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CQ-6218      TCGA-CQ-6219      TCGA-CQ-6221      TCGA-CQ-6222 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CQ-6223      TCGA-CQ-6224      TCGA-CQ-6227      TCGA-CQ-6228 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CQ-7063      TCGA-CQ-7072      TCGA-CQ-A4C6      TCGA-CQ-A4C7 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CQ-A4C9      TCGA-CQ-A4CB      TCGA-CQ-A4CG      TCGA-CQ-A4CI 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-5247      TCGA-CR-5250      TCGA-CR-6467      TCGA-CR-6471 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-6473      TCGA-CR-6474      TCGA-CR-6482      TCGA-CR-6487 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-6491      TCGA-CR-6492      TCGA-CR-6493      TCGA-CR-7364 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-7367      TCGA-CR-7368      TCGA-CR-7369      TCGA-CR-7370 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-7371      TCGA-CR-7373      TCGA-CR-7374      TCGA-CR-7376 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-7377      TCGA-CR-7379      TCGA-CR-7383      TCGA-CR-7385 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-7386      TCGA-CR-7388      TCGA-CR-7389      TCGA-CR-7390 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-7392      TCGA-CR-7394      TCGA-CR-7395      TCGA-CR-7398 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-7399      TCGA-CR-7401      TCGA-CR-7402      TCGA-CV-6436 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-6933      TCGA-CV-6934      TCGA-CV-6936      TCGA-CV-6941 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-6945      TCGA-CV-6952      TCGA-CV-6961      TCGA-CV-7095 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-7097      TCGA-CV-7235      TCGA-CV-7242      TCGA-CV-7245 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-7248      TCGA-CV-7250      TCGA-CV-7254      TCGA-CV-7261 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-7263      TCGA-CV-7406      TCGA-CV-7410      TCGA-CV-7418 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-7422      TCGA-CV-7424      TCGA-CV-7427      TCGA-CV-7430 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-7432      TCGA-CV-7433      TCGA-CV-7434      TCGA-CV-7440 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-7446      TCGA-CV-7568      TCGA-CV-A45Y      TCGA-CV-A45Z 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-A460      TCGA-CV-A464      TCGA-CV-A468      TCGA-CV-A6JD 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-A6JN      TCGA-CV-A6JO      TCGA-CV-A6JU      TCGA-CV-A6JZ 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-A6K1      TCGA-CV-A6K2      TCGA-CX-7082      TCGA-CX-7085 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CX-7086      TCGA-CX-7219      TCGA-D6-6516      TCGA-D6-6517 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-D6-6823      TCGA-D6-6824      TCGA-D6-6825      TCGA-D6-6827 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-D6-8568      TCGA-D6-8569      TCGA-D6-A4Z9      TCGA-D6-A4ZB 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-D6-A6EK      TCGA-D6-A6EP      TCGA-DQ-5625      TCGA-DQ-5629 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-DQ-5630      TCGA-DQ-5631      TCGA-DQ-7588      TCGA-DQ-7589 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-DQ-7590      TCGA-DQ-7591      TCGA-DQ-7592      TCGA-DQ-7593 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-DQ-7595      TCGA-F7-7848      TCGA-F7-8489      TCGA-F7-A50G 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-F7-A50I      TCGA-F7-A50J      TCGA-F7-A61S      TCGA-F7-A61V 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-F7-A61W      TCGA-F7-A620      TCGA-F7-A623      TCGA-H7-7774 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-H7-A6C4      TCGA-H7-A6C5      TCGA-HD-7753      TCGA-HD-7754 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-HD-7832      TCGA-HD-8634      TCGA-HD-8635      TCGA-HD-A634 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-HD-A6I0      TCGA-HL-7533      TCGA-IQ-7631      TCGA-IQ-7632 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-IQ-A61E      TCGA-IQ-A61G      TCGA-IQ-A61H      TCGA-IQ-A61K 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-KU-A66S      TCGA-KU-A6H7      TCGA-KU-A6H8      TCGA-MT-A51W 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-MT-A51X      TCGA-MT-A67D      TCGA-MZ-A6I9      TCGA-MZ-A7D7 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-P3-A5Q6      TCGA-P3-A6SW      TCGA-P3-A6SX      TCGA-P3-A6T0 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-P3-A6T4      TCGA-P3-A6T5      TCGA-P3-A6T7      TCGA-P3-A6T8 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-QK-A6IG      TCGA-QK-A6IJ      TCGA-RS-A6TP      TCGA-T2-A6WZ 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-T2-A6X0      TCGA-T2-A6X2      TCGA-TN-A7HI      TCGA-TN-A7HL 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-UF-A718      TCGA-UF-A71B      TCGA-UF-A71D      TCGA-UF-A7J9 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-UF-A7JC      TCGA-UF-A7JD      TCGA-UF-A7JF      TCGA-UF-A7JH 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-UF-A7JJ      TCGA-UF-A7JS      TCGA-WA-A7GZ      TCGA-WA-A7H4 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
D35V10, continuous
[1] "Remove cluster labels:" "CBWD1 MUTATED"         
clus
  CBWD1 MUTATED CBWD1 WILD-TYPE 
              2             270 
     TCGA-BA-4074      TCGA-BA-4075      TCGA-BA-4076      TCGA-BA-4077 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-BA-4078      TCGA-BA-5149      TCGA-BA-5151      TCGA-BA-5556 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-BA-6868      TCGA-BA-6869      TCGA-BA-6870      TCGA-BA-6871 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-BA-6872      TCGA-BA-6873      TCGA-BA-7269      TCGA-BA-A6DA 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-BA-A6DG      TCGA-BB-4225      TCGA-BB-4228      TCGA-BB-7871 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-BB-8596      TCGA-BB-A5HY      TCGA-BB-A6UM      TCGA-BB-A6UO 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-4727      TCGA-CN-4728      TCGA-CN-4730      TCGA-CN-4736 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-4738      TCGA-CN-4739      TCGA-CN-4741      TCGA-CN-4742 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-5358      TCGA-CN-5359      TCGA-CN-5360      TCGA-CN-5361 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-5363      TCGA-CN-5365      TCGA-CN-5366      TCGA-CN-5367 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-6010      TCGA-CN-6011      TCGA-CN-6012      TCGA-CN-6016 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-6017      TCGA-CN-6021      TCGA-CN-6023      TCGA-CN-6024 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-6989      TCGA-CN-6992      TCGA-CN-6994      TCGA-CN-6997 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-6998      TCGA-CN-A498      TCGA-CN-A49B      TCGA-CN-A49C 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-A63T      TCGA-CN-A63U      TCGA-CN-A63V      TCGA-CN-A641 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CN-A6UY      TCGA-CN-A6V3      TCGA-CN-A6V6      TCGA-CQ-5323 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CQ-5324      TCGA-CQ-5325      TCGA-CQ-5330      TCGA-CQ-5331 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CQ-5333      TCGA-CQ-6218      TCGA-CQ-6219      TCGA-CQ-6221 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CQ-6222      TCGA-CQ-6223      TCGA-CQ-6224      TCGA-CQ-6227 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CQ-6228      TCGA-CQ-7063      TCGA-CQ-7072      TCGA-CQ-A4C6 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CQ-A4C7      TCGA-CQ-A4C9      TCGA-CQ-A4CB      TCGA-CQ-A4CI 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-5247      TCGA-CR-5248      TCGA-CR-5250      TCGA-CR-6467 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-6471      TCGA-CR-6473      TCGA-CR-6474      TCGA-CR-6477 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-6478      TCGA-CR-6482      TCGA-CR-6487      TCGA-CR-6491 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-6492      TCGA-CR-6493      TCGA-CR-7364      TCGA-CR-7365 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-7367      TCGA-CR-7368      TCGA-CR-7369      TCGA-CR-7370 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-7371      TCGA-CR-7373      TCGA-CR-7374      TCGA-CR-7376 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-7377      TCGA-CR-7383      TCGA-CR-7385      TCGA-CR-7386 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-7388      TCGA-CR-7389      TCGA-CR-7390      TCGA-CR-7391 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-7392      TCGA-CR-7394      TCGA-CR-7395      TCGA-CR-7397 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CR-7399      TCGA-CR-7401      TCGA-CR-7402      TCGA-CV-5430 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-5431      TCGA-CV-5432      TCGA-CV-5435      TCGA-CV-5436 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-5440      TCGA-CV-5443      TCGA-CV-5966      TCGA-CV-5970 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-5976      TCGA-CV-6433      TCGA-CV-6436      TCGA-CV-6441 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-6934      TCGA-CV-6935      TCGA-CV-6936      TCGA-CV-6941 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-6943      TCGA-CV-6945      TCGA-CV-6952      TCGA-CV-6954 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-6960      TCGA-CV-6961      TCGA-CV-7091      TCGA-CV-7095 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-7097      TCGA-CV-7099      TCGA-CV-7100      TCGA-CV-7101 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-7102      TCGA-CV-7180      TCGA-CV-7183      TCGA-CV-7235 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-7242      TCGA-CV-7245      TCGA-CV-7248      TCGA-CV-7250 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-7254      TCGA-CV-7261      TCGA-CV-7406      TCGA-CV-7410 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-7418      TCGA-CV-7422      TCGA-CV-7424      TCGA-CV-7427 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-7430      TCGA-CV-7432      TCGA-CV-7433      TCGA-CV-7434 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-7435      TCGA-CV-7440      TCGA-CV-7446      TCGA-CV-7568 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-A45Q      TCGA-CV-A45Y      TCGA-CV-A45Z      TCGA-CV-A460 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-A461      TCGA-CV-A464      TCGA-CV-A468      TCGA-CV-A6JD 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-A6JE      TCGA-CV-A6JN      TCGA-CV-A6JO      TCGA-CV-A6JU 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CV-A6JY      TCGA-CV-A6JZ      TCGA-CV-A6K1      TCGA-CV-A6K2 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-CX-7086      TCGA-CX-7219      TCGA-D6-6516      TCGA-D6-6517 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-D6-6823      TCGA-D6-6824      TCGA-D6-6825      TCGA-D6-6827 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-D6-8568      TCGA-D6-8569      TCGA-D6-A4Z9      TCGA-D6-A4ZB 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-D6-A6EK      TCGA-D6-A6EP      TCGA-D6-A74Q      TCGA-DQ-5625 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-DQ-5629      TCGA-DQ-5630      TCGA-DQ-5631      TCGA-DQ-7588 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-DQ-7589      TCGA-DQ-7590      TCGA-DQ-7591      TCGA-DQ-7592 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-DQ-7593      TCGA-DQ-7595      TCGA-F7-7848      TCGA-F7-8489 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-F7-A50G      TCGA-F7-A50I      TCGA-F7-A50J      TCGA-F7-A61S 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-F7-A61V      TCGA-F7-A61W      TCGA-F7-A620      TCGA-F7-A623 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-H7-7774      TCGA-H7-A6C4      TCGA-H7-A6C5      TCGA-H7-A76A 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-HD-8634      TCGA-HD-8635      TCGA-HD-A634      TCGA-HD-A6I0 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-HL-7533      TCGA-IQ-7631      TCGA-IQ-7632      TCGA-IQ-A61E 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-IQ-A61G      TCGA-KU-A66S      TCGA-KU-A6H7      TCGA-KU-A6H8 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-MT-A51W      TCGA-MT-A51X      TCGA-MT-A67D      TCGA-MZ-A6I9 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-MZ-A7D7      TCGA-P3-A6SX      TCGA-P3-A6T0      TCGA-P3-A6T4 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-P3-A6T8      TCGA-QK-A6IG      TCGA-QK-A6IJ      TCGA-RS-A6TP 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-TN-A7HI      TCGA-TN-A7HL      TCGA-UF-A718      TCGA-UF-A71B 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-UF-A71D      TCGA-UF-A7J9      TCGA-UF-A7JC      TCGA-UF-A7JD 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-UF-A7JF      TCGA-UF-A7JH      TCGA-UF-A7JJ      TCGA-UF-A7JS 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-WA-A7GZ      TCGA-WA-A7H4 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
D35V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CBWD1 MUTATED                                  0     0
  CBWD1 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CBWD1 MUTATED                           0     5
  CBWD1 WILD-TYPE                        36   436
D35V12, multiclass
                                  clus
vv                                 CBWD1 MUTATED CBWD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              36
  WHITE                                        5             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
  CBWD1 MUTATED     0   5
  CBWD1 WILD-TYPE  25 440
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD1 MUTATED      0    5
  CBWD1 WILD-TYPE   25  440
                        clus
vv                       CBWD1 MUTATED CBWD1 WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO             5             440
[1] 2 2
[1] FALSE

Clustering(36) Variable = RGL4 MUTATION ANALYSIS
D36V1, survival
                sevent
clus2              0   1
  RGL4 MUTATED     6   1
  RGL4 WILD-TYPE 297 200
  RGL4 MUTATED RGL4 WILD-TYPE 
             7            497 
  RGL4 MUTATED RGL4 WILD-TYPE 
             1            200 
$`RGL4 MUTATED`
TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6482 TCGA-CR-7388 TCGA-CV-7091 TCGA-D6-6516 
       43.04        34.52        11.34        27.06       111.16        25.41 
TCGA-DQ-5625 
       35.54 

$`RGL4 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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       40.44        37.84        12.89        26.86        32.65        21.11 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       24.92        41.10        12.99        20.55        14.33        43.73 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        41.69        13.05        33.11        34.36         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       12.39        35.54        55.27         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        22.45        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       20.71        30.67        20.68        20.65        19.53        20.68 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        14.20         6.74         9.07         9.24        36.49 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       11.08        10.45        20.09        12.95        24.16         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        14.10        11.74        35.01        14.56        17.59 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       12.85        29.72        21.21         7.40        17.29        15.91 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       11.44         5.75         4.41        12.07         2.70        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
        7.33         9.80         7.69         6.18        48.20        39.68 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        46.75        45.80        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        34.75        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        51.29        33.11        16.73 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        28.83        64.11        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        32.81        25.81        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
       50.01        39.52        36.99        18.54        16.90         6.02 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       11.90        10.22        11.64         7.69        12.46        11.51 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       15.75         9.27        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       32.78        47.01        12.89        29.82        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       29.85        29.52        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        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      126.08        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-7095 
       28.34         2.50         4.14        64.83       126.15        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 
       24.99       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        22.03         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-D6-6515 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       18.84        34.36        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-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       12.36        15.88         7.63        14.30        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        11.11        58.45        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        18.90        25.48        20.45         9.83        12.13 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       12.10        10.65        11.18        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        19.23        18.94        12.62         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-7917 
       21.11         6.77         0.07         0.16        25.74         1.22 
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        12.76 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        19.33        11.84        13.55         0.07        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
        5.29        11.54        11.84        13.35        18.15        12.43 
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 
        3.68        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 
       56.75        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        11.74        17.65         7.30        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO 
        9.34        12.72        18.64        14.79        12.43        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        13.68        43.59        54.67         2.83        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       41.16        42.02        44.65        62.27        17.95        24.16 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       49.22        21.86        16.11        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 

  RGL4 MUTATED RGL4 WILD-TYPE 
         11.34           0.07 
  RGL4 MUTATED RGL4 WILD-TYPE 
        111.16         210.97 
  RGL4 MUTATED RGL4 WILD-TYPE 
         34.52          18.41 
[1] "11.3 - 111.2 (34.5)" "0.1 - 211.0 (18.4)" 
[1] "hr=" "4.2"
D36V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  RGL4 MUTATED         2        1         0         0         0
  RGL4 WILD-TYPE      23       75        77       248        11
D36V3, multiclass
           clus
vv          RGL4 MUTATED RGL4 WILD-TYPE
  STAGE I              2             23
  STAGE II             1             75
  STAGE III            0             77
  STAGE IVA            0            248
  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
  RGL4 MUTATED       2   1   0   0
  RGL4 WILD-TYPE    46 130  98 168
D36V4, multiclass
       clus
vv      RGL4 MUTATED RGL4 WILD-TYPE
  T0+T1            2             46
  T2               1            130
  T3               0             98
  T4               0            168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RGL4 MUTATED     3   0   0   0
  RGL4 WILD-TYPE 171  65 161   7
D36V5, multiclass
    clus
vv   RGL4 MUTATED RGL4 WILD-TYPE
  N0            3            171
  N1            0             65
  N2            0            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"
D36V6, binary
                cls
clus               0   1
  RGL4 MUTATED     3   4
  RGL4 WILD-TYPE 136 363
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGL4 MUTATED      3    4
  RGL4 WILD-TYPE  136  363
        clus
vv       RGL4 MUTATED RGL4 WILD-TYPE
  FEMALE            3            136
  MALE              4            363
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  RGL4 MUTATED                                       7
  RGL4 WILD-TYPE                                   491
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  RGL4 MUTATED                                                             0
  RGL4 WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  RGL4 MUTATED                                                     0
  RGL4 WILD-TYPE                                                   7
D36V7, multiclass
                                                             clus
vv                                                            RGL4 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                                                            RGL4 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"
D36V8, binary
                cls
clus               0   1
  RGL4 MUTATED     0   7
  RGL4 WILD-TYPE  83 416
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGL4 MUTATED      0    7
  RGL4 WILD-TYPE   83  416
     clus
vv    RGL4 MUTATED RGL4 WILD-TYPE
  NO             0             83
  YES            7            416
[1] 2 2
[1] FALSE
D36V9, continuous
D36V10, continuous
D36V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RGL4 MUTATED                                  0     0
  RGL4 WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RGL4 MUTATED                           1     6
  RGL4 WILD-TYPE                        35   435
D36V12, multiclass
                                  clus
vv                                 RGL4 MUTATED RGL4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             35
  WHITE                                       6            435
[1] 4 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
  RGL4 MUTATED     0   7
  RGL4 WILD-TYPE  25 438
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGL4 MUTATED      0    7
  RGL4 WILD-TYPE   25  438
                        clus
vv                       RGL4 MUTATED RGL4 WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO            7            438
[1] 2 2
[1] FALSE

Clustering(37) Variable = HUWE1 MUTATION ANALYSIS
D37V1, survival
                 sevent
clus2               0   1
  HUWE1 MUTATED    24  20
  HUWE1 WILD-TYPE 279 181
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             44             460 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             20             181 
$`HUWE1 MUTATED`
TCGA-BA-5557 TCGA-BB-A6UO TCGA-CN-A63Y TCGA-CN-A642 TCGA-CQ-5330 TCGA-CQ-5332 
       20.48         8.81         5.75         2.70        45.80        10.42 
TCGA-CQ-5334 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CB TCGA-CR-5248 TCGA-CR-6471 
        4.24        43.04        28.83        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        15.88        58.45        35.54        11.18         0.46 
TCGA-MT-A67F TCGA-P3-A6T5 TCGA-QK-A652 TCGA-QK-A6II TCGA-RS-A6TO TCGA-T2-A6WX 
       12.62        29.00        11.74         9.34        12.72         6.87 
TCGA-T2-A6X2 TCGA-UF-A7JT 
       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        53.79 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       57.44        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         7.76        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        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44        37.84 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.65        21.11        24.92        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        33.11        34.36         8.58        12.39        35.54 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       55.27         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        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        14.56        17.59        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 
       21.21         7.40        17.29        15.91        11.44         4.41 
TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
       12.07        10.09         7.33         9.80         7.69         6.18 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        39.68        21.50         2.93        54.58        46.75 
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        34.75        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        51.29        33.11        16.73        41.88 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE 
       64.11        44.48        11.61        23.24        32.81        25.81 
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 
       11.51        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        31.10        29.85 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       29.52        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        94.88        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       126.08        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        24.99 
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        22.03 
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-D6-6515 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 
       18.84        34.36        13.25         9.60        23.05        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        14.30        13.94        12.10        12.79        11.11 
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        18.90        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 
       20.45         9.83        12.13        12.10        10.65        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        19.23        18.94        12.62 
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         6.77         0.07         0.16        25.74 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
        1.22        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 
       12.76        14.50        19.33        11.84        13.55         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
       14.47         5.29        11.54        11.84        13.35        18.15 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       12.43        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q6 
        3.68        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 
       56.75        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       75.55        18.97         2.04        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.07        17.65         7.30        16.70        12.72        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-TN-A7HI 
       14.79        12.43        16.96        15.91         7.10        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.25        13.68        43.59        54.67         2.83        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       41.16        42.02        44.65        62.27        17.95        24.16 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       49.22        21.86        16.11        13.94        20.75        22.36 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        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 
         18.180          18.655 
[1] "0.5 - 76.5 (18.2)"  "0.1 - 211.0 (18.7)"
[1] "hr=" "1.3"
D37V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  HUWE1 MUTATED         1        6         8        21         1
  HUWE1 WILD-TYPE      24       70        69       227        10
D37V3, multiclass
           clus
vv          HUWE1 MUTATED HUWE1 WILD-TYPE
  STAGE I               1              24
  STAGE II              6              70
  STAGE III             8              69
  STAGE IVA            21             227
  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    44 122  92 150
D37V4, multiclass
       clus
vv      HUWE1 MUTATED HUWE1 WILD-TYPE
  T0+T1             4              44
  T2                9             122
  T3                6              92
  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 157  59 151   6
D37V5, multiclass
    clus
vv   HUWE1 MUTATED HUWE1 WILD-TYPE
  N0            17             157
  N1             6              59
  N2            10             151
  N3             1               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                 cls
clus                0   1
  HUWE1 MUTATED    19  26
  HUWE1 WILD-TYPE 120 341
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED     19   26
  HUWE1 WILD-TYPE  120  341
        clus
vv       HUWE1 MUTATED HUWE1 WILD-TYPE
  FEMALE            19             120
  MALE              26             341
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  HUWE1 MUTATED                                      45
  HUWE1 WILD-TYPE                                   453
                 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
D37V7, 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                                   453
  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"
D37V8, binary
                 cls
clus                0   1
  HUWE1 MUTATED     5  40
  HUWE1 WILD-TYPE  78 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED      5   40
  HUWE1 WILD-TYPE   78  383
     clus
vv    HUWE1 MUTATED HUWE1 WILD-TYPE
  NO              5              78
  YES            40             383
[1] 2 2
[1] FALSE
D37V9, continuous
D37V10, continuous
D37V11, 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                        36   401
D37V12, multiclass
                                  clus
vv                                 HUWE1 MUTATED HUWE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              36
  WHITE                                       40             401
[1] 4 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
  HUWE1 MUTATED     4  39
  HUWE1 WILD-TYPE  21 406
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED      4   39
  HUWE1 WILD-TYPE   21  406
                        clus
vv                       HUWE1 MUTATED HUWE1 WILD-TYPE
  HISPANIC OR LATINO                 4              21
  NOT HISPANIC OR LATINO            39             406
[1] 2 2
[1] FALSE

Clustering(38) Variable = HNRNPL MUTATION ANALYSIS
D38V1, survival
                  sevent
clus2                0   1
  HNRNPL MUTATED     4   7
  HNRNPL WILD-TYPE 299 194
  HNRNPL MUTATED HNRNPL WILD-TYPE 
              11              493 
  HNRNPL MUTATED HNRNPL WILD-TYPE 
               7              194 
$`HNRNPL MUTATED`
TCGA-CN-4729 TCGA-CN-6018 TCGA-CN-6023 TCGA-CR-7377 TCGA-CV-6948 TCGA-CV-6952 
       12.89        19.07        36.49         9.17        42.38         6.08 
TCGA-CV-6953 TCGA-CV-A45Q TCGA-DQ-5631 TCGA-P3-A6T8 TCGA-QK-A6VB 
       53.95       169.38        18.02        13.15        14.79 

$`HNRNPL 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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       40.44        37.84        26.86        32.65        21.11        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       35.54        55.27         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        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
       30.67        20.68        20.65        19.53        20.68        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        6.74         9.07         9.24        11.08        10.45        20.09 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       12.95        24.16         3.68        17.42        14.10        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        14.56        17.59        12.85        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        17.29        15.91        11.44         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        10.09         7.33         9.80         7.69 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
        6.18        48.20        39.68        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       46.75        45.80        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        34.75 
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 
       51.29        33.11        16.73        43.04        41.88        28.83 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       64.11        44.48        11.61        23.24        29.36        32.81 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       25.81        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        11.51 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       15.75         9.27        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
       31.96        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        29.82        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       29.85        29.52        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        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6954 
      126.08        19.79        12.03        15.09        30.08        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       10.98         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       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-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-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        24.99       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 
       22.03         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-D6-6515 
       10.42        10.42        10.55        18.84        34.36        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        15.88 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        14.30        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        35.54        30.94        33.86        14.04        18.90 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       25.48        20.45         9.83        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       11.18        37.18        21.63        20.25         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        12.62         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         6.77 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        0.07         0.16        25.74         1.22        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        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        13.55         0.07        14.47         5.29        11.54 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       11.84        13.35        18.15        12.43        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         3.68        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        56.75        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-QK-A64Z TCGA-QK-A652 
        2.04        29.00        12.99        16.01        21.07        11.74 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       17.65         7.30        16.70         9.34        12.72        18.64 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       12.43        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        13.68        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        43.36        41.16        42.02        44.65        62.27 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.16        49.22        21.86        16.11        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 

  HNRNPL MUTATED HNRNPL WILD-TYPE 
            6.08             0.07 
  HNRNPL MUTATED HNRNPL WILD-TYPE 
          169.38           210.97 
  HNRNPL MUTATED HNRNPL WILD-TYPE 
           18.02            18.67 
[1] "6.1 - 169.4 (18.0)" "0.1 - 211.0 (18.7)"
[1] "hr=" "1.2"
D38V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  HNRNPL MUTATED         0        0         2         6         1
  HNRNPL WILD-TYPE      25       76        75       242        10
D38V3, multiclass
           clus
vv          HNRNPL MUTATED HNRNPL WILD-TYPE
  STAGE I                0               25
  STAGE II               0               76
  STAGE III              2               75
  STAGE IVA              6              242
  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
  HNRNPL MUTATED       0   1   3   5
  HNRNPL WILD-TYPE    48 130  95 163
D38V4, multiclass
       clus
vv      HNRNPL MUTATED HNRNPL WILD-TYPE
  T0+T1              0               48
  T2                 1              130
  T3                 3               95
  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
  HNRNPL MUTATED     2   1   5   1
  HNRNPL WILD-TYPE 172  64 156   6
D38V5, multiclass
    clus
vv   HNRNPL MUTATED HNRNPL WILD-TYPE
  N0              2              172
  N1              1               64
  N2              5              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"
D38V6, binary
                  cls
clus                 0   1
  HNRNPL MUTATED     5   6
  HNRNPL WILD-TYPE 134 361
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPL MUTATED      5    6
  HNRNPL WILD-TYPE  134  361
        clus
vv       HNRNPL MUTATED HNRNPL WILD-TYPE
  FEMALE              5              134
  MALE                6              361
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  HNRNPL MUTATED                                      11
  HNRNPL WILD-TYPE                                   487
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  HNRNPL MUTATED                                                             0
  HNRNPL WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  HNRNPL MUTATED                                                     0
  HNRNPL WILD-TYPE                                                   7
D38V7, multiclass
                                                             clus
vv                                                            HNRNPL 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                                                            HNRNPL 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"
D38V8, binary
                  cls
clus                 0   1
  HNRNPL MUTATED     2   9
  HNRNPL WILD-TYPE  81 414
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPL MUTATED      2    9
  HNRNPL WILD-TYPE   81  414
     clus
vv    HNRNPL MUTATED HNRNPL WILD-TYPE
  NO               2               81
  YES              9              414
[1] 2 2
[1] FALSE
D38V9, continuous
D38V10, continuous
D38V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNRNPL MUTATED                                  0     0
  HNRNPL WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HNRNPL MUTATED                           0    11
  HNRNPL WILD-TYPE                        36   430
D38V12, multiclass
                                  clus
vv                                 HNRNPL MUTATED HNRNPL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               36
  WHITE                                        11              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"
D38V13, binary
                  cls
clus                 0   1
  HNRNPL MUTATED     0  11
  HNRNPL WILD-TYPE  25 434
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPL MUTATED      0   11
  HNRNPL WILD-TYPE   25  434
                        clus
vv                       HNRNPL MUTATED HNRNPL WILD-TYPE
  HISPANIC OR LATINO                  0               25
  NOT HISPANIC OR LATINO             11              434
[1] 2 2
[1] FALSE

Clustering(39) Variable = ITGB1 MUTATION ANALYSIS
D39V1, survival
                 sevent
clus2               0   1
  ITGB1 MUTATED     8   6
  ITGB1 WILD-TYPE 295 195
  ITGB1 MUTATED ITGB1 WILD-TYPE 
             14             490 
  ITGB1 MUTATED ITGB1 WILD-TYPE 
              6             195 
$`ITGB1 MUTATED`
TCGA-BB-7871 TCGA-CN-A497 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CR-7368 TCGA-CR-7380 
       24.66        35.01        10.42         4.24        40.93        19.92 
TCGA-CV-6003 TCGA-CV-6953 TCGA-CV-6962 TCGA-CV-7252 TCGA-D6-6516 TCGA-F7-A623 
       54.74        53.95         4.14         4.96        25.41        20.25 
TCGA-HD-A6I0 TCGA-QK-A6VB 
        6.90        14.79 

$`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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       37.84        12.89        26.86        32.65        21.11        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       35.54        55.27         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        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        20.68        20.65        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       14.20         6.74         9.07         9.24        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       14.10        11.74        14.56        17.59        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        17.29        15.91        11.44         5.75 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.69         6.18        48.20        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-6218 
       54.58        46.75        45.80        45.99        11.21        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        34.75        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        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       33.11        16.73        43.04        41.88        28.83        64.11 
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        32.81        25.81 
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        11.51        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 
        9.27        47.18        39.16        47.34        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-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       34.06        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        31.10        29.85        29.52 
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        94.88        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-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       126.08        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6955 
       42.38        15.09        30.08         6.08        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 
        7.13         8.42        28.34         2.50        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-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        24.99       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        22.03         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-D6-6515 TCGA-D6-6517 TCGA-D6-6823 
       10.55        18.84        34.36        13.25         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-A6EO TCGA-D6-A6EP 
       17.72        12.36        15.88         7.63        14.30        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        35.54        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        18.90        25.48        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
        9.83        12.13        12.10        10.65        11.18        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        19.23        18.94        12.62 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
        0.46        17.85        11.80        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         6.77         0.07         0.16        25.74 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
        1.22        14.66        22.03        12.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         3.65        34.75        15.95        12.76 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        19.33        11.84        13.55         0.07        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
        5.29        11.54        11.84        13.35        18.15        12.43 
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 
        3.68        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 
       56.75        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        11.74        17.65         7.30        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP 
        9.34        12.72        18.64        12.43        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 
       13.68        43.59        54.67         2.83        43.36        41.16 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       42.02        44.65        62.27        17.95        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       21.86        16.11        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 

  ITGB1 MUTATED ITGB1 WILD-TYPE 
           4.14            0.07 
  ITGB1 MUTATED ITGB1 WILD-TYPE 
          54.74          210.97 
  ITGB1 MUTATED ITGB1 WILD-TYPE 
         20.085          18.590 
[1] "4.1 - 54.7 (20.1)"  "0.1 - 211.0 (18.6)"
[1] "hr=" "1.3"
D39V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  ITGB1 MUTATED         1        0         4         8         1
  ITGB1 WILD-TYPE      24       76        73       240        10
D39V3, multiclass
           clus
vv          ITGB1 MUTATED ITGB1 WILD-TYPE
  STAGE I               1              24
  STAGE II              0              76
  STAGE III             4              73
  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       3   1   3   7
  ITGB1 WILD-TYPE    45 130  95 161
D39V4, multiclass
       clus
vv      ITGB1 MUTATED ITGB1 WILD-TYPE
  T0+T1             3              45
  T2                1             130
  T3                3              95
  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   4   3   0
  ITGB1 WILD-TYPE 168  61 158   7
D39V5, multiclass
    clus
vv   ITGB1 MUTATED ITGB1 WILD-TYPE
  N0             6             168
  N1             4              61
  N2             3             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"
D39V6, binary
                 cls
clus                0   1
  ITGB1 MUTATED     4  10
  ITGB1 WILD-TYPE 135 357
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB1 MUTATED      4   10
  ITGB1 WILD-TYPE  135  357
        clus
vv       ITGB1 MUTATED ITGB1 WILD-TYPE
  FEMALE             4             135
  MALE              10             357
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  ITGB1 MUTATED                                      14
  ITGB1 WILD-TYPE                                   484
                 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
D39V7, multiclass
                                                             clus
vv                                                            ITGB1 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                                                            ITGB1 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"
D39V8, binary
                 cls
clus                0   1
  ITGB1 MUTATED     1  13
  ITGB1 WILD-TYPE  82 410
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB1 MUTATED      1   13
  ITGB1 WILD-TYPE   82  410
     clus
vv    ITGB1 MUTATED ITGB1 WILD-TYPE
  NO              1              82
  YES            13             410
[1] 2 2
[1] FALSE
D39V9, continuous
D39V10, continuous
D39V11, 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                        35   429
D39V12, multiclass
                                  clus
vv                                 ITGB1 MUTATED ITGB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              35
  WHITE                                       12             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"
D39V13, binary
                 cls
clus                0   1
  ITGB1 MUTATED     1  13
  ITGB1 WILD-TYPE  24 432
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB1 MUTATED      1   13
  ITGB1 WILD-TYPE   24  432
                        clus
vv                       ITGB1 MUTATED ITGB1 WILD-TYPE
  HISPANIC OR LATINO                 1              24
  NOT HISPANIC OR LATINO            13             432
[1] 2 2
[1] FALSE

Clustering(40) Variable = B2M MUTATION ANALYSIS
D40V1, survival
               sevent
clus2             0   1
  B2M MUTATED     5   2
  B2M WILD-TYPE 298 199
  B2M MUTATED B2M WILD-TYPE 
            7           497 
  B2M MUTATED B2M WILD-TYPE 
            2           199 
$`B2M MUTATED`
TCGA-BB-7871 TCGA-CR-5243 TCGA-CR-7404 TCGA-CV-7099 TCGA-H7-A76A TCGA-QK-A6II 
       24.66        84.23        48.39         7.99         6.77         9.34 
TCGA-T2-A6X2 
       32.45 

$`B2M 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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       37.84        12.89        26.86        32.65        21.11        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       35.54        55.27         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        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        20.68        20.65        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       14.20         6.74         9.07         9.24        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        46.75        45.80        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        34.75        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        51.29        33.11        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        28.83        64.11        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        32.81        25.81        14.14        12.46        31.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-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 
       11.51        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        31.10        29.85        29.52        30.58         7.10 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 
        5.13         5.95        35.41        29.95       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
      129.21       108.95        76.24        19.20        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       54.74        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        9.70         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       126.08        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-7100 TCGA-CV-7101 TCGA-CV-7102 
      111.16        18.81        12.66         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        24.99       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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        34.36        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        15.88         7.63        14.30 
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        35.54 
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        18.90        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45         9.83        12.13        12.10        10.65        11.18 
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        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       12.62         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
       13.38        15.16        13.61        21.11         0.07         0.16 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       25.74         1.22        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        12.76        14.50        19.33        11.84        13.55 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
        0.07        14.47         5.29        11.54        11.84        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        12.43        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         3.68        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        56.75        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        11.74        17.65 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
        7.30        16.70        12.72        18.64        14.79        12.43 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-TN-A7HI 
       12.72        16.96         6.87        15.91         7.10        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.25        13.68        43.59        54.67         2.83        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       41.16        42.02        44.65        62.27        17.95        24.16 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       49.22        21.86        16.11        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 

  B2M MUTATED B2M WILD-TYPE 
         6.77          0.07 
  B2M MUTATED B2M WILD-TYPE 
        84.23        210.97 
  B2M MUTATED B2M WILD-TYPE 
        24.66         18.64 
[1] "6.8 - 84.2 (24.7)"  "0.1 - 211.0 (18.6)"
[1] "hr=" "1.4"
D40V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  B2M MUTATED         0        1         1         2         0
  B2M WILD-TYPE      25       75        76       246        11
D40V3, multiclass
           clus
vv          B2M MUTATED B2M WILD-TYPE
  STAGE I             0            25
  STAGE II            1            75
  STAGE III           1            76
  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
  B2M MUTATED       0   1   1   2
  B2M WILD-TYPE    48 130  97 166
D40V4, multiclass
       clus
vv      B2M MUTATED B2M WILD-TYPE
  T0+T1           0            48
  T2              1           130
  T3              1            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
  B2M MUTATED     1   0   3   0
  B2M WILD-TYPE 173  65 158   7
D40V5, multiclass
    clus
vv   B2M MUTATED B2M WILD-TYPE
  N0           1           173
  N1           0            65
  N2           3           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"
D40V6, binary
               cls
clus              0   1
  B2M MUTATED     2   5
  B2M WILD-TYPE 137 362
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      2    5
  B2M WILD-TYPE  137  362
        clus
vv       B2M MUTATED B2M WILD-TYPE
  FEMALE           2           137
  MALE             5           362
[1] 2 2
[1] FALSE
               vv
clus            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  B2M MUTATED                                       7
  B2M WILD-TYPE                                   491
               vv
clus            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  B2M MUTATED                                                             0
  B2M WILD-TYPE                                                           1
               vv
clus            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  B2M MUTATED                                                     0
  B2M WILD-TYPE                                                   7
D40V7, multiclass
                                                             clus
vv                                                            B2M 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                                                            B2M 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"
D40V8, binary
               cls
clus              0   1
  B2M MUTATED     0   7
  B2M WILD-TYPE  83 416
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      0    7
  B2M WILD-TYPE   83  416
     clus
vv    B2M MUTATED B2M WILD-TYPE
  NO            0            83
  YES           7           416
[1] 2 2
[1] FALSE
D40V9, continuous
D40V10, continuous
D40V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  B2M MUTATED                                  0     0
  B2M WILD-TYPE                                2    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  B2M MUTATED                           0     7
  B2M WILD-TYPE                        36   434
D40V12, multiclass
                                  clus
vv                                 B2M MUTATED B2M WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  0            36
  WHITE                                      7           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"
D40V13, binary
               cls
clus              0   1
  B2M MUTATED     0   6
  B2M WILD-TYPE  25 439
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      0    6
  B2M WILD-TYPE   25  439
                        clus
vv                       B2M MUTATED B2M WILD-TYPE
  HISPANIC OR LATINO               0            25
  NOT HISPANIC OR LATINO           6           439
[1] 2 2
[1] FALSE

Clustering(41) Variable = LRRC37B MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  LRRC37B MUTATED    12   4
  LRRC37B WILD-TYPE 291 197
  LRRC37B MUTATED LRRC37B WILD-TYPE 
               16               488 
  LRRC37B MUTATED LRRC37B WILD-TYPE 
                4               197 
$`LRRC37B MUTATED`
TCGA-BB-7870 TCGA-CN-6989 TCGA-CN-A63W TCGA-CQ-7064 TCGA-CR-5248 TCGA-CR-6481 
       66.28        20.09        11.44        51.29        54.67        10.22 
TCGA-CR-7388 TCGA-CV-6961 TCGA-CV-A6JY TCGA-CX-7085 TCGA-DQ-5629 TCGA-HD-8314 
       27.06         2.50        21.24        10.55        30.94        22.03 
TCGA-KU-A6H7 TCGA-P3-A5QF TCGA-QK-A6VC TCGA-WA-A7H4 
       12.43        10.85        12.43        14.56 

$`LRRC37B 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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       37.84        12.89        26.86        32.65        21.11        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       35.54        55.27         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        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        20.68        20.65        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       14.20         6.74         9.07         9.24        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       10.45        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        14.56        17.59        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       21.21         7.40        17.29        15.91         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        10.09         7.33         9.80         7.69 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
        6.18        48.20        39.68        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       46.75        45.80        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        34.75 
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-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       33.11        16.73        43.04        41.88        28.83        64.11 
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        32.81        25.81 
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-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-6482 TCGA-CR-6484 
       18.54        16.90         6.02        11.90        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        11.51        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       39.16        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 
       19.92        26.17        17.13        32.78        47.01        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       29.82        30.02        31.10        29.85        29.52        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        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        7.07        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-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       126.08        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-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        24.99       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-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
       22.03         3.62        23.47        19.92        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.42        18.84        34.36        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        15.88         7.63        14.30 
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        35.54 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
       33.86        18.02        14.04        18.90        25.48        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
        9.83        12.13        12.10        10.65        11.18        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        19.23        18.94        12.62 
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         6.77         0.07         0.16 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
       25.74         1.22        14.66        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 
       12.76        14.50        19.33        11.84        13.55         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
       14.47         5.29        11.54        11.84        13.35        18.15 
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 
        3.68        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 
       56.75        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-A6II 
       21.07        11.74        17.65         7.30        16.70         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       12.72        18.64        14.79        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        13.68 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       43.59        54.67         2.83        43.36        41.16        42.02 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        62.27        17.95        24.16        49.22        21.86 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       16.11        13.94        20.75        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ 
       17.03        20.55 

  LRRC37B MUTATED LRRC37B WILD-TYPE 
             2.50              0.07 
  LRRC37B MUTATED LRRC37B WILD-TYPE 
            66.28            210.97 
  LRRC37B MUTATED LRRC37B WILD-TYPE 
           17.325            18.655 
[1] "2.5 - 66.3 (17.3)"  "0.1 - 211.0 (18.7)"
[1] "hr=" "1.4"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  LRRC37B MUTATED         1        2         2         7         0
  LRRC37B WILD-TYPE      24       74        75       241        11
D41V3, multiclass
           clus
vv          LRRC37B MUTATED LRRC37B WILD-TYPE
  STAGE I                 1                24
  STAGE II                2                74
  STAGE III               2                75
  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
  LRRC37B MUTATED       2   3   2   5
  LRRC37B WILD-TYPE    46 128  96 163
D41V4, multiclass
       clus
vv      LRRC37B MUTATED LRRC37B WILD-TYPE
  T0+T1               2                46
  T2                  3               128
  T3                  2                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
  LRRC37B MUTATED     5   3   4   0
  LRRC37B WILD-TYPE 169  62 157   7
D41V5, multiclass
    clus
vv   LRRC37B MUTATED LRRC37B WILD-TYPE
  N0               5               169
  N1               3                62
  N2               4               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"
D41V6, binary
                   cls
clus                  0   1
  LRRC37B MUTATED     6  10
  LRRC37B WILD-TYPE 133 357
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRC37B MUTATED      6   10
  LRRC37B WILD-TYPE  133  357
        clus
vv       LRRC37B MUTATED LRRC37B WILD-TYPE
  FEMALE               6               133
  MALE                10               357
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  LRRC37B MUTATED                                      15
  LRRC37B WILD-TYPE                                   483
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  LRRC37B MUTATED                                                             0
  LRRC37B WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  LRRC37B MUTATED                                                     1
  LRRC37B WILD-TYPE                                                   6
D41V7, multiclass
                                                             clus
vv                                                            LRRC37B 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                       1
                                                             clus
vv                                                            LRRC37B 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                         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"
D41V8, binary
                   cls
clus                  0   1
  LRRC37B MUTATED     2  14
  LRRC37B WILD-TYPE  81 409
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRC37B MUTATED      2   14
  LRRC37B WILD-TYPE   81  409
     clus
vv    LRRC37B MUTATED LRRC37B WILD-TYPE
  NO                2                81
  YES              14               409
[1] 2 2
[1] FALSE
D41V9, continuous
D41V10, continuous
D41V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRC37B MUTATED                                  0     0
  LRRC37B WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  LRRC37B MUTATED                           1    15
  LRRC37B WILD-TYPE                        35   426
D41V12, multiclass
                                  clus
vv                                 LRRC37B MUTATED LRRC37B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                35
  WHITE                                         15               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"
D41V13, binary
                   cls
clus                  0   1
  LRRC37B MUTATED     0  16
  LRRC37B WILD-TYPE  25 429
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRC37B MUTATED      0   16
  LRRC37B WILD-TYPE   25  429
                        clus
vv                       LRRC37B MUTATED LRRC37B WILD-TYPE
  HISPANIC OR LATINO                   0                25
  NOT HISPANIC OR LATINO              16               429
[1] 2 2
[1] FALSE

Clustering(42) Variable = PPFIA4 MUTATION ANALYSIS
D42V1, survival
                  sevent
clus2                0   1
  PPFIA4 MUTATED    11   3
  PPFIA4 WILD-TYPE 292 198
  PPFIA4 MUTATED PPFIA4 WILD-TYPE 
              14              490 
  PPFIA4 MUTATED PPFIA4 WILD-TYPE 
               3              198 
$`PPFIA4 MUTATED`
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-CN-4727 TCGA-CN-5369 TCGA-CQ-A4CG TCGA-CR-7365 
        7.10        14.47        40.44        12.49        14.14        39.16 
TCGA-CR-7385 TCGA-CV-6951 TCGA-CX-7086 TCGA-D6-6516 TCGA-F7-A624 TCGA-H7-7774 
       32.78        30.08        18.84        25.41        12.43        13.38 
TCGA-MT-A67D TCGA-UF-A71D 
        1.84        41.16 

$`PPFIA4 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 
       53.79        57.44        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         7.76        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG 
       30.18        27.95        11.54         5.69         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        94.62         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.35        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-4728 TCGA-CN-4729 
       12.69        23.70        38.04         4.67        37.84        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
       26.86        32.65        21.11        24.92        41.10        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        43.73        27.58        41.69        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 
       33.11        34.36         8.58        12.39        35.54        55.27 
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 
       22.45        56.94        20.71        30.67        20.68        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
       19.53        20.68        19.07        14.20         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        9.24        36.49        11.08        10.45        20.09        12.95 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 
       24.16         3.68        17.42        14.10        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       14.56        17.59        12.85        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       17.29        15.91        11.44         5.75         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
        2.70        10.09         7.33         9.80         7.69         6.18 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        39.68        21.50         2.93        54.58        46.75 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       45.80        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        34.75        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        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       33.11        16.73        43.04        41.88        28.83        64.11 
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        32.81        25.81 
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        11.51        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       47.18        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       19.92        26.17        17.13        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        31.10        29.85        29.52        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        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        7.07        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-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       126.08        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       42.38        15.09         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-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        24.99       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 
       22.03         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6517 
       10.42        10.42        10.55        34.36        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        15.88         7.63        14.30 
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        35.54 
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        18.90        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45         9.83        12.13        12.10        10.65        11.18 
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        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-8501 
       12.62         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         6.77         0.07         0.16        25.74 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
        1.22        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 
       12.76        14.50        19.33        11.84        13.55         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
       14.47         5.29        11.54        11.84        13.35        18.15 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F 
       12.43        10.75        14.37         7.96        30.05        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q6 
        3.68        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 
       56.75        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        11.74        17.65         7.30        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO 
        9.34        12.72        18.64        14.79        12.43        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        13.68        43.59        54.67         2.83        43.36 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       42.02        44.65        62.27        17.95        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       21.86        16.11        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 

  PPFIA4 MUTATED PPFIA4 WILD-TYPE 
            1.84             0.07 
  PPFIA4 MUTATED PPFIA4 WILD-TYPE 
           41.16           210.97 
  PPFIA4 MUTATED PPFIA4 WILD-TYPE 
          16.655           18.655 
[1] "1.8 - 41.2 (16.7)"  "0.1 - 211.0 (18.7)"
[1] "hr=" "1.6"
D42V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  PPFIA4 MUTATED         2        3         2         6         0
  PPFIA4 WILD-TYPE      23       73        75       242        11
D42V3, multiclass
           clus
vv          PPFIA4 MUTATED PPFIA4 WILD-TYPE
  STAGE I                2               23
  STAGE II               3               73
  STAGE III              2               75
  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
  PPFIA4 MUTATED       3   3   2   6
  PPFIA4 WILD-TYPE    45 128  96 162
D42V4, multiclass
       clus
vv      PPFIA4 MUTATED PPFIA4 WILD-TYPE
  T0+T1              3               45
  T2                 3              128
  T3                 2               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
  PPFIA4 MUTATED    10   1   1   0
  PPFIA4 WILD-TYPE 164  64 160   7
D42V5, multiclass
    clus
vv   PPFIA4 MUTATED PPFIA4 WILD-TYPE
  N0             10              164
  N1              1               64
  N2              1              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"
D42V6, binary
                  cls
clus                 0   1
  PPFIA4 MUTATED     6   8
  PPFIA4 WILD-TYPE 133 359
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPFIA4 MUTATED      6    8
  PPFIA4 WILD-TYPE  133  359
        clus
vv       PPFIA4 MUTATED PPFIA4 WILD-TYPE
  FEMALE              6              133
  MALE                8              359
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  PPFIA4 MUTATED                                      14
  PPFIA4 WILD-TYPE                                   484
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  PPFIA4 MUTATED                                                             0
  PPFIA4 WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  PPFIA4 MUTATED                                                     0
  PPFIA4 WILD-TYPE                                                   7
D42V7, multiclass
                                                             clus
vv                                                            PPFIA4 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                                                            PPFIA4 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"
D42V8, binary
                  cls
clus                 0   1
  PPFIA4 MUTATED     3  11
  PPFIA4 WILD-TYPE  80 412
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPFIA4 MUTATED      3   11
  PPFIA4 WILD-TYPE   80  412
     clus
vv    PPFIA4 MUTATED PPFIA4 WILD-TYPE
  NO               3               80
  YES             11              412
[1] 2 2
[1] FALSE
D42V9, continuous
D42V10, continuous
D42V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPFIA4 MUTATED                                  0     0
  PPFIA4 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PPFIA4 MUTATED                           1    13
  PPFIA4 WILD-TYPE                        35   428
D42V12, multiclass
                                  clus
vv                                 PPFIA4 MUTATED PPFIA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               35
  WHITE                                        13              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"
D42V13, binary
                  cls
clus                 0   1
  PPFIA4 MUTATED     0  13
  PPFIA4 WILD-TYPE  25 432
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPFIA4 MUTATED      0   13
  PPFIA4 WILD-TYPE   25  432
                        clus
vv                       PPFIA4 MUTATED PPFIA4 WILD-TYPE
  HISPANIC OR LATINO                  0               25
  NOT HISPANIC OR LATINO             13              432
[1] 2 2
[1] FALSE

Clustering(43) Variable = PIK3R1 MUTATION ANALYSIS
D43V1, survival
                  sevent
clus2                0   1
  PIK3R1 MUTATED     9   0
  PIK3R1 WILD-TYPE 294 201
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               9              495 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               0              201 
$`PIK3R1 MUTATED`
TCGA-BB-7870 TCGA-CN-4729 TCGA-CN-A49C TCGA-CR-5248 TCGA-CR-6492 TCGA-DQ-5625 
       66.28        12.89        21.21        54.67        15.75        35.54 
TCGA-DQ-7596 TCGA-HL-7533 TCGA-QK-A6VB 
       11.18        34.75        14.79 

$`PIK3R1 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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       37.84        26.86        32.65        21.11        24.92        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        33.11        34.36         8.58        12.39        35.54 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       55.27         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        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        14.56        17.59        12.85        29.72 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        17.29        15.91        11.44         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        10.09         7.33         9.80         7.69 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
        6.18        48.20        39.68        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       46.75        45.80        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        34.75 
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 
       51.29        33.11        16.73        43.04        41.88        28.83 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       64.11        44.48        11.61        23.24        29.36        32.81 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       25.81        14.14        12.46        31.23        84.23        11.77 
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-6493 
       11.34        11.64         7.69        12.46        11.51         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        31.10        29.85 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       29.52        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        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       126.08 
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 
       24.99       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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        34.36        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-A6EO TCGA-D6-A6EP 
       17.72        12.36        15.88         7.63        14.30        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-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       18.02        14.04        18.90        25.48        20.45         9.83 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       12.13        12.10        10.65        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        19.23        18.94        12.62         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-7917 
       21.11         6.77         0.07         0.16        25.74         1.22 
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-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65         6.90        15.95        12.76        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       19.33        11.84        13.55         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       11.54        11.84        13.35        18.15        12.43        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         3.68 
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        56.75 
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        11.74        17.65         7.30        16.70         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       12.72        18.64        12.43        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        13.68 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       43.59        54.67         2.83        43.36        41.16        42.02 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        62.27        17.95        24.16        49.22        21.86 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       16.11        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 

  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           11.18             0.07 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           66.28           210.97 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           21.21            18.64 
[1] "11.2 - 66.3 (21.2)" "0.1 - 211.0 (18.6)"
[1] "hr="     "9200000"
D43V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  PIK3R1 MUTATED         0        0         2         2         0
  PIK3R1 WILD-TYPE      25       76        75       246        11
D43V3, multiclass
           clus
vv          PIK3R1 MUTATED PIK3R1 WILD-TYPE
  STAGE I                0               25
  STAGE II               0               76
  STAGE III              2               75
  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
  PIK3R1 MUTATED       0   2   0   2
  PIK3R1 WILD-TYPE    48 129  98 166
D43V4, multiclass
       clus
vv      PIK3R1 MUTATED PIK3R1 WILD-TYPE
  T0+T1              0               48
  T2                 2              129
  T3                 0               98
  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
  PIK3R1 MUTATED     2   2   0   0
  PIK3R1 WILD-TYPE 172  63 161   7
D43V5, multiclass
    clus
vv   PIK3R1 MUTATED PIK3R1 WILD-TYPE
  N0              2              172
  N1              2               63
  N2              0              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"
D43V6, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     1   8
  PIK3R1 WILD-TYPE 138 359
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      1    8
  PIK3R1 WILD-TYPE  138  359
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  FEMALE              1              138
  MALE                8              359
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  PIK3R1 MUTATED                                       9
  PIK3R1 WILD-TYPE                                   489
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  PIK3R1 MUTATED                                                             0
  PIK3R1 WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  PIK3R1 MUTATED                                                     0
  PIK3R1 WILD-TYPE                                                   7
D43V7, multiclass
                                                             clus
vv                                                            PIK3R1 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                                                            PIK3R1 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"
D43V8, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     1   8
  PIK3R1 WILD-TYPE  82 415
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      1    8
  PIK3R1 WILD-TYPE   82  415
     clus
vv    PIK3R1 MUTATED PIK3R1 WILD-TYPE
  NO               1               82
  YES              8              415
[1] 2 2
[1] FALSE
D43V9, continuous
D43V10, continuous
D43V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3R1 MUTATED                                  0     0
  PIK3R1 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3R1 MUTATED                           0     9
  PIK3R1 WILD-TYPE                        36   432
D43V12, multiclass
                                  clus
vv                                 PIK3R1 MUTATED PIK3R1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               36
  WHITE                                         9              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"
D43V13, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     0   9
  PIK3R1 WILD-TYPE  25 436
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      0    9
  PIK3R1 WILD-TYPE   25  436
                        clus
vv                       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  HISPANIC OR LATINO                  0               25
  NOT HISPANIC OR LATINO              9              436
[1] 2 2
[1] FALSE

Clustering(44) Variable = VPS33B MUTATION ANALYSIS
D44V1, survival
                  sevent
clus2                0   1
  VPS33B MUTATED     4   3
  VPS33B WILD-TYPE 299 198
  VPS33B MUTATED VPS33B WILD-TYPE 
               7              497 
  VPS33B MUTATED VPS33B WILD-TYPE 
               3              198 
$`VPS33B MUTATED`
TCGA-CN-5355 TCGA-CV-7177 TCGA-CV-7407 TCGA-DQ-5629 TCGA-F7-A623 TCGA-H7-7774 
       33.11        21.80        35.54        30.94        20.25        13.38 
TCGA-P3-A6SW 
       36.82 

$`VPS33B 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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       40.44        37.84        12.89        26.86        32.65        21.11 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       24.92        41.10        12.99        20.55        14.33        43.73 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       27.58        41.69        13.05        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       35.54        55.27         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        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        20.68        20.65        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       14.20         6.74         9.07         9.24        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        46.75        45.80        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        34.75        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        51.29        33.11        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        28.83        64.11        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        32.81        25.81        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        11.51        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        31.10        29.85        29.52        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        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        7.07        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-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       126.08        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-7178 
        9.01         5.26         1.84        52.31        12.92        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       10.75       130.88        77.16         4.73        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-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        24.99       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        22.03 
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        15.88         7.63 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       14.30        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 
       35.54        33.86        18.02        14.04        18.90        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45         9.83        12.13        12.10        10.65        11.18 
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        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-8501 
       12.62         0.46        17.85        11.80        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         6.77         0.07         0.16        25.74 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
        1.22        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 
       12.76        14.50        19.33        11.84        13.55         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
       14.47         5.29        11.54        11.84        13.35        18.15 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       12.43        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         3.68        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T0 
       15.78        56.75        51.25        10.85        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        11.74        17.65         7.30        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO 
        9.34        12.72        18.64        14.79        12.43        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        13.68        43.59        54.67         2.83        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       41.16        42.02        44.65        62.27        17.95        24.16 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       49.22        21.86        16.11        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 

  VPS33B MUTATED VPS33B WILD-TYPE 
           13.38             0.07 
  VPS33B MUTATED VPS33B WILD-TYPE 
           36.82           210.97 
  VPS33B MUTATED VPS33B WILD-TYPE 
           30.94            18.41 
[1] "13.4 - 36.8 (30.9)" "0.1 - 211.0 (18.4)"
[1] "hr=" "1.1"
D44V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  VPS33B MUTATED         0        2         0         3         1
  VPS33B WILD-TYPE      25       74        77       245        10
D44V3, multiclass
           clus
vv          VPS33B MUTATED VPS33B WILD-TYPE
  STAGE I                0               25
  STAGE II               2               74
  STAGE III              0               77
  STAGE IVA              3              245
  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
  VPS33B MUTATED       1   2   1   2
  VPS33B WILD-TYPE    47 129  97 166
D44V4, multiclass
       clus
vv      VPS33B MUTATED VPS33B WILD-TYPE
  T0+T1              1               47
  T2                 2              129
  T3                 1               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
  VPS33B MUTATED     2   0   1   1
  VPS33B WILD-TYPE 172  65 160   6
D44V5, multiclass
    clus
vv   VPS33B MUTATED VPS33B WILD-TYPE
  N0              2              172
  N1              0               65
  N2              1              160
  N3              1                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                  cls
clus                 0   1
  VPS33B MUTATED     3   4
  VPS33B WILD-TYPE 136 363
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS33B MUTATED      3    4
  VPS33B WILD-TYPE  136  363
        clus
vv       VPS33B MUTATED VPS33B WILD-TYPE
  FEMALE              3              136
  MALE                4              363
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  VPS33B MUTATED                                       6
  VPS33B WILD-TYPE                                   492
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  VPS33B MUTATED                                                             0
  VPS33B WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  VPS33B MUTATED                                                     1
  VPS33B WILD-TYPE                                                   6
D44V7, multiclass
                                                             clus
vv                                                            VPS33B 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                                                            VPS33B WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    492
  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"
D44V8, binary
                  cls
clus                 0   1
  VPS33B MUTATED     1   6
  VPS33B WILD-TYPE  82 417
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS33B MUTATED      1    6
  VPS33B WILD-TYPE   82  417
     clus
vv    VPS33B MUTATED VPS33B WILD-TYPE
  NO               1               82
  YES              6              417
[1] 2 2
[1] FALSE
D44V9, continuous
D44V10, continuous
D44V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VPS33B MUTATED                                  0     0
  VPS33B WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  VPS33B MUTATED                           1     6
  VPS33B WILD-TYPE                        35   435
D44V12, multiclass
                                  clus
vv                                 VPS33B MUTATED VPS33B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               35
  WHITE                                         6              435
[1] 4 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
  VPS33B MUTATED     0   7
  VPS33B WILD-TYPE  25 438
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS33B MUTATED      0    7
  VPS33B WILD-TYPE   25  438
                        clus
vv                       VPS33B MUTATED VPS33B WILD-TYPE
  HISPANIC OR LATINO                  0               25
  NOT HISPANIC OR LATINO              7              438
[1] 2 2
[1] FALSE

Clustering(45) Variable = C8ORF31 MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  C8ORF31 MUTATED     2   2
  C8ORF31 WILD-TYPE 301 199
  C8ORF31 MUTATED C8ORF31 WILD-TYPE 
                4               500 
  C8ORF31 MUTATED C8ORF31 WILD-TYPE 
                2               199 
$`C8ORF31 MUTATED`
TCGA-CN-5366 TCGA-CV-7568 TCGA-F7-7848 TCGA-F7-A624 
       11.84        30.48        37.18        12.43 

$`C8ORF31 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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       40.44        37.84        12.89        26.86        32.65        21.11 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       24.92        41.10        12.99        20.55        14.33        43.73 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        41.69        13.05        33.11        34.36         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       12.39        35.54        55.27         8.32        16.21        11.54 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.57        12.49         8.52        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        20.68        20.65        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       14.20         6.74         9.07         9.24        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        46.75        45.80        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        34.75        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        51.29        33.11        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        28.83        64.11        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        32.81        25.81        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        11.51        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        31.10        29.85        29.52        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        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        7.07        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-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       126.08        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-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-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 
      100.57        14.89        56.48       156.49         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       84.49        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       22.19        35.93        27.98        24.99       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 
       22.03         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-D6-6515 
       10.42        10.42        10.55        18.84        34.36        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        15.88 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        14.30        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        35.54        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 
       18.90        25.48        20.45         9.83        12.13        12.10 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       10.65        11.18        21.63        20.25         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        12.62         0.46        17.85        11.80        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         6.77         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
        0.16        25.74         1.22        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        12.76        14.50        19.33        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       13.55         0.07        14.47         5.29        11.54        11.84 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        12.43        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         3.68        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        56.75        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        11.74 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       17.65         7.30        16.70         9.34        12.72        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       14.79        12.43        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        13.68        43.59 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        43.36        41.16        42.02        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       62.27        17.95        24.16        49.22        21.86        16.11 
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 

  C8ORF31 MUTATED C8ORF31 WILD-TYPE 
            11.84              0.07 
  C8ORF31 MUTATED C8ORF31 WILD-TYPE 
            37.18            210.97 
  C8ORF31 MUTATED C8ORF31 WILD-TYPE 
           21.455            18.655 
[1] "11.8 - 37.2 (21.5)" "0.1 - 211.0 (18.7)"
[1] "hr=" "1.4"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  C8ORF31 MUTATED         0        1         0         3         0
  C8ORF31 WILD-TYPE      25       75        77       245        11
D45V3, multiclass
           clus
vv          C8ORF31 MUTATED C8ORF31 WILD-TYPE
  STAGE I                 0                25
  STAGE II                1                75
  STAGE III               0                77
  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
  C8ORF31 MUTATED       0   1   0   3
  C8ORF31 WILD-TYPE    48 130  98 165
D45V4, multiclass
       clus
vv      C8ORF31 MUTATED C8ORF31 WILD-TYPE
  T0+T1               0                48
  T2                  1               130
  T3                  0                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
  C8ORF31 MUTATED     0   1   1   0
  C8ORF31 WILD-TYPE 174  64 160   7
D45V5, multiclass
[1] "Remove cluster labels:" "C8ORF31 MUTATED"       
clus
  C8ORF31 MUTATED C8ORF31 WILD-TYPE 
                2               405 
       TCGA-BA-4074        TCGA-BA-4075        TCGA-BA-4077        TCGA-BA-5149 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-BA-5151        TCGA-BA-5152        TCGA-BA-5555        TCGA-BA-5556 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-BA-5557        TCGA-BA-6869        TCGA-BA-6873        TCGA-BA-7269 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-BA-A4IH        TCGA-BA-A4II        TCGA-BA-A6D8        TCGA-BA-A6DA 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-BA-A6DB        TCGA-BA-A6DD        TCGA-BA-A6DE        TCGA-BA-A6DF 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-BA-A6DJ        TCGA-BA-A6DL        TCGA-BB-4217        TCGA-BB-4223 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-BB-4224        TCGA-BB-4227        TCGA-BB-7861        TCGA-BB-7862 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-BB-7863        TCGA-BB-7864        TCGA-BB-7870        TCGA-BB-7871 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-BB-7872        TCGA-BB-8601        TCGA-BB-A5HU        TCGA-BB-A5HY 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-BB-A5HZ        TCGA-BB-A6UM        TCGA-BB-A6UO        TCGA-C9-A47Z 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-C9-A480        TCGA-CN-4723        TCGA-CN-4725        TCGA-CN-4726 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-4727        TCGA-CN-4728        TCGA-CN-4729        TCGA-CN-4730 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-4731        TCGA-CN-4733        TCGA-CN-4734        TCGA-CN-4735 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-4737        TCGA-CN-4738        TCGA-CN-4739        TCGA-CN-4740 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-4741        TCGA-CN-4742        TCGA-CN-5355        TCGA-CN-5356 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-5358        TCGA-CN-5359        TCGA-CN-5360        TCGA-CN-5361 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-5363        TCGA-CN-5364        TCGA-CN-5365        TCGA-CN-5367 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-5369        TCGA-CN-5370        TCGA-CN-5373        TCGA-CN-5374 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-6010        TCGA-CN-6011        TCGA-CN-6012        TCGA-CN-6013 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-6016        TCGA-CN-6017        TCGA-CN-6018        TCGA-CN-6019 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-6020        TCGA-CN-6022        TCGA-CN-6023        TCGA-CN-6024 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-6988        TCGA-CN-6989        TCGA-CN-6992        TCGA-CN-6994 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-6995        TCGA-CN-6996        TCGA-CN-6997        TCGA-CN-6998 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-A497        TCGA-CN-A498        TCGA-CN-A499        TCGA-CN-A49A 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-A49B        TCGA-CN-A63T        TCGA-CN-A63U        TCGA-CN-A63V 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-A63W        TCGA-CN-A63Y        TCGA-CN-A640        TCGA-CN-A641 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-A642        TCGA-CN-A6UY        TCGA-CN-A6V1        TCGA-CN-A6V3 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-A6V6        TCGA-CN-A6V7        TCGA-CQ-5323        TCGA-CQ-5324 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CQ-5325        TCGA-CQ-5326        TCGA-CQ-5327        TCGA-CQ-5329 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CQ-5330        TCGA-CQ-5332        TCGA-CQ-5333        TCGA-CQ-5334 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CQ-6218        TCGA-CQ-6219        TCGA-CQ-6220        TCGA-CQ-6222 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CQ-6223        TCGA-CQ-6224        TCGA-CQ-6225        TCGA-CQ-6227 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CQ-6228        TCGA-CQ-6229        TCGA-CQ-7064        TCGA-CQ-7065 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CQ-7067        TCGA-CQ-7068        TCGA-CQ-7069        TCGA-CQ-7071 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CQ-7072        TCGA-CQ-A4C6        TCGA-CQ-A4C7        TCGA-CQ-A4C9 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CQ-A4CB        TCGA-CQ-A4CD        TCGA-CQ-A4CE        TCGA-CQ-A4CG 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CQ-A4CH        TCGA-CQ-A4CI        TCGA-CR-5249        TCGA-CR-6467 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CR-6470        TCGA-CR-6471        TCGA-CR-6474        TCGA-CR-6484 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CR-6487        TCGA-CR-6488        TCGA-CR-6491        TCGA-CR-6492 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CR-6493        TCGA-CR-7364        TCGA-CR-7365        TCGA-CR-7367 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CR-7368        TCGA-CR-7369        TCGA-CR-7371        TCGA-CR-7372 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CR-7373        TCGA-CR-7376        TCGA-CR-7377        TCGA-CR-7379 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CR-7380        TCGA-CR-7382        TCGA-CR-7383        TCGA-CR-7386 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CR-7390        TCGA-CR-7391        TCGA-CR-7392        TCGA-CR-7393 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CR-7394        TCGA-CR-7395        TCGA-CR-7397        TCGA-CR-7398 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CR-7399        TCGA-CR-7401        TCGA-CV-5430        TCGA-CV-5431 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-5432        TCGA-CV-5434        TCGA-CV-5435        TCGA-CV-5436 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-5439        TCGA-CV-5440        TCGA-CV-5441        TCGA-CV-5442 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-5443        TCGA-CV-5444        TCGA-CV-5966        TCGA-CV-5970 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-5971        TCGA-CV-5973        TCGA-CV-5976        TCGA-CV-5977 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-5978        TCGA-CV-5979        TCGA-CV-6003        TCGA-CV-6433 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-6436        TCGA-CV-6441        TCGA-CV-6933        TCGA-CV-6934 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-6935        TCGA-CV-6936        TCGA-CV-6937        TCGA-CV-6939 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-6940        TCGA-CV-6941        TCGA-CV-6945        TCGA-CV-6948 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-6950        TCGA-CV-6951        TCGA-CV-6952        TCGA-CV-6953 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-6956        TCGA-CV-6959        TCGA-CV-6960        TCGA-CV-6961 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7089        TCGA-CV-7091        TCGA-CV-7100        TCGA-CV-7102 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7103        TCGA-CV-7104        TCGA-CV-7178        TCGA-CV-7183 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7235        TCGA-CV-7236        TCGA-CV-7238        TCGA-CV-7242 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7243        TCGA-CV-7245        TCGA-CV-7247        TCGA-CV-7248 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7250        TCGA-CV-7252        TCGA-CV-7253        TCGA-CV-7255 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7261        TCGA-CV-7406        TCGA-CV-7409        TCGA-CV-7410 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7411        TCGA-CV-7413        TCGA-CV-7414        TCGA-CV-7415 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7418        TCGA-CV-7421        TCGA-CV-7422        TCGA-CV-7424 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7429        TCGA-CV-7430        TCGA-CV-7432        TCGA-CV-7433 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7434        TCGA-CV-7435        TCGA-CV-7446        TCGA-CV-A45P 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-A45R        TCGA-CV-A45T        TCGA-CV-A45U        TCGA-CV-A45V 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-A45W        TCGA-CV-A45X        TCGA-CV-A45Y        TCGA-CV-A45Z 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-A460        TCGA-CV-A463        TCGA-CV-A464        TCGA-CV-A465 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-A468        TCGA-CV-A6JO        TCGA-CV-A6JT        TCGA-CV-A6JU 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-A6JY        TCGA-CV-A6JZ        TCGA-CV-A6K0        TCGA-CV-A6K1 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-A6K2        TCGA-CX-7082        TCGA-CX-7085        TCGA-CX-7086 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CX-7219        TCGA-D6-6515        TCGA-D6-6516        TCGA-D6-6517 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-D6-6823        TCGA-D6-6824        TCGA-D6-6825        TCGA-D6-6826 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-D6-6827        TCGA-D6-8568        TCGA-D6-8569        TCGA-D6-A4Z9 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-D6-A4ZB        TCGA-D6-A6EK        TCGA-D6-A6EM        TCGA-D6-A6EO 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-D6-A6EP        TCGA-D6-A6EQ        TCGA-D6-A6ES        TCGA-D6-A74Q 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-F7-8489        TCGA-F7-A50G        TCGA-F7-A50I        TCGA-F7-A50J 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-F7-A61S        TCGA-F7-A61V        TCGA-F7-A61W        TCGA-F7-A620 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-F7-A623        TCGA-H7-7774        TCGA-H7-8501        TCGA-H7-A6C4 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-H7-A6C5        TCGA-H7-A76A        TCGA-HD-7229        TCGA-HD-7753 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-HD-7754        TCGA-HD-7831        TCGA-HD-7832        TCGA-HD-7917 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-HD-8224        TCGA-HD-8314        TCGA-HD-8634        TCGA-HD-8635 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-HD-A4C1        TCGA-HD-A633        TCGA-HD-A634        TCGA-HD-A6HZ 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-HD-A6I0        TCGA-IQ-7630        TCGA-IQ-7631        TCGA-IQ-7632 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-IQ-A61E        TCGA-IQ-A61G        TCGA-IQ-A61H        TCGA-IQ-A61I 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-IQ-A61J        TCGA-IQ-A61K        TCGA-IQ-A61L        TCGA-IQ-A61O 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-KU-A66S        TCGA-KU-A66T        TCGA-KU-A6H7        TCGA-KU-A6H8 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-MT-A51W        TCGA-MT-A51X        TCGA-MT-A67A        TCGA-MT-A67D 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-MT-A67F        TCGA-MT-A67G        TCGA-MZ-A7D7        TCGA-P3-A5Q6 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-P3-A5QE        TCGA-P3-A5QF        TCGA-P3-A6SW        TCGA-P3-A6SX 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-P3-A6T0        TCGA-P3-A6T2        TCGA-P3-A6T3        TCGA-P3-A6T4 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-P3-A6T5        TCGA-P3-A6T7        TCGA-P3-A6T8        TCGA-QK-A652 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-QK-A6IG        TCGA-QK-A6IH        TCGA-QK-A6II        TCGA-QK-A6IJ 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-QK-A6VB        TCGA-QK-A6VC        TCGA-RS-A6TO        TCGA-RS-A6TP 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-T2-A6WZ        TCGA-T2-A6X2        TCGA-TN-A7HI        TCGA-TN-A7HJ 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-TN-A7HL        TCGA-UF-A718        TCGA-UF-A719        TCGA-UF-A71A 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-UF-A71B        TCGA-UF-A71D        TCGA-UF-A71E        TCGA-UF-A7J9 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-UF-A7JA        TCGA-UF-A7JC        TCGA-UF-A7JD        TCGA-UF-A7JF 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-UF-A7JH        TCGA-UF-A7JJ        TCGA-UF-A7JK        TCGA-UF-A7JO 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-UF-A7JS        TCGA-UF-A7JT        TCGA-UF-A7JV        TCGA-WA-A7GZ 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-WA-A7H4 
"C8ORF31 WILD-TYPE" 
D45V6, binary
                   cls
clus                  0   1
  C8ORF31 MUTATED     1   3
  C8ORF31 WILD-TYPE 138 364
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C8ORF31 MUTATED      1    3
  C8ORF31 WILD-TYPE  138  364
        clus
vv       C8ORF31 MUTATED C8ORF31 WILD-TYPE
  FEMALE               1               138
  MALE                 3               364
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  C8ORF31 MUTATED                                       4
  C8ORF31 WILD-TYPE                                   494
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  C8ORF31 MUTATED                                                             0
  C8ORF31 WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  C8ORF31 MUTATED                                                     0
  C8ORF31 WILD-TYPE                                                   7
D45V7, multiclass
                                                             clus
vv                                                            C8ORF31 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                                                            C8ORF31 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"
D45V8, binary
                   cls
clus                  0   1
  C8ORF31 MUTATED     1   3
  C8ORF31 WILD-TYPE  82 420
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C8ORF31 MUTATED      1    3
  C8ORF31 WILD-TYPE   82  420
     clus
vv    C8ORF31 MUTATED C8ORF31 WILD-TYPE
  NO                1                82
  YES               3               420
[1] 2 2
[1] FALSE
D45V9, continuous
D45V10, continuous
D45V11, continuous
[1] "Remove cluster labels:" "C8ORF31 MUTATED"       
clus
  C8ORF31 MUTATED C8ORF31 WILD-TYPE 
                2               394 
       TCGA-BA-4074        TCGA-BA-4075        TCGA-BA-4078        TCGA-BA-5149 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-BA-5151        TCGA-BA-5152        TCGA-BA-5555        TCGA-BA-5556 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-BA-5557        TCGA-BA-5558        TCGA-BA-5559        TCGA-BA-6869 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-BA-6872        TCGA-BA-6873        TCGA-BA-7269        TCGA-BA-A4IG 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-BA-A4IH        TCGA-BA-A4II        TCGA-BA-A6D8        TCGA-BA-A6DA 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-BA-A6DB        TCGA-BA-A6DD        TCGA-BA-A6DE        TCGA-BA-A6DF 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-BA-A6DJ        TCGA-BB-7861        TCGA-BB-7862        TCGA-BB-7863 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-BB-7864        TCGA-BB-7870        TCGA-BB-7871        TCGA-BB-7872 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-BB-8601        TCGA-BB-A5HU        TCGA-BB-A5HY        TCGA-BB-A5HZ 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-C9-A47Z        TCGA-CN-4723        TCGA-CN-4725        TCGA-CN-4726 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-4727        TCGA-CN-4728        TCGA-CN-4729        TCGA-CN-4730 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-4731        TCGA-CN-4733        TCGA-CN-4734        TCGA-CN-4735 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-4737        TCGA-CN-4738        TCGA-CN-4739        TCGA-CN-4740 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-4741        TCGA-CN-4742        TCGA-CN-5355        TCGA-CN-5356 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-5358        TCGA-CN-5359        TCGA-CN-5360        TCGA-CN-5361 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-5363        TCGA-CN-5364        TCGA-CN-5365        TCGA-CN-5367 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-5369        TCGA-CN-5370        TCGA-CN-5373        TCGA-CN-6010 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-6011        TCGA-CN-6012        TCGA-CN-6013        TCGA-CN-6016 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-6017        TCGA-CN-6018        TCGA-CN-6019        TCGA-CN-6020 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-6022        TCGA-CN-6023        TCGA-CN-6024        TCGA-CN-6988 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-6989        TCGA-CN-6992        TCGA-CN-6994        TCGA-CN-6995 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-6996        TCGA-CN-6997        TCGA-CN-6998        TCGA-CN-A497 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-A498        TCGA-CN-A499        TCGA-CN-A49A        TCGA-CN-A49B 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-A63T        TCGA-CN-A63U        TCGA-CN-A63V        TCGA-CN-A63W 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-A63Y        TCGA-CN-A640        TCGA-CN-A641        TCGA-CN-A642 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CN-A6UY        TCGA-CN-A6V1        TCGA-CN-A6V3        TCGA-CN-A6V6 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CQ-5323        TCGA-CQ-5324        TCGA-CQ-5325        TCGA-CQ-5326 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CQ-5327        TCGA-CQ-5329        TCGA-CQ-5330        TCGA-CQ-5332 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CQ-5333        TCGA-CQ-5334        TCGA-CQ-6218        TCGA-CQ-6219 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CQ-6220        TCGA-CQ-6222        TCGA-CQ-6223        TCGA-CQ-6224 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CQ-6225        TCGA-CQ-6227        TCGA-CQ-6228        TCGA-CQ-6229 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CQ-7064        TCGA-CQ-7065        TCGA-CQ-7067        TCGA-CQ-7068 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CQ-7069        TCGA-CQ-7071        TCGA-CQ-7072        TCGA-CQ-A4C6 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CQ-A4C7        TCGA-CQ-A4C9        TCGA-CQ-A4CB        TCGA-CQ-A4CD 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CQ-A4CE        TCGA-CQ-A4CG        TCGA-CQ-A4CH        TCGA-CQ-A4CI 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CR-6467        TCGA-CR-6470        TCGA-CR-6471        TCGA-CR-6474 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CR-6484        TCGA-CR-6488        TCGA-CR-6491        TCGA-CR-6492 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CR-6493        TCGA-CR-7364        TCGA-CR-7365        TCGA-CR-7367 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CR-7368        TCGA-CR-7369        TCGA-CR-7371        TCGA-CR-7372 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CR-7373        TCGA-CR-7376        TCGA-CR-7377        TCGA-CR-7379 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CR-7380        TCGA-CR-7382        TCGA-CR-7383        TCGA-CR-7386 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CR-7390        TCGA-CR-7391        TCGA-CR-7392        TCGA-CR-7393 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CR-7394        TCGA-CR-7397        TCGA-CR-7398        TCGA-CR-7399 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CR-7401        TCGA-CV-5430        TCGA-CV-5431        TCGA-CV-5432 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-5434        TCGA-CV-5435        TCGA-CV-5436        TCGA-CV-5439 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-5440        TCGA-CV-5441        TCGA-CV-5442        TCGA-CV-5443 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-5444        TCGA-CV-5966        TCGA-CV-5970        TCGA-CV-5971 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-5973        TCGA-CV-5976        TCGA-CV-5977        TCGA-CV-5978 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-5979        TCGA-CV-6003        TCGA-CV-6433        TCGA-CV-6436 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-6441        TCGA-CV-6933        TCGA-CV-6934        TCGA-CV-6935 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-6936        TCGA-CV-6939        TCGA-CV-6940        TCGA-CV-6941 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-6945        TCGA-CV-6948        TCGA-CV-6950        TCGA-CV-6951 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-6952        TCGA-CV-6953        TCGA-CV-6954        TCGA-CV-6956 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-6959        TCGA-CV-6960        TCGA-CV-7089        TCGA-CV-7091 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7095        TCGA-CV-7101        TCGA-CV-7102        TCGA-CV-7103 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7104        TCGA-CV-7178        TCGA-CV-7180        TCGA-CV-7183 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7236        TCGA-CV-7242        TCGA-CV-7243        TCGA-CV-7245 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7248        TCGA-CV-7252        TCGA-CV-7254        TCGA-CV-7261 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7406        TCGA-CV-7409        TCGA-CV-7410        TCGA-CV-7411 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7414        TCGA-CV-7415        TCGA-CV-7418        TCGA-CV-7421 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7422        TCGA-CV-7424        TCGA-CV-7429        TCGA-CV-7430 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7432        TCGA-CV-7433        TCGA-CV-7434        TCGA-CV-7435 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-7446        TCGA-CV-A45O        TCGA-CV-A45P        TCGA-CV-A45Q 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-A45R        TCGA-CV-A45T        TCGA-CV-A45U        TCGA-CV-A45W 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-A45X        TCGA-CV-A45Y        TCGA-CV-A45Z        TCGA-CV-A460 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-A461        TCGA-CV-A463        TCGA-CV-A464        TCGA-CV-A465 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-A468        TCGA-CV-A6JD        TCGA-CV-A6JE        TCGA-CV-A6JM 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-A6JN        TCGA-CV-A6JO        TCGA-CV-A6JT        TCGA-CV-A6JU 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-A6JY        TCGA-CV-A6JZ        TCGA-CV-A6K0        TCGA-CV-A6K1 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CV-A6K2        TCGA-CX-7082        TCGA-CX-7085        TCGA-CX-7086 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-CX-7219        TCGA-D6-6516        TCGA-D6-6517        TCGA-D6-6823 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-D6-6825        TCGA-D6-6826        TCGA-D6-8568        TCGA-D6-8569 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-D6-A4Z9        TCGA-D6-A4ZB        TCGA-D6-A6EK        TCGA-D6-A6EM 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-D6-A6EO        TCGA-D6-A6EP        TCGA-D6-A6EQ        TCGA-D6-A6ES 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-D6-A74Q        TCGA-DQ-5624        TCGA-DQ-5625        TCGA-DQ-5629 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-DQ-5630        TCGA-DQ-5631        TCGA-DQ-7588        TCGA-DQ-7592 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-F7-A50G        TCGA-F7-A50J        TCGA-F7-A61S        TCGA-F7-A61V 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-F7-A61W        TCGA-F7-A620        TCGA-F7-A623        TCGA-H7-7774 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-H7-8501        TCGA-H7-A6C4        TCGA-H7-A6C5        TCGA-H7-A76A 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-HD-7754        TCGA-HD-7831        TCGA-HD-7832        TCGA-HD-7917 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-HD-8224        TCGA-HD-8314        TCGA-HD-8634        TCGA-HD-8635 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-HD-A4C1        TCGA-HD-A633        TCGA-HD-A634        TCGA-HD-A6HZ 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-HD-A6I0        TCGA-IQ-7630        TCGA-IQ-7631        TCGA-IQ-7632 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-IQ-A61E        TCGA-IQ-A61G        TCGA-IQ-A61H        TCGA-IQ-A61I 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-IQ-A61J        TCGA-IQ-A61K        TCGA-IQ-A61L        TCGA-IQ-A61O 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-KU-A66S        TCGA-KU-A66T        TCGA-KU-A6H7        TCGA-KU-A6H8 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-MT-A51X        TCGA-MT-A67A        TCGA-MT-A67D        TCGA-MT-A67F 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-MT-A67G        TCGA-MZ-A7D7        TCGA-P3-A5Q6        TCGA-P3-A5QE 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-P3-A5QF        TCGA-P3-A6SX        TCGA-P3-A6T0        TCGA-P3-A6T2 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-P3-A6T3        TCGA-P3-A6T4        TCGA-P3-A6T5        TCGA-P3-A6T7 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-P3-A6T8        TCGA-QK-A652        TCGA-QK-A6IG        TCGA-QK-A6IH 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-QK-A6II        TCGA-QK-A6IJ        TCGA-QK-A6VB        TCGA-QK-A6VC 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-RS-A6TO        TCGA-T2-A6WX        TCGA-T2-A6WZ        TCGA-T2-A6X0 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-TN-A7HI        TCGA-TN-A7HJ        TCGA-TN-A7HL        TCGA-UF-A718 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-UF-A719        TCGA-UF-A71A        TCGA-UF-A71B        TCGA-UF-A71D 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-UF-A71E        TCGA-UF-A7J9        TCGA-UF-A7JA        TCGA-UF-A7JC 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-UF-A7JD        TCGA-UF-A7JF        TCGA-UF-A7JH        TCGA-UF-A7JJ 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-UF-A7JK        TCGA-UF-A7JO        TCGA-UF-A7JS        TCGA-UF-A7JT 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
       TCGA-UF-A7JV        TCGA-UP-A6WW 
"C8ORF31 WILD-TYPE" "C8ORF31 WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C8ORF31 MUTATED                                  0     0
  C8ORF31 WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C8ORF31 MUTATED                           0     4
  C8ORF31 WILD-TYPE                        36   437
D45V12, multiclass
                                  clus
vv                                 C8ORF31 MUTATED C8ORF31 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                36
  WHITE                                          4               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"
D45V13, binary
                   cls
clus                  0   1
  C8ORF31 MUTATED     0   4
  C8ORF31 WILD-TYPE  25 441
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C8ORF31 MUTATED      0    4
  C8ORF31 WILD-TYPE   25  441
                        clus
vv                       C8ORF31 MUTATED C8ORF31 WILD-TYPE
  HISPANIC OR LATINO                   0                25
  NOT HISPANIC OR LATINO               4               441
[1] 2 2
[1] FALSE

Clustering(46) Variable = NCOR1 MUTATION ANALYSIS
D46V1, survival
                 sevent
clus2               0   1
  NCOR1 MUTATED    11   7
  NCOR1 WILD-TYPE 292 194
  NCOR1 MUTATED NCOR1 WILD-TYPE 
             18             486 
  NCOR1 MUTATED NCOR1 WILD-TYPE 
              7             194 
$`NCOR1 MUTATED`
TCGA-CN-6992 TCGA-CQ-5331 TCGA-CQ-A4CD TCGA-CR-6481 TCGA-CV-5444 TCGA-CV-6441 
       12.95        45.99        32.81        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        10.65        12.43        12.62        17.98        14.79 

$`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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       40.44        37.84        12.89        26.86        32.65        21.11 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       24.92        41.10        12.99        20.55        14.33        43.73 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        41.69        13.05        33.11        34.36         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       12.39        35.54        55.27         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        22.45        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       20.71        30.67        20.68        20.65        19.53        20.68 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        14.20         6.74         9.07         9.24        36.49 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       11.08        10.45        20.09        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 
        2.93        54.58        46.75        45.80        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 
       34.75        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        51.29        33.11        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       28.83        64.11        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 
       25.81        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        11.51        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        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       29.85        29.52        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        94.88 
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       126.08        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        24.99 
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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       15.88         7.63        14.30        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        35.54        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        18.90        25.48        20.45         9.83        12.13 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       12.10        11.18        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 
       19.23        18.94        12.62         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         6.77 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        0.07         0.16        25.74         1.22        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        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        13.55         0.07        14.47         5.29        11.54 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       11.84        13.35        18.15        12.43        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         3.68        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        56.75        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        11.74        17.65 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC 
        7.30        16.70         9.34        12.72        18.64        12.43 
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        13.68        43.59        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       43.36        41.16        42.02        44.65        62.27        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.16        49.22        21.86        16.11        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 
         13.870          18.825 
[1] "0.5 - 156.5 (13.9)" "0.1 - 211.0 (18.8)"
[1] "hr=" "1"  
D46V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  NCOR1 MUTATED         0        3         1        10         0
  NCOR1 WILD-TYPE      25       73        76       238        11
D46V3, multiclass
           clus
vv          NCOR1 MUTATED NCOR1 WILD-TYPE
  STAGE I               0              25
  STAGE II              3              73
  STAGE III             1              76
  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    48 127  95 160
D46V4, multiclass
       clus
vv      NCOR1 MUTATED NCOR1 WILD-TYPE
  T0+T1             0              48
  T2                4             127
  T3                3              95
  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 168  64 158   7
D46V5, multiclass
    clus
vv   NCOR1 MUTATED NCOR1 WILD-TYPE
  N0             6             168
  N1             1              64
  N2             3             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"
D46V6, binary
                 cls
clus                0   1
  NCOR1 MUTATED     6  12
  NCOR1 WILD-TYPE 133 355
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOR1 MUTATED      6   12
  NCOR1 WILD-TYPE  133  355
        clus
vv       NCOR1 MUTATED NCOR1 WILD-TYPE
  FEMALE             6             133
  MALE              12             355
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  NCOR1 MUTATED                                      18
  NCOR1 WILD-TYPE                                   480
                 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
D46V7, 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                                   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"
D46V8, binary
                 cls
clus                0   1
  NCOR1 MUTATED     1  17
  NCOR1 WILD-TYPE  82 406
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOR1 MUTATED      1   17
  NCOR1 WILD-TYPE   82  406
     clus
vv    NCOR1 MUTATED NCOR1 WILD-TYPE
  NO              1              82
  YES            17             406
[1] 2 2
[1] FALSE
D46V9, continuous
D46V10, continuous
D46V11, 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                        34   425
D46V12, multiclass
                                  clus
vv                                 NCOR1 MUTATED NCOR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              34
  WHITE                                       16             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"
D46V13, binary
                 cls
clus                0   1
  NCOR1 MUTATED     2  16
  NCOR1 WILD-TYPE  23 429
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOR1 MUTATED      2   16
  NCOR1 WILD-TYPE   23  429
                        clus
vv                       NCOR1 MUTATED NCOR1 WILD-TYPE
  HISPANIC OR LATINO                 2              23
  NOT HISPANIC OR LATINO            16             429
[1] 2 2
[1] FALSE

Clustering(47) Variable = SEH1L MUTATION ANALYSIS
D47V1, survival
                 sevent
clus2               0   1
  SEH1L MUTATED     2   2
  SEH1L WILD-TYPE 301 199
  SEH1L MUTATED SEH1L WILD-TYPE 
              4             500 
  SEH1L MUTATED SEH1L WILD-TYPE 
              2             199 
$`SEH1L MUTATED`
TCGA-BB-7870 TCGA-CQ-6225 TCGA-CQ-A4CH TCGA-UF-A71D 
       66.28        13.25        12.46        41.16 

$`SEH1L 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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       37.84        12.89        26.86        32.65        21.11        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       35.54        55.27         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        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        20.68        20.65        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       14.20         6.74         9.07         9.24        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        46.75        45.80        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-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       66.28        34.75        56.58         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        51.29        33.11        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       28.83        64.11        44.48        11.61        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       32.81        25.81        14.14        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        11.51 
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 
       31.10        29.85        29.52        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 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       54.74        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        9.70         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       126.08        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        24.99       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        22.03 
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        15.88         7.63 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       14.30        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 
       35.54        30.94        33.86        18.02        14.04        18.90 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       25.48        20.45         9.83        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       11.18        37.18        21.63        20.25         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        12.62         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         6.77 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        0.07         0.16        25.74         1.22        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        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        13.55         0.07        14.47         5.29        11.54 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       11.84        13.35        18.15        12.43        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         3.68        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        56.75        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 
       11.74        17.65         7.30        16.70         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       18.64        14.79        12.43        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        13.68 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
       43.59        54.67         2.83        43.36        42.02        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       62.27        17.95        24.16        49.22        21.86        16.11 
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 

  SEH1L MUTATED SEH1L WILD-TYPE 
          12.46            0.07 
  SEH1L MUTATED SEH1L WILD-TYPE 
          66.28          210.97 
  SEH1L MUTATED SEH1L WILD-TYPE 
         27.205          18.655 
[1] "12.5 - 66.3 (27.2)" "0.1 - 211.0 (18.7)"
[1] "hr=" "1.1"
D47V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  SEH1L MUTATED         0        1         1         2         0
  SEH1L WILD-TYPE      25       75        76       246        11
D47V3, multiclass
           clus
vv          SEH1L MUTATED SEH1L WILD-TYPE
  STAGE I               0              25
  STAGE II              1              75
  STAGE III             1              76
  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
  SEH1L MUTATED       0   1   1   2
  SEH1L WILD-TYPE    48 130  97 166
D47V4, multiclass
       clus
vv      SEH1L MUTATED SEH1L WILD-TYPE
  T0+T1             0              48
  T2                1             130
  T3                1              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
  SEH1L MUTATED     4   0   0   0
  SEH1L WILD-TYPE 170  65 161   7
D47V5, multiclass
    clus
vv   SEH1L MUTATED SEH1L WILD-TYPE
  N0             4             170
  N1             0              65
  N2             0             161
  N3             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                 cls
clus                0   1
  SEH1L MUTATED     1   3
  SEH1L WILD-TYPE 138 364
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEH1L MUTATED      1    3
  SEH1L WILD-TYPE  138  364
        clus
vv       SEH1L MUTATED SEH1L WILD-TYPE
  FEMALE             1             138
  MALE               3             364
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  SEH1L MUTATED                                       4
  SEH1L WILD-TYPE                                   494
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  SEH1L MUTATED                                                             0
  SEH1L WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  SEH1L MUTATED                                                     0
  SEH1L WILD-TYPE                                                   7
D47V7, multiclass
                                                             clus
vv                                                            SEH1L 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                                                            SEH1L 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"
D47V8, binary
                 cls
clus                0   1
  SEH1L MUTATED     0   4
  SEH1L WILD-TYPE  83 419
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEH1L MUTATED      0    4
  SEH1L WILD-TYPE   83  419
     clus
vv    SEH1L MUTATED SEH1L WILD-TYPE
  NO              0              83
  YES             4             419
[1] 2 2
[1] FALSE
D47V9, continuous
[1] "Remove cluster labels:" "SEH1L MUTATED"         
clus
  SEH1L MUTATED SEH1L WILD-TYPE 
              2             280 
     TCGA-BA-4074      TCGA-BA-4075      TCGA-BA-4076      TCGA-BA-4077 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-BA-4078      TCGA-BA-5149      TCGA-BA-5151      TCGA-BA-5555 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-BA-5556      TCGA-BA-6868      TCGA-BA-6869      TCGA-BA-6870 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-BA-6871      TCGA-BA-6872      TCGA-BA-6873      TCGA-BA-7269 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-BA-A4IF      TCGA-BA-A4IH      TCGA-BA-A4II      TCGA-BA-A6D8 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-BA-A6DA      TCGA-BA-A6DD      TCGA-BA-A6DE      TCGA-BA-A6DG 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-BA-A6DI      TCGA-BA-A6DJ      TCGA-BA-A6DL      TCGA-BB-4217 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-BB-4225      TCGA-BB-4227      TCGA-BB-4228      TCGA-BB-7862 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-BB-7864      TCGA-BB-7871      TCGA-BB-8596      TCGA-BB-A5HY 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-BB-A6UM      TCGA-BB-A6UO      TCGA-CN-4726      TCGA-CN-4727 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-4728      TCGA-CN-4729      TCGA-CN-4730      TCGA-CN-4731 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-4735      TCGA-CN-4736      TCGA-CN-4738      TCGA-CN-4739 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-4740      TCGA-CN-4741      TCGA-CN-4742      TCGA-CN-5355 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-5358      TCGA-CN-5359      TCGA-CN-5360      TCGA-CN-5361 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-5363      TCGA-CN-5365      TCGA-CN-5366      TCGA-CN-5367 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-5373      TCGA-CN-5374      TCGA-CN-6010      TCGA-CN-6011 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-6012      TCGA-CN-6016      TCGA-CN-6017      TCGA-CN-6019 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-6021      TCGA-CN-6023      TCGA-CN-6024      TCGA-CN-6988 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-6989      TCGA-CN-6992      TCGA-CN-6994      TCGA-CN-6997 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-6998      TCGA-CN-A498      TCGA-CN-A49B      TCGA-CN-A49C 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-A63T      TCGA-CN-A63U      TCGA-CN-A63V      TCGA-CN-A641 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-A642      TCGA-CN-A6UY      TCGA-CN-A6V3      TCGA-CN-A6V6 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CQ-5323      TCGA-CQ-5324      TCGA-CQ-5325      TCGA-CQ-5326 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CQ-5330      TCGA-CQ-5331      TCGA-CQ-5332      TCGA-CQ-5333 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CQ-6218      TCGA-CQ-6219      TCGA-CQ-6221      TCGA-CQ-6222 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CQ-6223      TCGA-CQ-6224      TCGA-CQ-6227      TCGA-CQ-6228 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CQ-7063      TCGA-CQ-7072      TCGA-CQ-A4C6      TCGA-CQ-A4C7 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CQ-A4C9      TCGA-CQ-A4CB      TCGA-CQ-A4CG      TCGA-CQ-A4CI 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CR-5247      TCGA-CR-5250      TCGA-CR-6467      TCGA-CR-6471 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CR-6473      TCGA-CR-6474      TCGA-CR-6482      TCGA-CR-6487 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CR-6491      TCGA-CR-6492      TCGA-CR-6493      TCGA-CR-7364 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CR-7367      TCGA-CR-7368      TCGA-CR-7369      TCGA-CR-7370 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CR-7371      TCGA-CR-7373      TCGA-CR-7374      TCGA-CR-7376 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CR-7377      TCGA-CR-7379      TCGA-CR-7383      TCGA-CR-7385 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CR-7386      TCGA-CR-7388      TCGA-CR-7389      TCGA-CR-7390 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CR-7392      TCGA-CR-7394      TCGA-CR-7395      TCGA-CR-7398 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CR-7399      TCGA-CR-7401      TCGA-CR-7402      TCGA-CV-6436 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-6933      TCGA-CV-6934      TCGA-CV-6936      TCGA-CV-6941 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-6945      TCGA-CV-6952      TCGA-CV-6961      TCGA-CV-7095 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-7097      TCGA-CV-7235      TCGA-CV-7242      TCGA-CV-7245 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-7248      TCGA-CV-7250      TCGA-CV-7254      TCGA-CV-7261 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-7263      TCGA-CV-7406      TCGA-CV-7410      TCGA-CV-7418 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-7422      TCGA-CV-7424      TCGA-CV-7427      TCGA-CV-7430 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-7432      TCGA-CV-7433      TCGA-CV-7434      TCGA-CV-7440 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-7446      TCGA-CV-7568      TCGA-CV-A45Y      TCGA-CV-A45Z 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-A460      TCGA-CV-A464      TCGA-CV-A468      TCGA-CV-A6JD 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-A6JN      TCGA-CV-A6JO      TCGA-CV-A6JU      TCGA-CV-A6JZ 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-A6K1      TCGA-CV-A6K2      TCGA-CX-7082      TCGA-CX-7085 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CX-7086      TCGA-CX-7219      TCGA-D6-6516      TCGA-D6-6517 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-D6-6823      TCGA-D6-6824      TCGA-D6-6825      TCGA-D6-6827 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-D6-8568      TCGA-D6-8569      TCGA-D6-A4Z9      TCGA-D6-A4ZB 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-D6-A6EK      TCGA-D6-A6EP      TCGA-DQ-5625      TCGA-DQ-5629 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-DQ-5630      TCGA-DQ-5631      TCGA-DQ-7588      TCGA-DQ-7589 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-DQ-7590      TCGA-DQ-7591      TCGA-DQ-7592      TCGA-DQ-7593 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-DQ-7595      TCGA-F7-7848      TCGA-F7-8489      TCGA-F7-A50G 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-F7-A50I      TCGA-F7-A50J      TCGA-F7-A61S      TCGA-F7-A61V 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-F7-A61W      TCGA-F7-A620      TCGA-F7-A623      TCGA-H7-7774 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-H7-A6C4      TCGA-H7-A6C5      TCGA-HD-7753      TCGA-HD-7754 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-HD-7832      TCGA-HD-8634      TCGA-HD-8635      TCGA-HD-A634 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-HD-A6I0      TCGA-HL-7533      TCGA-IQ-7631      TCGA-IQ-7632 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-IQ-A61E      TCGA-IQ-A61G      TCGA-IQ-A61H      TCGA-IQ-A61K 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-KU-A66S      TCGA-KU-A6H7      TCGA-KU-A6H8      TCGA-MT-A51W 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-MT-A51X      TCGA-MT-A67D      TCGA-MZ-A6I9      TCGA-MZ-A7D7 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-P3-A5Q6      TCGA-P3-A6SW      TCGA-P3-A6SX      TCGA-P3-A6T0 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-P3-A6T4      TCGA-P3-A6T5      TCGA-P3-A6T7      TCGA-P3-A6T8 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-QK-A6IG      TCGA-QK-A6II      TCGA-QK-A6IJ      TCGA-RS-A6TP 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-T2-A6WZ      TCGA-T2-A6X0      TCGA-T2-A6X2      TCGA-TN-A7HI 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-TN-A7HL      TCGA-UF-A718      TCGA-UF-A71B      TCGA-UF-A7J9 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-UF-A7JC      TCGA-UF-A7JD      TCGA-UF-A7JF      TCGA-UF-A7JH 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-UF-A7JJ      TCGA-UF-A7JS      TCGA-WA-A7GZ      TCGA-WA-A7H4 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
D47V10, continuous
[1] "Remove cluster labels:" "SEH1L MUTATED"         
clus
  SEH1L MUTATED SEH1L WILD-TYPE 
              1             271 
     TCGA-BA-4074      TCGA-BA-4075      TCGA-BA-4076      TCGA-BA-4077 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-BA-4078      TCGA-BA-5149      TCGA-BA-5151      TCGA-BA-5556 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-BA-6868      TCGA-BA-6869      TCGA-BA-6870      TCGA-BA-6871 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-BA-6872      TCGA-BA-6873      TCGA-BA-7269      TCGA-BA-A6DA 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-BA-A6DG      TCGA-BB-4225      TCGA-BB-4228      TCGA-BB-7871 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-BB-8596      TCGA-BB-A5HY      TCGA-BB-A6UM      TCGA-BB-A6UO 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-4727      TCGA-CN-4728      TCGA-CN-4730      TCGA-CN-4736 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-4738      TCGA-CN-4739      TCGA-CN-4741      TCGA-CN-4742 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-5358      TCGA-CN-5359      TCGA-CN-5360      TCGA-CN-5361 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-5363      TCGA-CN-5365      TCGA-CN-5366      TCGA-CN-5367 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-5370      TCGA-CN-6010      TCGA-CN-6011      TCGA-CN-6012 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-6016      TCGA-CN-6017      TCGA-CN-6021      TCGA-CN-6023 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-6024      TCGA-CN-6989      TCGA-CN-6992      TCGA-CN-6994 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-6997      TCGA-CN-6998      TCGA-CN-A498      TCGA-CN-A49B 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-A49C      TCGA-CN-A63T      TCGA-CN-A63U      TCGA-CN-A63V 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CN-A641      TCGA-CN-A6UY      TCGA-CN-A6V3      TCGA-CN-A6V6 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CQ-5323      TCGA-CQ-5324      TCGA-CQ-5325      TCGA-CQ-5330 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CQ-5331      TCGA-CQ-5333      TCGA-CQ-6218      TCGA-CQ-6219 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CQ-6221      TCGA-CQ-6222      TCGA-CQ-6223      TCGA-CQ-6224 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CQ-6227      TCGA-CQ-6228      TCGA-CQ-7063      TCGA-CQ-7072 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CQ-A4C6      TCGA-CQ-A4C7      TCGA-CQ-A4C9      TCGA-CQ-A4CB 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CQ-A4CI      TCGA-CR-5247      TCGA-CR-5248      TCGA-CR-5250 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CR-6467      TCGA-CR-6471      TCGA-CR-6473      TCGA-CR-6474 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CR-6477      TCGA-CR-6478      TCGA-CR-6482      TCGA-CR-6487 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CR-6491      TCGA-CR-6492      TCGA-CR-6493      TCGA-CR-7364 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CR-7365      TCGA-CR-7367      TCGA-CR-7368      TCGA-CR-7369 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CR-7370      TCGA-CR-7371      TCGA-CR-7373      TCGA-CR-7374 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CR-7376      TCGA-CR-7377      TCGA-CR-7383      TCGA-CR-7385 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CR-7386      TCGA-CR-7388      TCGA-CR-7389      TCGA-CR-7390 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CR-7391      TCGA-CR-7392      TCGA-CR-7394      TCGA-CR-7395 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CR-7397      TCGA-CR-7399      TCGA-CR-7401      TCGA-CR-7402 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-5430      TCGA-CV-5431      TCGA-CV-5432      TCGA-CV-5435 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-5436      TCGA-CV-5440      TCGA-CV-5443      TCGA-CV-5966 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-5970      TCGA-CV-5976      TCGA-CV-6433      TCGA-CV-6436 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-6441      TCGA-CV-6934      TCGA-CV-6935      TCGA-CV-6936 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-6941      TCGA-CV-6943      TCGA-CV-6945      TCGA-CV-6952 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-6954      TCGA-CV-6960      TCGA-CV-6961      TCGA-CV-7091 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-7095      TCGA-CV-7097      TCGA-CV-7099      TCGA-CV-7100 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-7101      TCGA-CV-7102      TCGA-CV-7180      TCGA-CV-7183 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-7235      TCGA-CV-7242      TCGA-CV-7245      TCGA-CV-7248 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-7250      TCGA-CV-7254      TCGA-CV-7261      TCGA-CV-7406 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-7410      TCGA-CV-7418      TCGA-CV-7422      TCGA-CV-7424 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-7427      TCGA-CV-7430      TCGA-CV-7432      TCGA-CV-7433 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-7434      TCGA-CV-7435      TCGA-CV-7440      TCGA-CV-7446 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-7568      TCGA-CV-A45Q      TCGA-CV-A45Y      TCGA-CV-A45Z 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-A460      TCGA-CV-A461      TCGA-CV-A464      TCGA-CV-A468 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-A6JD      TCGA-CV-A6JE      TCGA-CV-A6JN      TCGA-CV-A6JO 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-A6JU      TCGA-CV-A6JY      TCGA-CV-A6JZ      TCGA-CV-A6K1 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-CV-A6K2      TCGA-CX-7086      TCGA-CX-7219      TCGA-D6-6516 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-D6-6517      TCGA-D6-6823      TCGA-D6-6824      TCGA-D6-6825 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-D6-6827      TCGA-D6-8568      TCGA-D6-8569      TCGA-D6-A4Z9 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-D6-A4ZB      TCGA-D6-A6EK      TCGA-D6-A6EP      TCGA-D6-A74Q 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-DQ-5625      TCGA-DQ-5629      TCGA-DQ-5630      TCGA-DQ-5631 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-DQ-7588      TCGA-DQ-7589      TCGA-DQ-7590      TCGA-DQ-7591 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-DQ-7592      TCGA-DQ-7593      TCGA-DQ-7595      TCGA-F7-7848 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-F7-8489      TCGA-F7-A50G      TCGA-F7-A50I      TCGA-F7-A50J 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-F7-A61S      TCGA-F7-A61V      TCGA-F7-A61W      TCGA-F7-A620 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-F7-A623      TCGA-H7-7774      TCGA-H7-A6C4      TCGA-H7-A6C5 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-H7-A76A      TCGA-HD-8634      TCGA-HD-8635      TCGA-HD-A634 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-HD-A6I0      TCGA-HL-7533      TCGA-IQ-7631      TCGA-IQ-7632 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-IQ-A61E      TCGA-IQ-A61G      TCGA-KU-A66S      TCGA-KU-A6H7 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-KU-A6H8      TCGA-MT-A51W      TCGA-MT-A51X      TCGA-MT-A67D 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-MZ-A6I9      TCGA-MZ-A7D7      TCGA-P3-A6SX      TCGA-P3-A6T0 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-P3-A6T4      TCGA-P3-A6T8      TCGA-QK-A6IG      TCGA-QK-A6II 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-QK-A6IJ      TCGA-RS-A6TP      TCGA-TN-A7HI      TCGA-TN-A7HL 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-UF-A718      TCGA-UF-A71B      TCGA-UF-A7J9      TCGA-UF-A7JC 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-UF-A7JD      TCGA-UF-A7JF      TCGA-UF-A7JH      TCGA-UF-A7JJ 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-UF-A7JS      TCGA-WA-A7GZ      TCGA-WA-A7H4 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
D47V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SEH1L MUTATED                                  0     1
  SEH1L WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SEH1L MUTATED                           0     3
  SEH1L WILD-TYPE                        36   438
D47V12, multiclass
                                  clus
vv                                 SEH1L MUTATED SEH1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              36
  WHITE                                        3             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"
D47V13, binary
                 cls
clus                0   1
  SEH1L MUTATED     0   3
  SEH1L WILD-TYPE  25 442
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEH1L MUTATED      0    3
  SEH1L WILD-TYPE   25  442
                        clus
vv                       SEH1L MUTATED SEH1L WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO             3             442
[1] 2 2
[1] FALSE

Clustering(48) Variable = CUL3 MUTATION ANALYSIS
D48V1, survival
                sevent
clus2              0   1
  CUL3 MUTATED     9   5
  CUL3 WILD-TYPE 294 196
  CUL3 MUTATED CUL3 WILD-TYPE 
            14            490 
  CUL3 MUTATED CUL3 WILD-TYPE 
             5            196 
$`CUL3 MUTATED`
TCGA-BA-6869 TCGA-BB-8601 TCGA-CN-5360 TCGA-CN-5369 TCGA-CN-6019 TCGA-CN-6989 
       21.17        20.52        35.54        12.49        14.20        20.09 
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        43.36 

$`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 
       53.79        57.44        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         7.76        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        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44        37.84 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.65        21.11        24.92        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5361 
       13.05        33.11        34.36         8.58        12.39        55.27 
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 
       22.45        56.94        20.71        30.67        20.68        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       19.53        20.68        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 
       36.49        11.08        10.45        12.95        24.16         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       17.42        14.10        11.74        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        46.75        45.80        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        34.75        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        51.29        33.11        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        28.83        64.11        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        32.81        25.81        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 
       11.51        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        31.10        29.85        29.52        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        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      126.08        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        24.99 
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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       15.88         7.63        14.30        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        35.54        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        18.90        25.48        20.45         9.83        12.13 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       12.10        10.65        11.18        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        19.23        18.94        12.62         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-7917 
       21.11         6.77         0.07         0.16        25.74         1.22 
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        12.76 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        19.33        11.84        13.55         0.07        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
        5.29        11.54        11.84        13.35        18.15        12.43 
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 
        3.68        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 
       56.75        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        11.74        17.65         7.30        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO 
        9.34        12.72        18.64        14.79        12.43        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        13.68        43.59        54.67         2.83        41.16 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       42.02        44.65        62.27        17.95        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       21.86        16.11        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 
        23.555         18.380 
[1] "6.4 - 129.2 (23.6)" "0.1 - 211.0 (18.4)"
[1] "hr=" "1.4"
D48V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  CUL3 MUTATED         0        0         5         7         0
  CUL3 WILD-TYPE      25       76        72       241        11
D48V3, multiclass
           clus
vv          CUL3 MUTATED CUL3 WILD-TYPE
  STAGE I              0             25
  STAGE II             0             76
  STAGE III            5             72
  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    47 131  93 162
D48V4, multiclass
       clus
vv      CUL3 MUTATED CUL3 WILD-TYPE
  T0+T1            1             47
  T2               0            131
  T3               5             93
  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 167  63 158   7
D48V5, multiclass
    clus
vv   CUL3 MUTATED CUL3 WILD-TYPE
  N0            7            167
  N1            2             63
  N2            3            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"
D48V6, binary
                cls
clus               0   1
  CUL3 MUTATED     2  12
  CUL3 WILD-TYPE 137 355
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL3 MUTATED      2   12
  CUL3 WILD-TYPE  137  355
        clus
vv       CUL3 MUTATED CUL3 WILD-TYPE
  FEMALE            2            137
  MALE             12            355
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  CUL3 MUTATED                                      14
  CUL3 WILD-TYPE                                   484
                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
D48V7, 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                                  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"
D48V8, binary
                cls
clus               0   1
  CUL3 MUTATED     5   9
  CUL3 WILD-TYPE  78 414
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL3 MUTATED      5    9
  CUL3 WILD-TYPE   78  414
     clus
vv    CUL3 MUTATED CUL3 WILD-TYPE
  NO             5             78
  YES            9            414
[1] 2 2
[1] FALSE
D48V9, continuous
D48V10, continuous
D48V11, 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                        33   431
D48V12, multiclass
                                  clus
vv                                 CUL3 MUTATED CUL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   3             33
  WHITE                                      10            431
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V13, binary
                cls
clus               0   1
  CUL3 MUTATED     0  12
  CUL3 WILD-TYPE  25 433
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL3 MUTATED      0   12
  CUL3 WILD-TYPE   25  433
                        clus
vv                       CUL3 MUTATED CUL3 WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO           12            433
[1] 2 2
[1] FALSE

Clustering(49) Variable = NOTCH2 MUTATION ANALYSIS
D49V1, survival
                  sevent
clus2                0   1
  NOTCH2 MUTATED     9  10
  NOTCH2 WILD-TYPE 294 191
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
              19              485 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
              10              191 
$`NOTCH2 MUTATED`
TCGA-BA-6870 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-6018 TCGA-CN-6989 TCGA-CN-A498 
       14.83         4.67        40.44        19.07        20.09        14.56 
TCGA-CR-7364 TCGA-CR-7383 TCGA-CR-7394 TCGA-CV-6003 TCGA-CV-6937 TCGA-CV-7178 
       47.18        17.13        29.52        54.74        20.52        71.21 
TCGA-CV-7427 TCGA-CV-7568 TCGA-CV-A45P TCGA-DQ-5631 TCGA-MT-A67A TCGA-P3-A6SX 
      156.49        30.48        24.99        18.02        30.05        47.01 
TCGA-P3-A6T0 
       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 
       53.79        57.44        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         7.76        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        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.35        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        23.70        38.04        37.84        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
       26.86        32.65        21.11        24.92        41.10        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        43.73        27.58        41.69        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 
       33.11        34.36         8.58        12.39        35.54        55.27 
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        22.45        56.94        20.71        30.67        20.68 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
       20.65        19.53        20.68        14.20         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 
        9.24        36.49        11.08        10.45        12.95        24.16 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 
        3.68        17.42        14.10        11.74        35.01        17.59 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       12.85        29.72        21.21         7.40        17.29        15.91 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       11.44         5.75         4.41        12.07         2.70        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
        7.33         9.80         7.69         6.18        48.20        39.68 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        46.75        45.80        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        34.75        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        51.29        33.11        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       43.04        41.88        28.83        64.11        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        32.81        25.81        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        11.51        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        31.10        29.85        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 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
        5.46         4.73        21.90        26.43        11.24       126.08 
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        22.03 
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        15.88         7.63 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       14.30        13.94        12.10        12.79        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       35.54        30.94        33.86        14.04        18.90        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45         9.83        12.13        12.10        10.65        11.18 
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        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       12.62         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         6.77         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
        0.16        25.74         1.22        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        12.76        14.50        19.33        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       13.55         0.07        14.47         5.29        11.54        11.84 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        12.43        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         3.68        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        56.75        51.25        10.85        36.82 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        11.74        17.65         7.30        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO 
        9.34        12.72        18.64        14.79        12.43        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        13.68        43.59        54.67         2.83        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       41.16        42.02        44.65        62.27        17.95        24.16 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       49.22        21.86        16.11        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 

  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
            4.67             0.07 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
          156.49           210.97 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
           24.99            18.15 
[1] "4.7 - 156.5 (25.0)" "0.1 - 211.0 (18.1)"
[1] "hr=" "1"  
D49V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  NOTCH2 MUTATED         3        2         4         8         0
  NOTCH2 WILD-TYPE      22       74        73       240        11
D49V3, multiclass
           clus
vv          NOTCH2 MUTATED NOTCH2 WILD-TYPE
  STAGE I                3               22
  STAGE II               2               74
  STAGE III              4               73
  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
  NOTCH2 MUTATED       3   4   4   6
  NOTCH2 WILD-TYPE    45 127  94 162
D49V4, multiclass
       clus
vv      NOTCH2 MUTATED NOTCH2 WILD-TYPE
  T0+T1              3               45
  T2                 4              127
  T3                 4               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
  NOTCH2 MUTATED     9   2   4   0
  NOTCH2 WILD-TYPE 165  63 157   7
D49V5, multiclass
    clus
vv   NOTCH2 MUTATED NOTCH2 WILD-TYPE
  N0              9              165
  N1              2               63
  N2              4              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"
D49V6, binary
                  cls
clus                 0   1
  NOTCH2 MUTATED    11   8
  NOTCH2 WILD-TYPE 128 359
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED     11    8
  NOTCH2 WILD-TYPE  128  359
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  FEMALE             11              128
  MALE                8              359
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  NOTCH2 MUTATED                                      19
  NOTCH2 WILD-TYPE                                   479
                  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
D49V7, multiclass
                                                             clus
vv                                                            NOTCH2 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                                                            NOTCH2 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"
D49V8, binary
                  cls
clus                 0   1
  NOTCH2 MUTATED     4  15
  NOTCH2 WILD-TYPE  79 408
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      4   15
  NOTCH2 WILD-TYPE   79  408
     clus
vv    NOTCH2 MUTATED NOTCH2 WILD-TYPE
  NO               4               79
  YES             15              408
[1] 2 2
[1] FALSE
D49V9, continuous
D49V10, continuous
D49V11, 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    18
  NOTCH2 WILD-TYPE                        35   423
D49V12, multiclass
                                  clus
vv                                 NOTCH2 MUTATED NOTCH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               35
  WHITE                                        18              423
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V13, binary
                  cls
clus                 0   1
  NOTCH2 MUTATED     0  19
  NOTCH2 WILD-TYPE  25 426
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      0   19
  NOTCH2 WILD-TYPE   25  426
                        clus
vv                       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  HISPANIC OR LATINO                  0               25
  NOT HISPANIC OR LATINO             19              426
[1] 2 2
[1] FALSE

Clustering(50) Variable = YTHDF1 MUTATION ANALYSIS
D50V1, survival
                  sevent
clus2                0   1
  YTHDF1 MUTATED     2   4
  YTHDF1 WILD-TYPE 301 197
  YTHDF1 MUTATED YTHDF1 WILD-TYPE 
               6              498 
  YTHDF1 MUTATED YTHDF1 WILD-TYPE 
               4              197 
$`YTHDF1 MUTATED`
TCGA-BA-5152 TCGA-CN-5367 TCGA-CV-A6K2 TCGA-KU-A66S TCGA-TN-A7HI TCGA-UF-A71A 
       42.35        11.57        10.42        13.35        13.55         2.83 

$`YTHDF1 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        53.79 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       57.44        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         7.76        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        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       37.84        12.89        26.86        32.65        21.11        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       35.54        55.27         8.32        16.21        11.54        11.84 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
       12.49         8.52        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        14.56        17.59        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        17.29        15.91        11.44         5.75 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.69         6.18        48.20        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        46.75        45.80        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 
       34.75        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        51.29        33.11        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       28.83        64.11        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 
       32.81        25.81        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 
       11.51        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        31.10        29.85        29.52        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        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       126.08        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-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        24.99       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 
       22.03         3.62        21.24        23.47        19.92        22.52 
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        15.88         7.63 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       14.30        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 
       35.54        30.94        33.86        18.02        14.04        18.90 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       25.48        20.45         9.83        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       11.18        37.18        21.63        20.25         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        12.62         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         6.77 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        0.07         0.16        25.74         1.22        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        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        13.55         0.07        14.47         5.29        11.54 
TCGA-IQ-A61O TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       11.84        18.15        12.43        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         3.68        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        56.75        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        11.74 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       17.65         7.30        16.70         9.34        12.72        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       14.79        12.43        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        7.10        32.45        13.25        13.68        43.59        54.67 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       43.36        41.16        42.02        44.65        62.27        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.16        49.22        21.86        16.11        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 

  YTHDF1 MUTATED YTHDF1 WILD-TYPE 
            2.83             0.07 
  YTHDF1 MUTATED YTHDF1 WILD-TYPE 
           42.35           210.97 
  YTHDF1 MUTATED YTHDF1 WILD-TYPE 
          12.460           18.825 
[1] "2.8 - 42.4 (12.5)"  "0.1 - 211.0 (18.8)"
[1] "hr=" "2.8"
D50V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  YTHDF1 MUTATED         0        0         1         5         0
  YTHDF1 WILD-TYPE      25       76        76       243        11
D50V3, multiclass
           clus
vv          YTHDF1 MUTATED YTHDF1 WILD-TYPE
  STAGE I                0               25
  STAGE II               0               76
  STAGE III              1               76
  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
  YTHDF1 MUTATED       1   1   0   4
  YTHDF1 WILD-TYPE    47 130  98 164
D50V4, multiclass
       clus
vv      YTHDF1 MUTATED YTHDF1 WILD-TYPE
  T0+T1              1               47
  T2                 1              130
  T3                 0               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
  YTHDF1 MUTATED     2   1   3   0
  YTHDF1 WILD-TYPE 172  64 158   7
D50V5, multiclass
    clus
vv   YTHDF1 MUTATED YTHDF1 WILD-TYPE
  N0              2              172
  N1              1               64
  N2              3              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"
D50V6, binary
                  cls
clus                 0   1
  YTHDF1 MUTATED     2   4
  YTHDF1 WILD-TYPE 137 363
[1] "tbl2"
                  cls
clus               [,1] [,2]
  YTHDF1 MUTATED      2    4
  YTHDF1 WILD-TYPE  137  363
        clus
vv       YTHDF1 MUTATED YTHDF1 WILD-TYPE
  FEMALE              2              137
  MALE                4              363
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  YTHDF1 MUTATED                                       5
  YTHDF1 WILD-TYPE                                   493
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  YTHDF1 MUTATED                                                             0
  YTHDF1 WILD-TYPE                                                           1
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  YTHDF1 MUTATED                                                     1
  YTHDF1 WILD-TYPE                                                   6
D50V7, multiclass
                                                             clus
vv                                                            YTHDF1 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                      1
                                                             clus
vv                                                            YTHDF1 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"
D50V8, binary
                  cls
clus                 0   1
  YTHDF1 MUTATED     2   4
  YTHDF1 WILD-TYPE  81 419
[1] "tbl2"
                  cls
clus               [,1] [,2]
  YTHDF1 MUTATED      2    4
  YTHDF1 WILD-TYPE   81  419
     clus
vv    YTHDF1 MUTATED YTHDF1 WILD-TYPE
  NO               2               81
  YES              4              419
[1] 2 2
[1] FALSE
D50V9, continuous
D50V10, continuous
D50V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  YTHDF1 MUTATED                                  0     0
  YTHDF1 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  YTHDF1 MUTATED                           0     6
  YTHDF1 WILD-TYPE                        36   435
D50V12, multiclass
                                  clus
vv                                 YTHDF1 MUTATED YTHDF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               36
  WHITE                                         6              435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V13, binary
                  cls
clus                 0   1
  YTHDF1 MUTATED     0   5
  YTHDF1 WILD-TYPE  25 440
[1] "tbl2"
                  cls
clus               [,1] [,2]
  YTHDF1 MUTATED      0    5
  YTHDF1 WILD-TYPE   25  440
                        clus
vv                       YTHDF1 MUTATED YTHDF1 WILD-TYPE
  HISPANIC OR LATINO                  0               25
  NOT HISPANIC OR LATINO              5              440
[1] 2 2
[1] FALSE

Clustering(51) Variable = FOSL2 MUTATION ANALYSIS
D51V1, survival
                 sevent
clus2               0   1
  FOSL2 MUTATED     2   8
  FOSL2 WILD-TYPE 301 193
  FOSL2 MUTATED FOSL2 WILD-TYPE 
             10             494 
  FOSL2 MUTATED FOSL2 WILD-TYPE 
              8             193 
$`FOSL2 MUTATED`
TCGA-BA-4077 TCGA-BA-6872 TCGA-CN-6998 TCGA-CQ-5334 TCGA-CQ-7069 TCGA-CV-7099 
       37.28        12.62        11.74         4.24        41.88         7.99 
TCGA-CV-7104 TCGA-CV-7568 TCGA-DQ-5629 TCGA-HD-A6I0 
       12.92        30.48        30.94         6.90 

$`FOSL2 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-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        53.79 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 
       57.44        15.52        21.17        14.83         3.55         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
        7.76        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        94.62         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.35        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        23.70        38.04         4.67        40.44        37.84 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.65        21.11        24.92        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        33.11        34.36         8.58        12.39        35.54 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       55.27         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        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        14.56        17.59        12.85        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        17.29        15.91        11.44         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        10.09         7.33         9.80         7.69 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
        6.18        48.20        39.68        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 
       46.75        45.80        45.99        10.42        11.21        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        34.75        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        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       33.11        16.73        43.04        28.83        64.11        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        32.81        25.81        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        11.51        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        31.10        29.85 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       29.52        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        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       126.08 
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-7177 
       12.66         9.01         5.26         1.84        52.31        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        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-7427 TCGA-CV-7429 TCGA-CV-7430 
      100.57        14.89        56.48       156.49         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       84.49        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       22.19        35.93        27.98        24.99       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 
       22.03         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-D6-6515 
       10.42        10.42        10.55        18.84        34.36        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        15.88 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        14.30        13.94        12.10        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       58.45        35.54        33.86        18.02        14.04        18.90 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       25.48        20.45         9.83        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       11.18        37.18        21.63        20.25         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        12.62         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         6.77 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        0.07         0.16        25.74         1.22        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-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
       34.75        15.95        12.76        14.50        19.33        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       13.55         0.07        14.47         5.29        11.54        11.84 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        12.43        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         3.68        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        56.75        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        11.74 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       17.65         7.30        16.70         9.34        12.72        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       14.79        12.43        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        13.68        43.59 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        43.36        41.16        42.02        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       62.27        17.95        24.16        49.22        21.86        16.11 
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 

  FOSL2 MUTATED FOSL2 WILD-TYPE 
           4.24            0.07 
  FOSL2 MUTATED FOSL2 WILD-TYPE 
          41.88          210.97 
  FOSL2 MUTATED FOSL2 WILD-TYPE 
          12.77           18.74 
[1] "4.2 - 41.9 (12.8)"  "0.1 - 211.0 (18.7)"
[1] "hr=" "2.7"
D51V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  FOSL2 MUTATED         0        2         0         6         0
  FOSL2 WILD-TYPE      25       74        77       242        11
D51V3, multiclass
           clus
vv          FOSL2 MUTATED FOSL2 WILD-TYPE
  STAGE I               0              25
  STAGE II              2              74
  STAGE III             0              77
  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
  FOSL2 MUTATED       0   3   2   3
  FOSL2 WILD-TYPE    48 128  96 165
D51V4, multiclass
       clus
vv      FOSL2 MUTATED FOSL2 WILD-TYPE
  T0+T1             0              48
  T2                3             128
  T3                2              96
  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
  FOSL2 MUTATED     2   1   3   0
  FOSL2 WILD-TYPE 172  64 158   7
D51V5, multiclass
    clus
vv   FOSL2 MUTATED FOSL2 WILD-TYPE
  N0             2             172
  N1             1              64
  N2             3             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"
D51V6, binary
                 cls
clus                0   1
  FOSL2 MUTATED     5   5
  FOSL2 WILD-TYPE 134 362
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOSL2 MUTATED      5    5
  FOSL2 WILD-TYPE  134  362
        clus
vv       FOSL2 MUTATED FOSL2 WILD-TYPE
  FEMALE             5             134
  MALE               5             362
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  FOSL2 MUTATED                                      10
  FOSL2 WILD-TYPE                                   488
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  FOSL2 MUTATED                                                             0
  FOSL2 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  FOSL2 MUTATED                                                     0
  FOSL2 WILD-TYPE                                                   7
D51V7, multiclass
                                                             clus
vv                                                            FOSL2 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  10
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
                                                             clus
vv                                                            FOSL2 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"
D51V8, binary
                 cls
clus                0   1
  FOSL2 MUTATED     2   8
  FOSL2 WILD-TYPE  81 415
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOSL2 MUTATED      2    8
  FOSL2 WILD-TYPE   81  415
     clus
vv    FOSL2 MUTATED FOSL2 WILD-TYPE
  NO              2              81
  YES             8             415
[1] 2 2
[1] FALSE
D51V9, continuous
D51V10, continuous
D51V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FOSL2 MUTATED                                  0     0
  FOSL2 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FOSL2 MUTATED                           0    10
  FOSL2 WILD-TYPE                        36   431
D51V12, multiclass
                                  clus
vv                                 FOSL2 MUTATED FOSL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              36
  WHITE                                       10             431
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V13, binary
                 cls
clus                0   1
  FOSL2 MUTATED     0   9
  FOSL2 WILD-TYPE  25 436
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOSL2 MUTATED      0    9
  FOSL2 WILD-TYPE   25  436
                        clus
vv                       FOSL2 MUTATED FOSL2 WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO             9             436
[1] 2 2
[1] FALSE

Clustering(52) Variable = MYH9 MUTATION ANALYSIS
D52V1, survival
                sevent
clus2              0   1
  MYH9 MUTATED    13   9
  MYH9 WILD-TYPE 290 192
  MYH9 MUTATED MYH9 WILD-TYPE 
            22            482 
  MYH9 MUTATED MYH9 WILD-TYPE 
             9            192 
$`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        20.65         7.69 
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        22.03        17.85        15.95 
TCGA-P3-A6T2 TCGA-QK-A6VB TCGA-T2-A6X2 TCGA-UF-A7JJ 
       75.55        14.79        32.45        16.11 

$`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        53.79 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       57.44        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         7.76        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        94.62         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 
        4.41        18.35        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        23.70 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       38.04         4.67        40.44        37.84        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       32.65        21.11        24.92        41.10        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        43.73        27.58        41.69        13.05        33.11 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
       34.36         8.58        12.39        35.54        55.27         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 
       22.45        56.94        20.71        30.67        20.68        19.53 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       20.68        19.07        14.20         6.74         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
       36.49        11.08        10.45        20.09        12.95        24.16 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        3.68        17.42        14.10        11.74        35.01        14.56 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       17.59        12.85        29.72        21.21         7.40        17.29 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       15.91        11.44         5.75         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       10.09         7.33         9.80         6.18        48.20        39.68 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        46.75        45.80        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        34.75        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        51.29        33.11        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        28.83        64.11        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        32.81        25.81        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        11.51        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        31.10        29.85        29.52        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        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       126.08        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        24.99       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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        34.36        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        15.88         7.63        14.30 
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        35.54 
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        18.90        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45         9.83        12.13        12.10        10.65        11.18 
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        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
       12.62         0.46        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         6.77         0.07         0.16 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       25.74         1.22        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-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       12.76        14.50        19.33        11.84        13.55         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
       14.47         5.29        11.54        11.84        13.35        18.15 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       12.43        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         3.68        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        56.75        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        11.74        17.65         7.30        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP 
        9.34        12.72        18.64        12.43        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        13.68 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       43.59        54.67         2.83        43.36        41.16        42.02 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        62.27        17.95        24.16        49.22        21.86 
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 
         20.55          18.59 
[1] "0.8 - 169.4 (20.5)" "0.1 - 211.0 (18.6)"
[1] "hr=" "1.2"
D52V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  MYH9 MUTATED         1        4         5        10         0
  MYH9 WILD-TYPE      24       72        72       238        11
D52V3, multiclass
           clus
vv          MYH9 MUTATED MYH9 WILD-TYPE
  STAGE I              1             24
  STAGE II             4             72
  STAGE III            5             72
  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    46 124  93 161
D52V4, multiclass
       clus
vv      MYH9 MUTATED MYH9 WILD-TYPE
  T0+T1            2             46
  T2               7            124
  T3               5             93
  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 164  62 155   7
D52V5, multiclass
    clus
vv   MYH9 MUTATED MYH9 WILD-TYPE
  N0           10            164
  N1            3             62
  N2            6            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"
D52V6, binary
                cls
clus               0   1
  MYH9 MUTATED     4  18
  MYH9 WILD-TYPE 135 349
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH9 MUTATED      4   18
  MYH9 WILD-TYPE  135  349
        clus
vv       MYH9 MUTATED MYH9 WILD-TYPE
  FEMALE            4            135
  MALE             18            349
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  MYH9 MUTATED                                      21
  MYH9 WILD-TYPE                                   477
                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
D52V7, 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                                  477
  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"
D52V8, binary
                cls
clus               0   1
  MYH9 MUTATED     3  19
  MYH9 WILD-TYPE  80 404
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH9 MUTATED      3   19
  MYH9 WILD-TYPE   80  404
     clus
vv    MYH9 MUTATED MYH9 WILD-TYPE
  NO             3             80
  YES           19            404
[1] 2 2
[1] FALSE
D52V9, continuous
D52V10, continuous
D52V11, 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                        35   423
D52V12, multiclass
                                  clus
vv                                 MYH9 MUTATED MYH9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             35
  WHITE                                      18            423
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V13, binary
                cls
clus               0   1
  MYH9 MUTATED     2  17
  MYH9 WILD-TYPE  23 428
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH9 MUTATED      2   17
  MYH9 WILD-TYPE   23  428
                        clus
vv                       MYH9 MUTATED MYH9 WILD-TYPE
  HISPANIC OR LATINO                2             23
  NOT HISPANIC OR LATINO           17            428
[1] 2 2
[1] FALSE

Clustering(53) Variable = TP63 MUTATION ANALYSIS
D53V1, survival
                sevent
clus2              0   1
  TP63 MUTATED    10   2
  TP63 WILD-TYPE 293 199
  TP63 MUTATED TP63 WILD-TYPE 
            12            492 
  TP63 MUTATED TP63 WILD-TYPE 
             2            199 
$`TP63 MUTATED`
TCGA-BA-5152 TCGA-BA-A4IG TCGA-BA-A6D8 TCGA-CN-5364 TCGA-CN-6998 TCGA-CR-6492 
       42.35        28.11        27.95        16.21        11.74        15.75 
TCGA-CV-5440 TCGA-CV-6003 TCGA-CV-A6JU TCGA-D6-A6EM TCGA-HL-7533 TCGA-MT-A67A 
      107.51        54.74         3.62         7.63        34.75        30.05 

$`TP63 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        53.79 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       57.44        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA 
        4.01         7.76        29.42        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        94.62         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.41        18.35        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 
       23.70        38.04         4.67        40.44        37.84        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
       26.86        32.65        21.11        24.92        41.10        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        43.73        27.58        41.69        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 
       33.11        34.36         8.58        12.39        35.54        55.27 
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 
       22.45        56.94        20.71        30.67        20.68        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
       19.53        20.68        19.07        14.20         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        9.24        36.49        11.08        10.45        20.09        12.95 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A498 
       24.16         3.68        17.42        14.10        35.01        14.56 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       17.59        12.85        29.72        21.21         7.40        17.29 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       15.91        11.44         5.75         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       10.09         7.33         9.80         7.69         6.18        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       39.68        21.50         2.93        54.58        46.75        45.80 
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        34.75        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        51.29        33.11 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       16.73        43.04        41.88        28.83        64.11        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        32.81        25.81        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-6493 TCGA-CR-7364 
       11.64         7.69        12.46        11.51         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       39.16        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        29.82        30.02        31.10        29.85        29.52 
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-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       19.20        17.95        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
        7.07        43.23        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       126.08        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-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        24.99       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-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
       22.03        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-A6EO 
       24.95        25.32        17.72        12.36        15.88        14.30 
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        35.54 
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        18.90        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45         9.83        12.13        12.10        10.65        11.18 
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        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       12.62         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         6.77         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
        0.16        25.74         1.22        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        12.76        14.50        19.33        11.84        13.55 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
        0.07        14.47         5.29        11.54        11.84        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D 
       18.15        12.43        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         3.68        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        56.75        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        11.74        17.65         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       16.70         9.34        12.72        18.64        14.79        12.43 
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        13.68        43.59        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       43.36        41.16        42.02        44.65        62.27        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.16        49.22        21.86        16.11        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 

  TP63 MUTATED TP63 WILD-TYPE 
          3.62           0.07 
  TP63 MUTATED TP63 WILD-TYPE 
        107.51         210.97 
  TP63 MUTATED TP63 WILD-TYPE 
         28.03          18.59 
[1] "3.6 - 107.5 (28.0)" "0.1 - 211.0 (18.6)"
[1] "hr=" "2.8"
D53V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  TP63 MUTATED         1        1         2         5         1
  TP63 WILD-TYPE      24       75        75       243        10
D53V3, multiclass
           clus
vv          TP63 MUTATED TP63 WILD-TYPE
  STAGE I              1             24
  STAGE II             1             75
  STAGE III            2             75
  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
  TP63 MUTATED       2   3   1   5
  TP63 WILD-TYPE    46 128  97 163
D53V4, multiclass
       clus
vv      TP63 MUTATED TP63 WILD-TYPE
  T0+T1            2             46
  T2               3            128
  T3               1             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
  TP63 MUTATED     3   3   4   0
  TP63 WILD-TYPE 171  62 157   7
D53V5, multiclass
    clus
vv   TP63 MUTATED TP63 WILD-TYPE
  N0            3            171
  N1            3             62
  N2            4            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"
D53V6, binary
                cls
clus               0   1
  TP63 MUTATED     4   8
  TP63 WILD-TYPE 135 359
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED      4    8
  TP63 WILD-TYPE  135  359
        clus
vv       TP63 MUTATED TP63 WILD-TYPE
  FEMALE            4            135
  MALE              8            359
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  TP63 MUTATED                                      12
  TP63 WILD-TYPE                                   486
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  TP63 MUTATED                                                             0
  TP63 WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  TP63 MUTATED                                                     0
  TP63 WILD-TYPE                                                   7
D53V7, multiclass
                                                             clus
vv                                                            TP63 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                 12
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    0
                                                             clus
vv                                                            TP63 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"
D53V8, binary
                cls
clus               0   1
  TP63 MUTATED     4   8
  TP63 WILD-TYPE  79 415
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED      4    8
  TP63 WILD-TYPE   79  415
     clus
vv    TP63 MUTATED TP63 WILD-TYPE
  NO             4             79
  YES            8            415
[1] 2 2
[1] FALSE
D53V9, continuous
D53V10, continuous
D53V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP63 MUTATED                                  0     0
  TP63 WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP63 MUTATED                           1    11
  TP63 WILD-TYPE                        35   430
D53V12, multiclass
                                  clus
vv                                 TP63 MUTATED TP63 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             35
  WHITE                                      11            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"
D53V13, binary
                cls
clus               0   1
  TP63 MUTATED     0  11
  TP63 WILD-TYPE  25 434
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED      0   11
  TP63 WILD-TYPE   25  434
                        clus
vv                       TP63 MUTATED TP63 WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO           11            434
[1] 2 2
[1] FALSE

Clustering(54) Variable = DYSF MUTATION ANALYSIS
D54V1, survival
                sevent
clus2              0   1
  DYSF MUTATED    12   9
  DYSF WILD-TYPE 291 192
  DYSF MUTATED DYSF WILD-TYPE 
            21            483 
  DYSF MUTATED DYSF WILD-TYPE 
             9            192 
$`DYSF MUTATED`
TCGA-BA-6869 TCGA-BA-A6DA TCGA-BA-A6DF TCGA-BB-7870 TCGA-CN-4727 TCGA-CN-6016 
       21.17        11.54         7.82        66.28        40.44        19.53 
TCGA-CN-6995 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6228 TCGA-CR-7364 TCGA-CR-7398 
        3.68        10.42        11.21        14.99        47.18         5.13 
TCGA-CR-7402 TCGA-CV-7242 TCGA-CV-A45U TCGA-CV-A461 TCGA-CV-A6JT TCGA-D6-6516 
       29.95        36.00        35.47        67.86        22.03        25.41 
TCGA-HL-7533 TCGA-IQ-A61I TCGA-UF-A7JT 
       34.75         0.07        32.65 

$`DYSF 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 
       53.79        57.44        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         7.76        29.42        28.11        20.45        30.18 
TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DI 
       27.95         7.10         5.69        14.47         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        94.62         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.41        18.35        22.42        36.72        33.70        50.20 
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        23.70 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        37.84        12.89        26.86        32.65 
TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       21.11        24.92        41.10        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       43.73        27.58        41.69        13.05        33.11        34.36 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 
        8.58        12.39        35.54        55.27         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        22.45 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6017 
       56.94        20.71        30.67        20.68        20.65        20.68 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        14.20         6.74         9.07         9.24        36.49 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
       11.08        10.45        20.09        12.95        24.16        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5334 
        2.93        54.58        46.75        45.80        45.99         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        34.75 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       56.58        13.25         4.24        38.76        70.13        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       33.11        16.73        43.04        41.88        28.83        64.11 
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        32.81        25.81 
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        11.51        15.75 
TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        9.27        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        31.10        29.85 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 
       29.52        30.58         7.10         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        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        7.07        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-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       126.08        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-7238 
       71.21        10.75       130.88        77.16         4.73        47.47 
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        24.99       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
      159.65         1.05        45.96         6.51        88.87        48.20 
TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       60.43         0.76        56.61         7.07        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JU TCGA-CV-A6JY 
       35.34         6.38        29.79         6.48         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
       23.47        19.92        22.52        10.42        10.42        10.55 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       18.84        34.36        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-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       12.36        15.88         7.63        14.30        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        35.54        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        18.90        25.48        20.45         9.83 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
       12.13        12.10        10.65        11.18        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        19.23        18.94        12.62         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         6.77         0.07         0.16        25.74 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
        1.22        14.66        22.03        12.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         3.65         6.90        15.95        12.76 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K 
       14.50        19.33        11.84        13.55        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       11.54        11.84        13.35        18.15        12.43        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         3.68 
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        56.75 
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        11.74        17.65         7.30        16.70         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP 
       12.72        18.64        14.79        12.43        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 
       13.68        43.59        54.67         2.83        43.36        41.16 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       42.02        44.65        62.27        17.95        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JV 
       21.86        16.11        13.94        20.75        22.36         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

  DYSF MUTATED DYSF WILD-TYPE 
          0.07           0.07 
  DYSF MUTATED DYSF WILD-TYPE 
         67.86         210.97 
  DYSF MUTATED DYSF WILD-TYPE 
         22.03          18.41 
[1] "0.1 - 67.9 (22.0)"  "0.1 - 211.0 (18.4)"
[1] "hr=" "1.1"
D54V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DYSF MUTATED         1        4         3        10         0
  DYSF WILD-TYPE      24       72        74       238        11
D54V3, multiclass
           clus
vv          DYSF MUTATED DYSF WILD-TYPE
  STAGE I              1             24
  STAGE II             4             72
  STAGE III            3             74
  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
  DYSF MUTATED       3   4   3   8
  DYSF WILD-TYPE    45 127  95 160
D54V4, multiclass
       clus
vv      DYSF MUTATED DYSF WILD-TYPE
  T0+T1            3             45
  T2               4            127
  T3               3             95
  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
  DYSF MUTATED    13   1   4   0
  DYSF WILD-TYPE 161  64 157   7
D54V5, multiclass
    clus
vv   DYSF MUTATED DYSF WILD-TYPE
  N0           13            161
  N1            1             64
  N2            4            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"
D54V6, binary
                cls
clus               0   1
  DYSF MUTATED     6  15
  DYSF WILD-TYPE 133 352
[1] "tbl2"
                cls
clus             [,1] [,2]
  DYSF MUTATED      6   15
  DYSF WILD-TYPE  133  352
        clus
vv       DYSF MUTATED DYSF WILD-TYPE
  FEMALE            6            133
  MALE             15            352
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DYSF MUTATED                                      21
  DYSF WILD-TYPE                                   477
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DYSF MUTATED                                                             0
  DYSF WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DYSF MUTATED                                                     0
  DYSF WILD-TYPE                                                   7
D54V7, multiclass
                                                             clus
vv                                                            DYSF 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                    0
                                                             clus
vv                                                            DYSF WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                  477
  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"
D54V8, binary
                cls
clus               0   1
  DYSF MUTATED     4  17
  DYSF WILD-TYPE  79 406
[1] "tbl2"
                cls
clus             [,1] [,2]
  DYSF MUTATED      4   17
  DYSF WILD-TYPE   79  406
     clus
vv    DYSF MUTATED DYSF WILD-TYPE
  NO             4             79
  YES           17            406
[1] 2 2
[1] FALSE
D54V9, continuous
D54V10, continuous
D54V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DYSF MUTATED                                  0     0
  DYSF WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DYSF MUTATED                           1    20
  DYSF WILD-TYPE                        35   421
D54V12, multiclass
                                  clus
vv                                 DYSF MUTATED DYSF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             35
  WHITE                                      20            421
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V13, binary
                cls
clus               0   1
  DYSF MUTATED     0  20
  DYSF WILD-TYPE  25 425
[1] "tbl2"
                cls
clus             [,1] [,2]
  DYSF MUTATED      0   20
  DYSF WILD-TYPE   25  425
                        clus
vv                       DYSF MUTATED DYSF WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO           20            425
[1] 2 2
[1] FALSE

Clustering(55) Variable = TMEM2 MUTATION ANALYSIS
D55V1, survival
                 sevent
clus2               0   1
  TMEM2 MUTATED    11   6
  TMEM2 WILD-TYPE 292 195
  TMEM2 MUTATED TMEM2 WILD-TYPE 
             17             487 
  TMEM2 MUTATED TMEM2 WILD-TYPE 
              6             195 
$`TMEM2 MUTATED`
TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4740 TCGA-CN-5360 TCGA-CN-6011 TCGA-CN-6997 
       23.70        40.44        27.58        35.54        30.67        14.10 
TCGA-CN-A63U TCGA-CN-A6V1 TCGA-CR-7388 TCGA-CV-5440 TCGA-CV-6934 TCGA-CV-7104 
       17.29         7.33        27.06       107.51         2.14        12.92 
TCGA-CV-7253 TCGA-HD-A633 TCGA-IQ-7630 TCGA-P3-A5QF TCGA-UF-A71D 
       11.87        13.84        15.95        10.85        41.16 

$`TMEM2 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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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-4725 TCGA-CN-4726 TCGA-CN-4728 
        8.81         6.28        12.69        38.04         4.67        37.84 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.65        21.11        24.92        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 
       12.99        20.55        14.33        43.73        41.69        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5361 TCGA-CN-5363 
       33.11        34.36         8.58        12.39        55.27         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-6012 TCGA-CN-6013 TCGA-CN-6016 
       22.45        56.94        20.71        20.68        20.65        19.53 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       20.68        19.07        14.20         6.74         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
       36.49        11.08        10.45        20.09        12.95        24.16 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        14.56        17.59 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W 
       12.85        29.72        21.21         7.40        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V3 
        5.75         4.41        12.07         2.70        10.09         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.69         6.18        48.20        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        46.75        45.80        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 
       34.75        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        51.29        33.11        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       28.83        64.11        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 
       32.81        25.81        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 
       11.51        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-7398 
       31.10        29.85        29.52        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-5441 
      129.21       108.95        76.24        19.20        17.95        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 
       21.07        62.43         9.60        90.12         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       126.08 
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-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-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-A45Q 
       22.19        35.93        30.48        27.98        24.99       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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       15.88         7.63        14.30        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        35.54        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        18.90        25.48        20.45         9.83        12.13 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       12.10        10.65        11.18        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        19.23        18.94        12.62         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-7917 
       21.11         6.77         0.07         0.16        25.74         1.22 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 
       14.66        22.03        12.66        22.85         0.36         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        3.65         6.90        34.75        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        13.55         0.07        14.47         5.29        11.54 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       11.84        13.35        18.15        12.43        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         3.68        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        56.75        51.25 
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        11.74 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       17.65         7.30        16.70         9.34        12.72        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       14.79        12.43        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        13.68        43.59 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        43.36        42.02        44.65        62.27 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.16        49.22        21.86        16.11        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 

  TMEM2 MUTATED TMEM2 WILD-TYPE 
           2.14            0.07 
  TMEM2 MUTATED TMEM2 WILD-TYPE 
         107.51          210.97 
  TMEM2 MUTATED TMEM2 WILD-TYPE 
          17.29           18.67 
[1] "2.1 - 107.5 (17.3)" "0.1 - 211.0 (18.7)"
[1] "hr=" "1.1"
D55V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  TMEM2 MUTATED         0        1         0        15         0
  TMEM2 WILD-TYPE      25       75        77       233        11
D55V3, multiclass
           clus
vv          TMEM2 MUTATED TMEM2 WILD-TYPE
  STAGE I               0              25
  STAGE II              1              75
  STAGE III             0              77
  STAGE IVA            15             233
  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
  TMEM2 MUTATED       0   3   3  10
  TMEM2 WILD-TYPE    48 128  95 158
D55V4, multiclass
       clus
vv      TMEM2 MUTATED TMEM2 WILD-TYPE
  T0+T1             0              48
  T2                3             128
  T3                3              95
  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
  TMEM2 MUTATED     9   0   7   0
  TMEM2 WILD-TYPE 165  65 154   7
D55V5, multiclass
    clus
vv   TMEM2 MUTATED TMEM2 WILD-TYPE
  N0             9             165
  N1             0              65
  N2             7             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"
D55V6, binary
                 cls
clus                0   1
  TMEM2 MUTATED     5  12
  TMEM2 WILD-TYPE 134 355
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMEM2 MUTATED      5   12
  TMEM2 WILD-TYPE  134  355
        clus
vv       TMEM2 MUTATED TMEM2 WILD-TYPE
  FEMALE             5             134
  MALE              12             355
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  TMEM2 MUTATED                                      17
  TMEM2 WILD-TYPE                                   481
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  TMEM2 MUTATED                                                             0
  TMEM2 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  TMEM2 MUTATED                                                     0
  TMEM2 WILD-TYPE                                                   7
D55V7, multiclass
                                                             clus
vv                                                            TMEM2 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                                                            TMEM2 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                       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"
D55V8, binary
                 cls
clus                0   1
  TMEM2 MUTATED     6  11
  TMEM2 WILD-TYPE  77 412
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMEM2 MUTATED      6   11
  TMEM2 WILD-TYPE   77  412
     clus
vv    TMEM2 MUTATED TMEM2 WILD-TYPE
  NO              6              77
  YES            11             412
[1] 2 2
[1] FALSE
D55V9, continuous
D55V10, continuous
D55V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM2 MUTATED                                  0     0
  TMEM2 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TMEM2 MUTATED                           1    16
  TMEM2 WILD-TYPE                        35   425
D55V12, multiclass
                                  clus
vv                                 TMEM2 MUTATED TMEM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              35
  WHITE                                       16             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"
D55V13, binary
                 cls
clus                0   1
  TMEM2 MUTATED     1  13
  TMEM2 WILD-TYPE  24 432
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMEM2 MUTATED      1   13
  TMEM2 WILD-TYPE   24  432
                        clus
vv                       TMEM2 MUTATED TMEM2 WILD-TYPE
  HISPANIC OR LATINO                 1              24
  NOT HISPANIC OR LATINO            13             432
[1] 2 2
[1] FALSE

Clustering(56) Variable = PTPN14 MUTATION ANALYSIS
D56V1, survival
                  sevent
clus2                0   1
  PTPN14 MUTATED    11   3
  PTPN14 WILD-TYPE 292 198
  PTPN14 MUTATED PTPN14 WILD-TYPE 
              14              490 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
               3              198 
$`PTPN14 MUTATED`
TCGA-CN-4727 TCGA-CN-5363 TCGA-CN-A63U TCGA-CQ-5327 TCGA-CQ-7071 TCGA-CQ-A4C6 
       40.44         8.32        17.29        54.58        28.83        44.48 
TCGA-CR-7365 TCGA-CV-5430 TCGA-CV-5441 TCGA-CV-A6JD TCGA-D6-6516 TCGA-D6-A6ES 
       39.16       139.43        94.88         5.98        25.41        12.79 
TCGA-DQ-7588 TCGA-MT-A67F 
       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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       37.84        12.89        26.86        32.65        21.11        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       35.54        55.27        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        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        14.56        17.59        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
       21.21         7.40        15.91        11.44         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        10.09         7.33         9.80         7.69 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 
        6.18        48.20        39.68        21.50         2.93        46.75 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       45.80        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        34.75        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        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C7 
       33.11        16.73        43.04        41.88        64.11        11.61 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        32.81        25.81        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        11.51        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        31.10        29.85        29.52        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       126.08        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        24.99       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        22.03         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-D6-6515 TCGA-D6-6517 TCGA-D6-6823 
       10.55        18.84        34.36        13.25         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-A6EO TCGA-D6-A6EP 
       17.72        12.36        15.88         7.63        14.30        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        35.54        30.94        33.86 
TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       18.02        18.90        25.48        20.45         9.83        12.13 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       12.10        10.65        11.18        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        19.23        18.94        12.62         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-7917 
       21.11         6.77         0.07         0.16        25.74         1.22 
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        12.76 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        19.33        11.84        13.55         0.07        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
        5.29        11.54        11.84        13.35        18.15        12.43 
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         3.68 
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        56.75 
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        11.74        17.65         7.30        16.70         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP 
       12.72        18.64        14.79        12.43        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 
       13.68        43.59        54.67         2.83        43.36        41.16 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       42.02        44.65        62.27        17.95        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       21.86        16.11        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 

  PTPN14 MUTATED PTPN14 WILD-TYPE 
            5.98             0.07 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
          139.43           210.97 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
           27.12            18.59 
[1] "6.0 - 139.4 (27.1)" "0.1 - 211.0 (18.6)"
[1] "hr=" "2.4"
D56V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  PTPN14 MUTATED         1        1         1         8         1
  PTPN14 WILD-TYPE      24       75        76       240        10
D56V3, multiclass
           clus
vv          PTPN14 MUTATED PTPN14 WILD-TYPE
  STAGE I                1               24
  STAGE II               1               75
  STAGE III              1               76
  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   2   2   7
  PTPN14 WILD-TYPE    47 129  96 161
D56V4, multiclass
       clus
vv      PTPN14 MUTATED PTPN14 WILD-TYPE
  T0+T1              1               47
  T2                 2              129
  T3                 2               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
  PTPN14 MUTATED     6   1   4   1
  PTPN14 WILD-TYPE 168  64 157   6
D56V5, multiclass
    clus
vv   PTPN14 MUTATED PTPN14 WILD-TYPE
  N0              6              168
  N1              1               64
  N2              4              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"
D56V6, binary
                  cls
clus                 0   1
  PTPN14 MUTATED     4  10
  PTPN14 WILD-TYPE 135 357
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED      4   10
  PTPN14 WILD-TYPE  135  357
        clus
vv       PTPN14 MUTATED PTPN14 WILD-TYPE
  FEMALE              4              135
  MALE               10              357
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  PTPN14 MUTATED                                      14
  PTPN14 WILD-TYPE                                   484
                  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
D56V7, multiclass
                                                             clus
vv                                                            PTPN14 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                                                            PTPN14 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"
D56V8, binary
                  cls
clus                 0   1
  PTPN14 MUTATED     5   9
  PTPN14 WILD-TYPE  78 414
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED      5    9
  PTPN14 WILD-TYPE   78  414
     clus
vv    PTPN14 MUTATED PTPN14 WILD-TYPE
  NO               5               78
  YES              9              414
[1] 2 2
[1] FALSE
D56V9, continuous
D56V10, continuous
D56V11, 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    11
  PTPN14 WILD-TYPE                        35   430
D56V12, multiclass
                                  clus
vv                                 PTPN14 MUTATED PTPN14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               35
  WHITE                                        11              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"
D56V13, binary
                  cls
clus                 0   1
  PTPN14 MUTATED     1  13
  PTPN14 WILD-TYPE  24 432
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED      1   13
  PTPN14 WILD-TYPE   24  432
                        clus
vv                       PTPN14 MUTATED PTPN14 WILD-TYPE
  HISPANIC OR LATINO                  1               24
  NOT HISPANIC OR LATINO             13              432
[1] 2 2
[1] FALSE

Clustering(57) Variable = RBM10 MUTATION ANALYSIS
D57V1, survival
                 sevent
clus2               0   1
  RBM10 MUTATED     3   1
  RBM10 WILD-TYPE 300 200
  RBM10 MUTATED RBM10 WILD-TYPE 
              4             500 
  RBM10 MUTATED RBM10 WILD-TYPE 
              1             200 
$`RBM10 MUTATED`
TCGA-CN-4733 TCGA-CR-7382 TCGA-CV-5430 TCGA-CV-A463 
       21.11        26.17       139.43         0.76 

$`RBM10 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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4734 
       40.44        37.84        12.89        26.86        32.65        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       35.54        55.27         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        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        20.68        20.65        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       14.20         6.74         9.07         9.24        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        46.75        45.80        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        34.75        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        51.29        33.11        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        28.83        64.11        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        32.81        25.81        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        11.51        15.75         9.27        47.18        39.16 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
       47.34        40.93        35.84         3.45         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       29.23         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       17.13        32.78        47.01        27.06        12.89        29.82 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        31.10        29.85        29.52        30.58         7.10 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
        5.13         5.95        35.41        29.95        48.39        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
      129.21       108.95        76.24        19.20        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       54.74        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        9.70         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       126.08        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        24.99       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-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       60.43        67.86        56.61         7.07        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       35.34         6.38        29.79         6.48        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        34.36        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        15.88         7.63        14.30 
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        35.54 
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        18.90        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45         9.83        12.13        12.10        10.65        11.18 
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        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       12.62         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         6.77         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
        0.16        25.74         1.22        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        12.76        14.50        19.33        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       13.55         0.07        14.47         5.29        11.54        11.84 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        12.43        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         3.68        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        56.75        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        11.74 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       17.65         7.30        16.70         9.34        12.72        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       14.79        12.43        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        13.68        43.59 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        43.36        41.16        42.02        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       62.27        17.95        24.16        49.22        21.86        16.11 
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 

  RBM10 MUTATED RBM10 WILD-TYPE 
           0.76            0.07 
  RBM10 MUTATED RBM10 WILD-TYPE 
         139.43          210.97 
  RBM10 MUTATED RBM10 WILD-TYPE 
          23.64           18.59 
[1] "0.8 - 139.4 (23.6)" "0.1 - 211.0 (18.6)"
[1] "hr=" "2.2"
D57V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  RBM10 MUTATED         0        0         1         3         0
  RBM10 WILD-TYPE      25       76        76       245        11
D57V3, multiclass
           clus
vv          RBM10 MUTATED RBM10 WILD-TYPE
  STAGE I               0              25
  STAGE II              0              76
  STAGE III             1              76
  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
  RBM10 MUTATED       1   1   0   2
  RBM10 WILD-TYPE    47 130  98 166
D57V4, multiclass
       clus
vv      RBM10 MUTATED RBM10 WILD-TYPE
  T0+T1             1              47
  T2                1             130
  T3                0              98
  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
  RBM10 MUTATED     1   1   2   0
  RBM10 WILD-TYPE 173  64 159   7
D57V5, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  N0             1             173
  N1             1              64
  N2             2             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"
D57V6, binary
                 cls
clus                0   1
  RBM10 MUTATED     1   3
  RBM10 WILD-TYPE 138 364
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      1    3
  RBM10 WILD-TYPE  138  364
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  FEMALE             1             138
  MALE               3             364
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  RBM10 MUTATED                                       4
  RBM10 WILD-TYPE                                   494
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  RBM10 MUTATED                                                             0
  RBM10 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  RBM10 MUTATED                                                     0
  RBM10 WILD-TYPE                                                   7
D57V7, multiclass
                                                             clus
vv                                                            RBM10 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                                                            RBM10 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"
D57V8, binary
                 cls
clus                0   1
  RBM10 MUTATED     2   2
  RBM10 WILD-TYPE  81 421
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      2    2
  RBM10 WILD-TYPE   81  421
     clus
vv    RBM10 MUTATED RBM10 WILD-TYPE
  NO              2              81
  YES             2             421
[1] 2 2
[1] FALSE
D57V9, continuous
D57V10, continuous
[1] "Remove cluster labels:" "RBM10 MUTATED"         
clus
  RBM10 MUTATED RBM10 WILD-TYPE 
              1             271 
     TCGA-BA-4074      TCGA-BA-4075      TCGA-BA-4076      TCGA-BA-4077 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-BA-4078      TCGA-BA-5149      TCGA-BA-5151      TCGA-BA-5556 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-BA-6868      TCGA-BA-6869      TCGA-BA-6870      TCGA-BA-6871 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-BA-6872      TCGA-BA-6873      TCGA-BA-7269      TCGA-BA-A6DA 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-BA-A6DG      TCGA-BB-4225      TCGA-BB-4228      TCGA-BB-7871 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-BB-8596      TCGA-BB-A5HY      TCGA-BB-A6UM      TCGA-BB-A6UO 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CN-4727      TCGA-CN-4728      TCGA-CN-4730      TCGA-CN-4736 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CN-4738      TCGA-CN-4739      TCGA-CN-4741      TCGA-CN-4742 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CN-5358      TCGA-CN-5359      TCGA-CN-5360      TCGA-CN-5361 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CN-5363      TCGA-CN-5365      TCGA-CN-5366      TCGA-CN-5367 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CN-5370      TCGA-CN-6010      TCGA-CN-6011      TCGA-CN-6012 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CN-6016      TCGA-CN-6017      TCGA-CN-6021      TCGA-CN-6023 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CN-6024      TCGA-CN-6989      TCGA-CN-6992      TCGA-CN-6994 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CN-6997      TCGA-CN-6998      TCGA-CN-A498      TCGA-CN-A49B 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CN-A49C      TCGA-CN-A63T      TCGA-CN-A63U      TCGA-CN-A63V 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CN-A641      TCGA-CN-A6UY      TCGA-CN-A6V3      TCGA-CN-A6V6 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CQ-5323      TCGA-CQ-5324      TCGA-CQ-5325      TCGA-CQ-5330 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CQ-5331      TCGA-CQ-5333      TCGA-CQ-6218      TCGA-CQ-6219 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CQ-6221      TCGA-CQ-6222      TCGA-CQ-6223      TCGA-CQ-6224 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CQ-6227      TCGA-CQ-6228      TCGA-CQ-7063      TCGA-CQ-7072 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CQ-A4C6      TCGA-CQ-A4C7      TCGA-CQ-A4C9      TCGA-CQ-A4CB 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CQ-A4CI      TCGA-CR-5247      TCGA-CR-5248      TCGA-CR-5250 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CR-6467      TCGA-CR-6471      TCGA-CR-6473      TCGA-CR-6474 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CR-6477      TCGA-CR-6478      TCGA-CR-6482      TCGA-CR-6487 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CR-6491      TCGA-CR-6492      TCGA-CR-6493      TCGA-CR-7364 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CR-7365      TCGA-CR-7367      TCGA-CR-7368      TCGA-CR-7369 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CR-7370      TCGA-CR-7371      TCGA-CR-7373      TCGA-CR-7374 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CR-7376      TCGA-CR-7377      TCGA-CR-7383      TCGA-CR-7385 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CR-7386      TCGA-CR-7388      TCGA-CR-7389      TCGA-CR-7390 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CR-7391      TCGA-CR-7392      TCGA-CR-7394      TCGA-CR-7395 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CR-7397      TCGA-CR-7399      TCGA-CR-7401      TCGA-CR-7402 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CV-5431      TCGA-CV-5432      TCGA-CV-5435      TCGA-CV-5436 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CV-5440      TCGA-CV-5443      TCGA-CV-5966      TCGA-CV-5970 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CV-5976      TCGA-CV-6433      TCGA-CV-6436      TCGA-CV-6441 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CV-6934      TCGA-CV-6935      TCGA-CV-6936      TCGA-CV-6941 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CV-6943      TCGA-CV-6945      TCGA-CV-6952      TCGA-CV-6954 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CV-6960      TCGA-CV-6961      TCGA-CV-7091      TCGA-CV-7095 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CV-7097      TCGA-CV-7099      TCGA-CV-7100      TCGA-CV-7101 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CV-7102      TCGA-CV-7180      TCGA-CV-7183      TCGA-CV-7235 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CV-7242      TCGA-CV-7245      TCGA-CV-7248      TCGA-CV-7250 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CV-7254      TCGA-CV-7261      TCGA-CV-7406      TCGA-CV-7410 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CV-7418      TCGA-CV-7422      TCGA-CV-7424      TCGA-CV-7427 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CV-7430      TCGA-CV-7432      TCGA-CV-7433      TCGA-CV-7434 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CV-7435      TCGA-CV-7440      TCGA-CV-7446      TCGA-CV-7568 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CV-A45Q      TCGA-CV-A45Y      TCGA-CV-A45Z      TCGA-CV-A460 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CV-A461      TCGA-CV-A464      TCGA-CV-A468      TCGA-CV-A6JD 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CV-A6JE      TCGA-CV-A6JN      TCGA-CV-A6JO      TCGA-CV-A6JU 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CV-A6JY      TCGA-CV-A6JZ      TCGA-CV-A6K1      TCGA-CV-A6K2 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-CX-7086      TCGA-CX-7219      TCGA-D6-6516      TCGA-D6-6517 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-D6-6823      TCGA-D6-6824      TCGA-D6-6825      TCGA-D6-6827 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-D6-8568      TCGA-D6-8569      TCGA-D6-A4Z9      TCGA-D6-A4ZB 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-D6-A6EK      TCGA-D6-A6EP      TCGA-D6-A74Q      TCGA-DQ-5625 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-DQ-5629      TCGA-DQ-5630      TCGA-DQ-5631      TCGA-DQ-7588 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-DQ-7589      TCGA-DQ-7590      TCGA-DQ-7591      TCGA-DQ-7592 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-DQ-7593      TCGA-DQ-7595      TCGA-F7-7848      TCGA-F7-8489 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-F7-A50G      TCGA-F7-A50I      TCGA-F7-A50J      TCGA-F7-A61S 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-F7-A61V      TCGA-F7-A61W      TCGA-F7-A620      TCGA-F7-A623 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-H7-7774      TCGA-H7-A6C4      TCGA-H7-A6C5      TCGA-H7-A76A 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-HD-8634      TCGA-HD-8635      TCGA-HD-A634      TCGA-HD-A6I0 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-HL-7533      TCGA-IQ-7631      TCGA-IQ-7632      TCGA-IQ-A61E 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-IQ-A61G      TCGA-KU-A66S      TCGA-KU-A6H7      TCGA-KU-A6H8 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-MT-A51W      TCGA-MT-A51X      TCGA-MT-A67D      TCGA-MZ-A6I9 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-MZ-A7D7      TCGA-P3-A6SX      TCGA-P3-A6T0      TCGA-P3-A6T4 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-P3-A6T8      TCGA-QK-A6IG      TCGA-QK-A6II      TCGA-QK-A6IJ 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-RS-A6TP      TCGA-TN-A7HI      TCGA-TN-A7HL      TCGA-UF-A718 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-UF-A71B      TCGA-UF-A71D      TCGA-UF-A7J9      TCGA-UF-A7JC 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-UF-A7JD      TCGA-UF-A7JF      TCGA-UF-A7JH      TCGA-UF-A7JJ 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-UF-A7JS      TCGA-WA-A7GZ      TCGA-WA-A7H4 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
D57V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM10 MUTATED                                  0     0
  RBM10 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBM10 MUTATED                           0     4
  RBM10 WILD-TYPE                        36   437
D57V12, multiclass
                                  clus
vv                                 RBM10 MUTATED RBM10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              36
  WHITE                                        4             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"
D57V13, binary
                 cls
clus                0   1
  RBM10 MUTATED     2   2
  RBM10 WILD-TYPE  23 443
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      2    2
  RBM10 WILD-TYPE   23  443
                        clus
vv                       RBM10 MUTATED RBM10 WILD-TYPE
  HISPANIC OR LATINO                 2              23
  NOT HISPANIC OR LATINO             2             443
[1] 2 2
[1] FALSE

Clustering(58) Variable = IRF2 MUTATION ANALYSIS
D58V1, survival
                sevent
clus2              0   1
  IRF2 MUTATED     6   1
  IRF2 WILD-TYPE 297 200
  IRF2 MUTATED IRF2 WILD-TYPE 
             7            497 
  IRF2 MUTATED IRF2 WILD-TYPE 
             1            200 
$`IRF2 MUTATED`
TCGA-BA-A6DA TCGA-CN-4734 TCGA-CV-6953 TCGA-CV-A6K1 TCGA-DQ-7594 TCGA-T2-A6X2 
       11.54        24.92        53.95        22.52        12.10        32.45 
TCGA-TN-A7HL 
       13.68 

$`IRF2 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 
       53.79        57.44        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         7.76        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       30.18        27.95         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        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       37.84        12.89        26.86        32.65        21.11        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        33.11        34.36         8.58        12.39        35.54 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       55.27         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        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        14.56        17.59        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        17.29        15.91        11.44         5.75 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.69         6.18        48.20        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        46.75        45.80        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 
       34.75        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        51.29        33.11        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       28.83        64.11        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 
       32.81        25.81        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 
       11.51        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        31.10        29.85        29.52        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        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       126.08        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       15.09        30.08         6.08        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        24.99       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        22.03 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7082 
        3.62        21.24        23.47        19.92        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        34.36        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        15.88         7.63        14.30 
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        35.54 
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        18.90        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       20.45         9.83        12.13        10.65        11.18        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        19.23        18.94        12.62 
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         6.77         0.07         0.16 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       25.74         1.22        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        12.76        14.50        19.33        11.84        13.55 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
        0.07        14.47         5.29        11.54        11.84        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        12.43        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         3.68        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        56.75        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        11.74        17.65 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        16.70         9.34        12.72        18.64        14.79 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       12.43        12.72        16.96         6.87        15.91         7.10 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.55        13.25        43.59        54.67         2.83        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       41.16        42.02        44.65        62.27        17.95        24.16 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       49.22        21.86        16.11        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 

  IRF2 MUTATED IRF2 WILD-TYPE 
         11.54           0.07 
  IRF2 MUTATED IRF2 WILD-TYPE 
         53.95         210.97 
  IRF2 MUTATED IRF2 WILD-TYPE 
         22.52          18.64 
[1] "11.5 - 54.0 (22.5)" "0.1 - 211.0 (18.6)"
[1] "hr=" "2.7"
D58V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  IRF2 MUTATED         0        1         2         3         0
  IRF2 WILD-TYPE      25       75        75       245        11
D58V3, multiclass
           clus
vv          IRF2 MUTATED IRF2 WILD-TYPE
  STAGE I              0             25
  STAGE II             1             75
  STAGE III            2             75
  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
  IRF2 MUTATED       0   1   3   2
  IRF2 WILD-TYPE    48 130  95 166
D58V4, multiclass
       clus
vv      IRF2 MUTATED IRF2 WILD-TYPE
  T0+T1            0             48
  T2               1            130
  T3               3             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
  IRF2 MUTATED     4   0   2   0
  IRF2 WILD-TYPE 170  65 159   7
D58V5, multiclass
    clus
vv   IRF2 MUTATED IRF2 WILD-TYPE
  N0            4            170
  N1            0             65
  N2            2            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"
D58V6, binary
                cls
clus               0   1
  IRF2 MUTATED     2   5
  IRF2 WILD-TYPE 137 362
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF2 MUTATED      2    5
  IRF2 WILD-TYPE  137  362
        clus
vv       IRF2 MUTATED IRF2 WILD-TYPE
  FEMALE            2            137
  MALE              5            362
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  IRF2 MUTATED                                       7
  IRF2 WILD-TYPE                                   491
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  IRF2 MUTATED                                                             0
  IRF2 WILD-TYPE                                                           1
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  IRF2 MUTATED                                                     0
  IRF2 WILD-TYPE                                                   7
D58V7, multiclass
                                                             clus
vv                                                            IRF2 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                                                            IRF2 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"
D58V8, binary
                cls
clus               0   1
  IRF2 MUTATED     1   6
  IRF2 WILD-TYPE  82 417
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF2 MUTATED      1    6
  IRF2 WILD-TYPE   82  417
     clus
vv    IRF2 MUTATED IRF2 WILD-TYPE
  NO             1             82
  YES            6            417
[1] 2 2
[1] FALSE
D58V9, continuous
D58V10, continuous
D58V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IRF2 MUTATED                                  0     0
  IRF2 WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IRF2 MUTATED                           0     7
  IRF2 WILD-TYPE                        36   434
D58V12, multiclass
                                  clus
vv                                 IRF2 MUTATED IRF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             36
  WHITE                                       7            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"
D58V13, binary
                cls
clus               0   1
  IRF2 MUTATED     0   7
  IRF2 WILD-TYPE  25 438
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF2 MUTATED      0    7
  IRF2 WILD-TYPE   25  438
                        clus
vv                       IRF2 MUTATED IRF2 WILD-TYPE
  HISPANIC OR LATINO                0             25
  NOT HISPANIC OR LATINO            7            438
[1] 2 2
[1] FALSE

Clustering(59) Variable = AMPD1 MUTATION ANALYSIS
D59V1, survival
                 sevent
clus2               0   1
  AMPD1 MUTATED     3   3
  AMPD1 WILD-TYPE 300 198
  AMPD1 MUTATED AMPD1 WILD-TYPE 
              6             498 
  AMPD1 MUTATED AMPD1 WILD-TYPE 
              3             198 
$`AMPD1 MUTATED`
TCGA-BA-4078 TCGA-BA-A6DA TCGA-CN-A63U TCGA-CV-7440 TCGA-HD-A633 TCGA-P3-A6T5 
        9.07        11.54        17.29        22.19        13.84        29.00 

$`AMPD1 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        53.79 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       57.44        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         7.76        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-4223 TCGA-BB-4224 
       11.05        13.38        20.48         6.15        94.62         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.35        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        23.70        38.04         4.67        40.44        37.84 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 
       12.89        26.86        32.65        21.11        24.92        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        33.11        34.36         8.58        12.39        35.54 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       55.27         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        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        14.56        17.59        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
       21.21         7.40        15.91        11.44         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        10.09         7.33         9.80         7.69 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
        6.18        48.20        39.68        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       46.75        45.80        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        34.75 
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 
       51.29        33.11        16.73        43.04        41.88        28.83 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       64.11        44.48        11.61        23.24        29.36        32.81 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       25.81        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        11.51 
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 
       31.10        29.85        29.52        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 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       54.74        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        9.70         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       126.08        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-7446 TCGA-CV-7568 
        7.17       153.86        16.64         6.38        35.93        30.48 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        24.99       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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        34.36        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        15.88         7.63        14.30 
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        35.54 
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        18.90        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45         9.83        12.13        12.10        10.65        11.18 
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        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       12.62         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         6.77         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
        0.16        25.74         1.22        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        12.76        14.50        19.33        11.84        13.55 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
        0.07        14.47         5.29        11.54        11.84        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        12.43        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         3.68        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        56.75        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 
       47.01        19.00        75.55        18.97         2.04        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        11.74        17.65         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       16.70         9.34        12.72        18.64        14.79        12.43 
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        13.68        43.59        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       43.36        41.16        42.02        44.65        62.27        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.16        49.22        21.86        16.11        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 

  AMPD1 MUTATED AMPD1 WILD-TYPE 
           9.07            0.07 
  AMPD1 MUTATED AMPD1 WILD-TYPE 
          29.00          210.97 
  AMPD1 MUTATED AMPD1 WILD-TYPE 
         15.565          18.740 
[1] "9.1 - 29.0 (15.6)"  "0.1 - 211.0 (18.7)"
[1] "hr=" "1.7"
D59V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMPD1 MUTATED         0        1         0         4         0
  AMPD1 WILD-TYPE      25       75        77       244        11
D59V3, multiclass
           clus
vv          AMPD1 MUTATED AMPD1 WILD-TYPE
  STAGE I               0              25
  STAGE II              1              75
  STAGE III             0              77
  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
  AMPD1 MUTATED       0   1   1   3
  AMPD1 WILD-TYPE    48 130  97 165
D59V4, multiclass
       clus
vv      AMPD1 MUTATED AMPD1 WILD-TYPE
  T0+T1             0              48
  T2                1             130
  T3                1              97
  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
  AMPD1 MUTATED     2   0   2   0
  AMPD1 WILD-TYPE 172  65 159   7
D59V5, multiclass
    clus
vv   AMPD1 MUTATED AMPD1 WILD-TYPE
  N0             2             172
  N1             0              65
  N2             2             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"
D59V6, binary
                 cls
clus                0   1
  AMPD1 MUTATED     2   4
  AMPD1 WILD-TYPE 137 363
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD1 MUTATED      2    4
  AMPD1 WILD-TYPE  137  363
        clus
vv       AMPD1 MUTATED AMPD1 WILD-TYPE
  FEMALE             2             137
  MALE               4             363
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMPD1 MUTATED                                       6
  AMPD1 WILD-TYPE                                   492
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMPD1 MUTATED                                                             0
  AMPD1 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMPD1 MUTATED                                                     0
  AMPD1 WILD-TYPE                                                   7
D59V7, multiclass
                                                             clus
vv                                                            AMPD1 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                                                            AMPD1 WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   492
  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"
D59V8, binary
                 cls
clus                0   1
  AMPD1 MUTATED     1   5
  AMPD1 WILD-TYPE  82 418
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD1 MUTATED      1    5
  AMPD1 WILD-TYPE   82  418
     clus
vv    AMPD1 MUTATED AMPD1 WILD-TYPE
  NO              1              82
  YES             5             418
[1] 2 2
[1] FALSE
D59V9, continuous
D59V10, continuous
D59V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMPD1 MUTATED                                  0     0
  AMPD1 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AMPD1 MUTATED                           0     6
  AMPD1 WILD-TYPE                        36   435
D59V12, multiclass
                                  clus
vv                                 AMPD1 MUTATED AMPD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              36
  WHITE                                        6             435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V13, binary
                 cls
clus                0   1
  AMPD1 MUTATED     0   6
  AMPD1 WILD-TYPE  25 439
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD1 MUTATED      0    6
  AMPD1 WILD-TYPE   25  439
                        clus
vv                       AMPD1 MUTATED AMPD1 WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO             6             439
[1] 2 2
[1] FALSE

Clustering(60) Variable = ZMYM1 MUTATION ANALYSIS
D60V1, survival
                 sevent
clus2               0   1
  ZMYM1 MUTATED     2   7
  ZMYM1 WILD-TYPE 301 194
  ZMYM1 MUTATED ZMYM1 WILD-TYPE 
              9             495 
  ZMYM1 MUTATED ZMYM1 WILD-TYPE 
              7             194 
$`ZMYM1 MUTATED`
TCGA-BA-4078 TCGA-CN-6011 TCGA-CQ-5332 TCGA-CR-6481 TCGA-CR-7371 TCGA-CV-7104 
        9.07        30.67        10.42        10.22         3.09        12.92 
TCGA-CV-A45Q TCGA-P3-A6T4 TCGA-QK-A6II 
      169.38         2.04         9.34 

$`ZMYM1 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        53.79 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       57.44        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         7.76        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        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       37.84        12.89        26.86        32.65        21.11        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       35.54        55.27         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        22.45        56.94        20.71 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        14.56        17.59        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        17.29        15.91        11.44         5.75 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.69         6.18        48.20        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        46.75        45.80        45.99        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        34.75 
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 
       51.29        33.11        16.73        43.04        41.88        28.83 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       64.11        44.48        11.61        23.24        29.36        32.81 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       25.81        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        11.51        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-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.45        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        31.10        29.85 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       29.52        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        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       126.08 
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-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-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        24.99 
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        22.03         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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       15.88         7.63        14.30        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        35.54        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        18.90        25.48        20.45         9.83        12.13 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       12.10        10.65        11.18        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        19.23        18.94        12.62         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-7917 
       21.11         6.77         0.07         0.16        25.74         1.22 
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        12.76 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        19.33        11.84        13.55         0.07        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
        5.29        11.54        11.84        13.35        18.15        12.43 
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 
        3.68        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 
       56.75        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-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ 
       21.07        11.74        17.65         7.30        16.70        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       18.64        14.79        12.43        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        13.68 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       43.59        54.67         2.83        43.36        41.16        42.02 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        62.27        17.95        24.16        49.22        21.86 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       16.11        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 

  ZMYM1 MUTATED ZMYM1 WILD-TYPE 
           2.04            0.07 
  ZMYM1 MUTATED ZMYM1 WILD-TYPE 
         169.38          210.97 
  ZMYM1 MUTATED ZMYM1 WILD-TYPE 
          10.22           18.84 
[1] "2.0 - 169.4 (10.2)" "0.1 - 211.0 (18.8)"
[1] "hr=" "2.1"
D60V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  ZMYM1 MUTATED         0        0         2         4         0
  ZMYM1 WILD-TYPE      25       76        75       244        11
D60V3, multiclass
           clus
vv          ZMYM1 MUTATED ZMYM1 WILD-TYPE
  STAGE I               0              25
  STAGE II              0              76
  STAGE III             2              75
  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
  ZMYM1 MUTATED       0   1   2   3
  ZMYM1 WILD-TYPE    48 130  96 165
D60V4, multiclass
       clus
vv      ZMYM1 MUTATED ZMYM1 WILD-TYPE
  T0+T1             0              48
  T2                1             130
  T3                2              96
  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
  ZMYM1 MUTATED     2   2   2   0
  ZMYM1 WILD-TYPE 172  63 159   7
D60V5, multiclass
    clus
vv   ZMYM1 MUTATED ZMYM1 WILD-TYPE
  N0             2             172
  N1             2              63
  N2             2             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"
D60V6, binary
                 cls
clus                0   1
  ZMYM1 MUTATED     3   6
  ZMYM1 WILD-TYPE 136 361
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM1 MUTATED      3    6
  ZMYM1 WILD-TYPE  136  361
        clus
vv       ZMYM1 MUTATED ZMYM1 WILD-TYPE
  FEMALE             3             136
  MALE               6             361
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  ZMYM1 MUTATED                                       9
  ZMYM1 WILD-TYPE                                   489
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  ZMYM1 MUTATED                                                             0
  ZMYM1 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  ZMYM1 MUTATED                                                     0
  ZMYM1 WILD-TYPE                                                   7
D60V7, multiclass
                                                             clus
vv                                                            ZMYM1 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                                                            ZMYM1 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"
D60V8, binary
                 cls
clus                0   1
  ZMYM1 MUTATED     2   7
  ZMYM1 WILD-TYPE  81 416
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM1 MUTATED      2    7
  ZMYM1 WILD-TYPE   81  416
     clus
vv    ZMYM1 MUTATED ZMYM1 WILD-TYPE
  NO              2              81
  YES             7             416
[1] 2 2
[1] FALSE
D60V9, continuous
D60V10, continuous
D60V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZMYM1 MUTATED                                  0     0
  ZMYM1 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZMYM1 MUTATED                           0     9
  ZMYM1 WILD-TYPE                        36   432
D60V12, multiclass
                                  clus
vv                                 ZMYM1 MUTATED ZMYM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              36
  WHITE                                        9             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"
D60V13, binary
                 cls
clus                0   1
  ZMYM1 MUTATED     0   9
  ZMYM1 WILD-TYPE  25 436
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM1 MUTATED      0    9
  ZMYM1 WILD-TYPE   25  436
                        clus
vv                       ZMYM1 MUTATED ZMYM1 WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO             9             436
[1] 2 2
[1] FALSE

Clustering(61) Variable = LCP1 MUTATION ANALYSIS
D61V1, survival
                sevent
clus2              0   1
  LCP1 MUTATED     8   7
  LCP1 WILD-TYPE 295 194
  LCP1 MUTATED LCP1 WILD-TYPE 
            15            489 
  LCP1 MUTATED LCP1 WILD-TYPE 
             7            194 
$`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        11.44        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        10.65        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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       40.44        37.84        12.89        26.86        32.65        21.11 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       24.92        41.10        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        33.11        34.36         8.58        12.39        35.54 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       55.27         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        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       11.74        14.56        17.59        12.85        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
        7.40        17.29        15.91         5.75         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
        2.70        10.09         7.33         9.80         7.69         6.18 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        39.68        21.50         2.93        54.58        46.75 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       45.80        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        34.75        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        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       33.11        16.73        43.04        41.88        28.83        64.11 
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        32.81        25.81 
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        11.51        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        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       29.85        29.52        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        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       126.08 
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        24.99       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        22.03 
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-D6-6517 
       10.42        10.55        18.84        34.36        13.25         9.60 
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-A6EO TCGA-D6-A6EP 
       17.72        12.36        15.88         7.63        14.30        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5631 
       12.10        12.79        11.11        58.45        35.54        18.02 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       14.04        18.90        25.48        20.45         9.83        12.13 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       12.10        11.18        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 
       19.23        18.94        12.62         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-7917 TCGA-HD-8224 
        6.77         0.07         0.16        25.74         1.22        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        12.76        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       19.33        11.84        13.55         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       11.54        11.84        13.35        18.15        12.43        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         3.68 
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        56.75 
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 
       11.74        17.65         7.30        16.70         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       18.64        14.79        12.43        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        13.68 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       43.59        54.67         2.83        43.36        41.16        42.02 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        62.27        17.95        24.16        49.22        21.86 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       16.11        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 
         25.41          18.35 
[1] "0.5 - 156.5 (25.4)" "0.1 - 211.0 (18.4)"
[1] "hr=" "1.1"
D61V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  LCP1 MUTATED         2        3         1         5         0
  LCP1 WILD-TYPE      23       73        76       243        11
D61V3, multiclass
           clus
vv          LCP1 MUTATED LCP1 WILD-TYPE
  STAGE I              2             23
  STAGE II             3             73
  STAGE III            1             76
  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    44 127  97 165
D61V4, multiclass
       clus
vv      LCP1 MUTATED LCP1 WILD-TYPE
  T0+T1            4             44
  T2               4            127
  T3               1             97
  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 170  64 157   7
D61V5, multiclass
    clus
vv   LCP1 MUTATED LCP1 WILD-TYPE
  N0            4            170
  N1            1             64
  N2            4            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"
D61V6, binary
                cls
clus               0   1
  LCP1 MUTATED     4  11
  LCP1 WILD-TYPE 135 356
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCP1 MUTATED      4   11
  LCP1 WILD-TYPE  135  356
        clus
vv       LCP1 MUTATED LCP1 WILD-TYPE
  FEMALE            4            135
  MALE             11            356
[1] 2 2
[1] FALSE
                vv
clus             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  LCP1 MUTATED                                      15
  LCP1 WILD-TYPE                                   483
                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
D61V7, 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                                  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"
D61V8, binary
                cls
clus               0   1
  LCP1 MUTATED     4  11
  LCP1 WILD-TYPE  79 412
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCP1 MUTATED      4   11
  LCP1 WILD-TYPE   79  412
     clus
vv    LCP1 MUTATED LCP1 WILD-TYPE
  NO             4             79
  YES           11            412
[1] 2 2
[1] FALSE
D61V9, continuous
D61V10, continuous
D61V11, 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                        36   428
D61V12, multiclass
                                  clus
vv                                 LCP1 MUTATED LCP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             36
  WHITE                                      13            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"
D61V13, binary
                cls
clus               0   1
  LCP1 MUTATED     1  14
  LCP1 WILD-TYPE  24 431
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCP1 MUTATED      1   14
  LCP1 WILD-TYPE   24  431
                        clus
vv                       LCP1 MUTATED LCP1 WILD-TYPE
  HISPANIC OR LATINO                1             24
  NOT HISPANIC OR LATINO           14            431
[1] 2 2
[1] FALSE

Clustering(62) Variable = SLC9A6 MUTATION ANALYSIS
D62V1, survival
                  sevent
clus2                0   1
  SLC9A6 MUTATED     1   4
  SLC9A6 WILD-TYPE 302 197
  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
               5              499 
  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
               4              197 
$`SLC9A6 MUTATED`
TCGA-CN-4742 TCGA-CV-6952 TCGA-CV-7438 TCGA-IQ-A61J TCGA-P3-A6T7 
       13.05         6.08         6.38        14.47        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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       40.44        37.84        12.89        26.86        32.65        21.11 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       24.92        41.10        12.99        20.55        14.33        43.73 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       27.58        41.69        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       35.54        55.27         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        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        20.68        20.65        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       14.20         6.74         9.07         9.24        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        46.75        45.80        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        34.75        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        51.29        33.11        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        28.83        64.11        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        32.81        25.81        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        11.51        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        31.10        29.85        29.52        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        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        7.07        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-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       126.08        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        24.99       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        22.03 
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        15.88         7.63 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       14.30        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 
       35.54        30.94        33.86        18.02        14.04        18.90 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       25.48        20.45         9.83        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       11.18        37.18        21.63        20.25         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        12.62         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         6.77 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        0.07         0.16        25.74         1.22        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        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       11.84        13.55         0.07         5.29        11.54        11.84 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        12.43        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         3.68        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        56.75        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        11.74        17.65 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        16.70         9.34        12.72        18.64        14.79 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       12.43        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        13.68        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        43.36        41.16        42.02        44.65        62.27 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.16        49.22        21.86        16.11        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 
           16.01           210.97 
  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
           13.05            18.84 
[1] "6.1 - 16.0 (13.1)"  "0.1 - 211.0 (18.8)"
[1] "hr=" "4.3"
D62V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  SLC9A6 MUTATED         1        0         0         4         0
  SLC9A6 WILD-TYPE      24       76        77       244        11
D62V3, multiclass
           clus
vv          SLC9A6 MUTATED SLC9A6 WILD-TYPE
  STAGE I                1               24
  STAGE II               0               76
  STAGE III              0               77
  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    47 130  96 167
D62V4, multiclass
       clus
vv      SLC9A6 MUTATED SLC9A6 WILD-TYPE
  T0+T1              1               47
  T2                 1              130
  T3                 2               96
  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 174  65 157   7
D62V5, multiclass
    clus
vv   SLC9A6 MUTATED SLC9A6 WILD-TYPE
  N0              0              174
  N1              0               65
  N2              4              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"
D62V6, binary
                  cls
clus                 0   1
  SLC9A6 MUTATED     3   2
  SLC9A6 WILD-TYPE 136 365
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A6 MUTATED      3    2
  SLC9A6 WILD-TYPE  136  365
        clus
vv       SLC9A6 MUTATED SLC9A6 WILD-TYPE
  FEMALE              3              136
  MALE                2              365
[1] 2 2
[1] FALSE
                  vv
clus               HEAD AND NECK SQUAMOUS CELL CARCINOMA
  SLC9A6 MUTATED                                       5
  SLC9A6 WILD-TYPE                                   493
                  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
D62V7, 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                                    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"
D62V8, binary
                  cls
clus                 0   1
  SLC9A6 MUTATED     1   4
  SLC9A6 WILD-TYPE  82 419
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A6 MUTATED      1    4
  SLC9A6 WILD-TYPE   82  419
     clus
vv    SLC9A6 MUTATED SLC9A6 WILD-TYPE
  NO               1               82
  YES              4              419
[1] 2 2
[1] FALSE
D62V9, continuous
D62V10, continuous
[1] "Remove cluster labels:" "SLC9A6 MUTATED"        
clus
  SLC9A6 MUTATED SLC9A6 WILD-TYPE 
               2              270 
      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-6941 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-6943       TCGA-CV-6945       TCGA-CV-6954       TCGA-CV-6960 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-6961       TCGA-CV-7091       TCGA-CV-7095       TCGA-CV-7097 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7099       TCGA-CV-7100       TCGA-CV-7101       TCGA-CV-7102 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7180       TCGA-CV-7183       TCGA-CV-7235       TCGA-CV-7242 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7245       TCGA-CV-7248       TCGA-CV-7250       TCGA-CV-7254 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7261       TCGA-CV-7406       TCGA-CV-7410       TCGA-CV-7418 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7422       TCGA-CV-7424       TCGA-CV-7427       TCGA-CV-7430 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7432       TCGA-CV-7433       TCGA-CV-7434       TCGA-CV-7435 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-7440       TCGA-CV-7446       TCGA-CV-7568       TCGA-CV-A45Q 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-A45Y       TCGA-CV-A45Z       TCGA-CV-A460       TCGA-CV-A461 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-A464       TCGA-CV-A468       TCGA-CV-A6JD       TCGA-CV-A6JE 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-A6JN       TCGA-CV-A6JO       TCGA-CV-A6JU       TCGA-CV-A6JY 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CV-A6JZ       TCGA-CV-A6K1       TCGA-CV-A6K2       TCGA-CX-7086 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-CX-7219       TCGA-D6-6516       TCGA-D6-6517       TCGA-D6-6823 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-D6-6824       TCGA-D6-6825       TCGA-D6-6827       TCGA-D6-8568 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-D6-8569       TCGA-D6-A4Z9       TCGA-D6-A4ZB       TCGA-D6-A6EK 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-D6-A6EP       TCGA-D6-A74Q       TCGA-DQ-5625       TCGA-DQ-5629 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-DQ-5630       TCGA-DQ-5631       TCGA-DQ-7588       TCGA-DQ-7589 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-DQ-7590       TCGA-DQ-7591       TCGA-DQ-7592       TCGA-DQ-7593 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-DQ-7595       TCGA-F7-7848       TCGA-F7-8489       TCGA-F7-A50G 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-F7-A50I       TCGA-F7-A50J       TCGA-F7-A61S       TCGA-F7-A61V 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-F7-A61W       TCGA-F7-A620       TCGA-F7-A623       TCGA-H7-7774 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-H7-A6C4       TCGA-H7-A6C5       TCGA-H7-A76A       TCGA-HD-8634 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-HD-8635       TCGA-HD-A634       TCGA-HD-A6I0       TCGA-HL-7533 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-IQ-7631       TCGA-IQ-7632       TCGA-IQ-A61E       TCGA-IQ-A61G 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-KU-A66S       TCGA-KU-A6H7       TCGA-KU-A6H8       TCGA-MT-A51W 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-MT-A51X       TCGA-MT-A67D       TCGA-MZ-A6I9       TCGA-MZ-A7D7 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-P3-A6SX       TCGA-P3-A6T0       TCGA-P3-A6T4       TCGA-P3-A6T8 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-QK-A6IG       TCGA-QK-A6II       TCGA-QK-A6IJ       TCGA-RS-A6TP 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-TN-A7HI       TCGA-TN-A7HL       TCGA-UF-A718       TCGA-UF-A71B 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-UF-A71D       TCGA-UF-A7J9       TCGA-UF-A7JC       TCGA-UF-A7JD 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-UF-A7JF       TCGA-UF-A7JH       TCGA-UF-A7JJ       TCGA-UF-A7JS 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
      TCGA-WA-A7GZ       TCGA-WA-A7H4 
"SLC9A6 WILD-TYPE" "SLC9A6 WILD-TYPE" 
D62V11, 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                        36   436
D62V12, multiclass
                                  clus
vv                                 SLC9A6 MUTATED SLC9A6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               36
  WHITE                                         5              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"
D62V13, binary
                  cls
clus                 0   1
  SLC9A6 MUTATED     0   5
  SLC9A6 WILD-TYPE  25 440
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A6 MUTATED      0    5
  SLC9A6 WILD-TYPE   25  440
                        clus
vv                       SLC9A6 MUTATED SLC9A6 WILD-TYPE
  HISPANIC OR LATINO                  0               25
  NOT HISPANIC OR LATINO              5              440
[1] 2 2
[1] FALSE

Clustering(63) Variable = CCNG2 MUTATION ANALYSIS
D63V1, survival
                 sevent
clus2               0   1
  CCNG2 MUTATED     2   1
  CCNG2 WILD-TYPE 301 200
  CCNG2 MUTATED CCNG2 WILD-TYPE 
              3             501 
  CCNG2 MUTATED CCNG2 WILD-TYPE 
              1             200 
$`CCNG2 MUTATED`
TCGA-BA-4077 TCGA-CQ-A4C6 TCGA-CX-7086 
       37.28        44.48        18.84 

$`CCNG2 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-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        53.79 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       57.44        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         7.76        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        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       37.84        12.89        26.86        32.65        21.11        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       35.54        55.27         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        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        20.68        20.65        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       14.20         6.74         9.07         9.24        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        46.75        45.80        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        34.75        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        51.29        33.11        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        28.83        64.11        11.61        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       32.81        25.81        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 
       11.51        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        31.10        29.85        29.52        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        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       126.08        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-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        24.99       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 
       22.03         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.42        10.55        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        15.88         7.63 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       14.30        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 
       35.54        30.94        33.86        18.02        14.04        18.90 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       25.48        20.45         9.83        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       11.18        37.18        21.63        20.25         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        12.62         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         6.77 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        0.07         0.16        25.74         1.22        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        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        13.55         0.07        14.47         5.29        11.54 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       11.84        13.35        18.15        12.43        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         3.68        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        56.75        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 
       11.74        17.65         7.30        16.70         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       18.64        14.79        12.43        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        13.68 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       43.59        54.67         2.83        43.36        41.16        42.02 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        62.27        17.95        24.16        49.22        21.86 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       16.11        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 

  CCNG2 MUTATED CCNG2 WILD-TYPE 
          18.84            0.07 
  CCNG2 MUTATED CCNG2 WILD-TYPE 
          44.48          210.97 
  CCNG2 MUTATED CCNG2 WILD-TYPE 
          37.28           18.54 
[1] "18.8 - 44.5 (37.3)" "0.1 - 211.0 (18.5)"
[1] "hr=" "1.5"
D63V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  CCNG2 MUTATED         0        1         1         1         0
  CCNG2 WILD-TYPE      25       75        76       247        11
D63V3, multiclass
           clus
vv          CCNG2 MUTATED CCNG2 WILD-TYPE
  STAGE I               0              25
  STAGE II              1              75
  STAGE III             1              76
  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
  CCNG2 MUTATED       0   1   1   1
  CCNG2 WILD-TYPE    48 130  97 167
D63V4, multiclass
       clus
vv      CCNG2 MUTATED CCNG2 WILD-TYPE
  T0+T1             0              48
  T2                1             130
  T3                1              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
  CCNG2 MUTATED     2   1   0   0
  CCNG2 WILD-TYPE 172  64 161   7
D63V5, multiclass
    clus
vv   CCNG2 MUTATED CCNG2 WILD-TYPE
  N0             2             172
  N1             1              64
  N2             0             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"
D63V6, binary
                 cls
clus                0   1
  CCNG2 MUTATED     1   2
  CCNG2 WILD-TYPE 138 365
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCNG2 MUTATED      1    2
  CCNG2 WILD-TYPE  138  365
        clus
vv       CCNG2 MUTATED CCNG2 WILD-TYPE
  FEMALE             1             138
  MALE               2             365
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  CCNG2 MUTATED                                       3
  CCNG2 WILD-TYPE                                   495
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  CCNG2 MUTATED                                                             0
  CCNG2 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  CCNG2 MUTATED                                                     0
  CCNG2 WILD-TYPE                                                   7
D63V7, multiclass
                                                             clus
vv                                                            CCNG2 MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   3
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
                                                             clus
vv                                                            CCNG2 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"
D63V8, binary
                 cls
clus                0   1
  CCNG2 MUTATED     0   3
  CCNG2 WILD-TYPE  83 420
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCNG2 MUTATED      0    3
  CCNG2 WILD-TYPE   83  420
     clus
vv    CCNG2 MUTATED CCNG2 WILD-TYPE
  NO              0              83
  YES             3             420
[1] 2 2
[1] FALSE
D63V9, continuous
D63V10, continuous
D63V11, continuous
[1] "Remove cluster labels:" "CCNG2 MUTATED"         
clus
  CCNG2 MUTATED CCNG2 WILD-TYPE 
              2             394 
     TCGA-BA-4074      TCGA-BA-4075      TCGA-BA-4078      TCGA-BA-5149 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-BA-5151      TCGA-BA-5152      TCGA-BA-5555      TCGA-BA-5556 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-BA-5557      TCGA-BA-5558      TCGA-BA-5559      TCGA-BA-6869 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-BA-6872      TCGA-BA-6873      TCGA-BA-7269      TCGA-BA-A4IG 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-BA-A4IH      TCGA-BA-A4II      TCGA-BA-A6D8      TCGA-BA-A6DA 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-BA-A6DB      TCGA-BA-A6DD      TCGA-BA-A6DE      TCGA-BA-A6DF 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-BA-A6DJ      TCGA-BB-7861      TCGA-BB-7862      TCGA-BB-7863 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-BB-7864      TCGA-BB-7870      TCGA-BB-7871      TCGA-BB-7872 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-BB-8601      TCGA-BB-A5HU      TCGA-BB-A5HY      TCGA-BB-A5HZ 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-C9-A47Z      TCGA-CN-4723      TCGA-CN-4725      TCGA-CN-4726 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CN-4727      TCGA-CN-4728      TCGA-CN-4729      TCGA-CN-4730 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CN-4731      TCGA-CN-4733      TCGA-CN-4734      TCGA-CN-4735 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CN-4737      TCGA-CN-4738      TCGA-CN-4739      TCGA-CN-4740 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CN-4741      TCGA-CN-4742      TCGA-CN-5355      TCGA-CN-5356 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CN-5358      TCGA-CN-5359      TCGA-CN-5360      TCGA-CN-5361 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CN-5363      TCGA-CN-5364      TCGA-CN-5365      TCGA-CN-5366 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CN-5367      TCGA-CN-5369      TCGA-CN-5370      TCGA-CN-5373 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CN-6010      TCGA-CN-6011      TCGA-CN-6012      TCGA-CN-6013 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CN-6016      TCGA-CN-6017      TCGA-CN-6018      TCGA-CN-6019 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CN-6020      TCGA-CN-6022      TCGA-CN-6023      TCGA-CN-6024 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CN-6988      TCGA-CN-6989      TCGA-CN-6992      TCGA-CN-6994 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CN-6995      TCGA-CN-6996      TCGA-CN-6997      TCGA-CN-6998 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CN-A497      TCGA-CN-A498      TCGA-CN-A499      TCGA-CN-A49A 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CN-A49B      TCGA-CN-A63T      TCGA-CN-A63U      TCGA-CN-A63V 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CN-A63W      TCGA-CN-A63Y      TCGA-CN-A640      TCGA-CN-A641 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CN-A642      TCGA-CN-A6UY      TCGA-CN-A6V1      TCGA-CN-A6V3 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CN-A6V6      TCGA-CQ-5323      TCGA-CQ-5324      TCGA-CQ-5325 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CQ-5326      TCGA-CQ-5327      TCGA-CQ-5329      TCGA-CQ-5330 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CQ-5332      TCGA-CQ-5333      TCGA-CQ-5334      TCGA-CQ-6218 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CQ-6219      TCGA-CQ-6220      TCGA-CQ-6222      TCGA-CQ-6223 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CQ-6224      TCGA-CQ-6225      TCGA-CQ-6227      TCGA-CQ-6228 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CQ-6229      TCGA-CQ-7064      TCGA-CQ-7065      TCGA-CQ-7067 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CQ-7068      TCGA-CQ-7069      TCGA-CQ-7071      TCGA-CQ-7072 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CQ-A4C7      TCGA-CQ-A4C9      TCGA-CQ-A4CB      TCGA-CQ-A4CD 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CQ-A4CE      TCGA-CQ-A4CG      TCGA-CQ-A4CH      TCGA-CQ-A4CI 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CR-6467      TCGA-CR-6470      TCGA-CR-6471      TCGA-CR-6474 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CR-6484      TCGA-CR-6488      TCGA-CR-6491      TCGA-CR-6492 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CR-6493      TCGA-CR-7364      TCGA-CR-7365      TCGA-CR-7367 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CR-7368      TCGA-CR-7369      TCGA-CR-7371      TCGA-CR-7372 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CR-7373      TCGA-CR-7376      TCGA-CR-7377      TCGA-CR-7379 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CR-7380      TCGA-CR-7382      TCGA-CR-7383      TCGA-CR-7386 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CR-7390      TCGA-CR-7391      TCGA-CR-7392      TCGA-CR-7393 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CR-7394      TCGA-CR-7397      TCGA-CR-7398      TCGA-CR-7399 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CR-7401      TCGA-CV-5430      TCGA-CV-5431      TCGA-CV-5432 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-5434      TCGA-CV-5435      TCGA-CV-5436      TCGA-CV-5439 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-5440      TCGA-CV-5441      TCGA-CV-5442      TCGA-CV-5443 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-5444      TCGA-CV-5966      TCGA-CV-5970      TCGA-CV-5971 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-5973      TCGA-CV-5976      TCGA-CV-5977      TCGA-CV-5978 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-5979      TCGA-CV-6003      TCGA-CV-6433      TCGA-CV-6436 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-6441      TCGA-CV-6933      TCGA-CV-6934      TCGA-CV-6935 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-6936      TCGA-CV-6939      TCGA-CV-6940      TCGA-CV-6941 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-6945      TCGA-CV-6948      TCGA-CV-6950      TCGA-CV-6951 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-6952      TCGA-CV-6953      TCGA-CV-6954      TCGA-CV-6956 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-6959      TCGA-CV-6960      TCGA-CV-7089      TCGA-CV-7091 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-7095      TCGA-CV-7101      TCGA-CV-7102      TCGA-CV-7103 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-7104      TCGA-CV-7178      TCGA-CV-7180      TCGA-CV-7183 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-7236      TCGA-CV-7242      TCGA-CV-7243      TCGA-CV-7245 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-7248      TCGA-CV-7252      TCGA-CV-7254      TCGA-CV-7261 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-7406      TCGA-CV-7409      TCGA-CV-7410      TCGA-CV-7411 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-7414      TCGA-CV-7415      TCGA-CV-7418      TCGA-CV-7421 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-7422      TCGA-CV-7424      TCGA-CV-7429      TCGA-CV-7430 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-7432      TCGA-CV-7433      TCGA-CV-7434      TCGA-CV-7435 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-7446      TCGA-CV-A45O      TCGA-CV-A45P      TCGA-CV-A45Q 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-A45R      TCGA-CV-A45T      TCGA-CV-A45U      TCGA-CV-A45W 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-A45X      TCGA-CV-A45Y      TCGA-CV-A45Z      TCGA-CV-A460 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-A461      TCGA-CV-A463      TCGA-CV-A464      TCGA-CV-A465 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-A468      TCGA-CV-A6JD      TCGA-CV-A6JE      TCGA-CV-A6JM 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-A6JN      TCGA-CV-A6JO      TCGA-CV-A6JT      TCGA-CV-A6JU 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-A6JY      TCGA-CV-A6JZ      TCGA-CV-A6K0      TCGA-CV-A6K1 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-CV-A6K2      TCGA-CX-7082      TCGA-CX-7085      TCGA-CX-7219 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-D6-6516      TCGA-D6-6517      TCGA-D6-6823      TCGA-D6-6825 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-D6-6826      TCGA-D6-8568      TCGA-D6-8569      TCGA-D6-A4Z9 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-D6-A4ZB      TCGA-D6-A6EK      TCGA-D6-A6EM      TCGA-D6-A6EO 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-D6-A6EP      TCGA-D6-A6EQ      TCGA-D6-A6ES      TCGA-D6-A74Q 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-DQ-5624      TCGA-DQ-5625      TCGA-DQ-5629      TCGA-DQ-5630 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-DQ-5631      TCGA-DQ-7588      TCGA-DQ-7592      TCGA-F7-7848 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-F7-A50G      TCGA-F7-A50J      TCGA-F7-A61S      TCGA-F7-A61V 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-F7-A61W      TCGA-F7-A620      TCGA-F7-A623      TCGA-H7-7774 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-H7-8501      TCGA-H7-A6C4      TCGA-H7-A6C5      TCGA-H7-A76A 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-HD-7754      TCGA-HD-7831      TCGA-HD-7832      TCGA-HD-7917 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-HD-8224      TCGA-HD-8314      TCGA-HD-8634      TCGA-HD-8635 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-HD-A4C1      TCGA-HD-A633      TCGA-HD-A634      TCGA-HD-A6HZ 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-HD-A6I0      TCGA-IQ-7630      TCGA-IQ-7631      TCGA-IQ-7632 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-IQ-A61E      TCGA-IQ-A61G      TCGA-IQ-A61H      TCGA-IQ-A61I 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-IQ-A61J      TCGA-IQ-A61K      TCGA-IQ-A61L      TCGA-IQ-A61O 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-KU-A66S      TCGA-KU-A66T      TCGA-KU-A6H7      TCGA-KU-A6H8 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-MT-A51X      TCGA-MT-A67A      TCGA-MT-A67D      TCGA-MT-A67F 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-MT-A67G      TCGA-MZ-A7D7      TCGA-P3-A5Q6      TCGA-P3-A5QE 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-P3-A5QF      TCGA-P3-A6SX      TCGA-P3-A6T0      TCGA-P3-A6T2 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-P3-A6T3      TCGA-P3-A6T4      TCGA-P3-A6T5      TCGA-P3-A6T7 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-P3-A6T8      TCGA-QK-A652      TCGA-QK-A6IG      TCGA-QK-A6IH 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-QK-A6II      TCGA-QK-A6IJ      TCGA-QK-A6VB      TCGA-QK-A6VC 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-RS-A6TO      TCGA-T2-A6WX      TCGA-T2-A6WZ      TCGA-T2-A6X0 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-TN-A7HI      TCGA-TN-A7HJ      TCGA-TN-A7HL      TCGA-UF-A718 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-UF-A719      TCGA-UF-A71A      TCGA-UF-A71B      TCGA-UF-A71D 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-UF-A71E      TCGA-UF-A7J9      TCGA-UF-A7JA      TCGA-UF-A7JC 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-UF-A7JD      TCGA-UF-A7JF      TCGA-UF-A7JH      TCGA-UF-A7JJ 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-UF-A7JK      TCGA-UF-A7JO      TCGA-UF-A7JS      TCGA-UF-A7JT 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
     TCGA-UF-A7JV      TCGA-UP-A6WW 
"CCNG2 WILD-TYPE" "CCNG2 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCNG2 MUTATED                                  0     1
  CCNG2 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CCNG2 MUTATED                           1     1
  CCNG2 WILD-TYPE                        35   440
D63V12, multiclass
                                  clus
vv                                 CCNG2 MUTATED CCNG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              35
  WHITE                                        1             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"
D63V13, binary
                 cls
clus                0   1
  CCNG2 MUTATED     0   3
  CCNG2 WILD-TYPE  25 442
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCNG2 MUTATED      0    3
  CCNG2 WILD-TYPE   25  442
                        clus
vv                       CCNG2 MUTATED CCNG2 WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO             3             442
[1] 2 2
[1] FALSE

Clustering(64) Variable = TACR2 MUTATION ANALYSIS
D64V1, survival
                 sevent
clus2               0   1
  TACR2 MUTATED     4   0
  TACR2 WILD-TYPE 299 201
  TACR2 MUTATED TACR2 WILD-TYPE 
              4             500 
  TACR2 MUTATED TACR2 WILD-TYPE 
              0             201 
$`TACR2 MUTATED`
TCGA-BB-7870 TCGA-CN-6016 TCGA-D6-6517 TCGA-F7-A624 
       66.28        19.53         9.60        12.43 

$`TACR2 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 
       53.79        57.44        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         7.76        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 
       94.62         9.14         4.60         4.41        18.35        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        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 
       37.84        12.89        26.86        32.65        21.11        24.92 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       35.54        55.27         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        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       30.67        20.68        20.65        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        14.56        17.59        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        17.29        15.91        11.44         5.75 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.69         6.18        48.20        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        46.75        45.80        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 
       34.75        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        51.29        33.11        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       28.83        64.11        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 
       32.81        25.81        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 
       11.51        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        31.10        29.85        29.52        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        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       126.08        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-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        24.99       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 
       22.03         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-D6-6515 
       10.42        10.42        10.55        18.84        34.36        13.25 
TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
       25.41        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        15.88         7.63 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       14.30        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 
       35.54        30.94        33.86        18.02        14.04        18.90 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       25.48        20.45         9.83        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       11.18        37.18        21.63        20.25         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        12.62         0.46        17.85        11.80        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         6.77         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
        0.16        25.74         1.22        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        12.76        14.50        19.33        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       13.55         0.07        14.47         5.29        11.54        11.84 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        12.43        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         3.68        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        56.75        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        11.74 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       17.65         7.30        16.70         9.34        12.72        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       14.79        12.43        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        13.68        43.59 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        43.36        41.16        42.02        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       62.27        17.95        24.16        49.22        21.86        16.11 
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 

  TACR2 MUTATED TACR2 WILD-TYPE 
           9.60            0.07 
  TACR2 MUTATED TACR2 WILD-TYPE 
          66.28          210.97 
  TACR2 MUTATED TACR2 WILD-TYPE 
         15.980          18.655 
[1] "9.6 - 66.3 (16.0)"  "0.1 - 211.0 (18.7)"
[1] "hr="     "3300000"
D64V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  TACR2 MUTATED         0        1         1         2         0
  TACR2 WILD-TYPE      25       75        76       246        11
D64V3, multiclass
           clus
vv          TACR2 MUTATED TACR2 WILD-TYPE
  STAGE I               0              25
  STAGE II              1              75
  STAGE III             1              76
  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
  TACR2 MUTATED       0   1   1   2
  TACR2 WILD-TYPE    48 130  97 166
D64V4, multiclass
       clus
vv      TACR2 MUTATED TACR2 WILD-TYPE
  T0+T1             0              48
  T2                1             130
  T3                1              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
  TACR2 MUTATED     2   1   0   0
  TACR2 WILD-TYPE 172  64 161   7
D64V5, multiclass
    clus
vv   TACR2 MUTATED TACR2 WILD-TYPE
  N0             2             172
  N1             1              64
  N2             0             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"
D64V6, binary
                 cls
clus                0   1
  TACR2 MUTATED     0   4
  TACR2 WILD-TYPE 139 363
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TACR2 MUTATED      0    4
  TACR2 WILD-TYPE  139  363
        clus
vv       TACR2 MUTATED TACR2 WILD-TYPE
  FEMALE             0             139
  MALE               4             363
[1] 2 2
[1] FALSE
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  TACR2 MUTATED                                       4
  TACR2 WILD-TYPE                                   494
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  TACR2 MUTATED                                                             0
  TACR2 WILD-TYPE                                                           1
                 vv
clus              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  TACR2 MUTATED                                                     0
  TACR2 WILD-TYPE                                                   7
D64V7, multiclass
                                                             clus
vv                                                            TACR2 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                                                            TACR2 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"
D64V8, binary
                 cls
clus                0   1
  TACR2 MUTATED     1   3
  TACR2 WILD-TYPE  82 420
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TACR2 MUTATED      1    3
  TACR2 WILD-TYPE   82  420
     clus
vv    TACR2 MUTATED TACR2 WILD-TYPE
  NO              1              82
  YES             3             420
[1] 2 2
[1] FALSE
D64V9, continuous
D64V10, continuous
[1] "Remove cluster labels:" "TACR2 MUTATED"         
clus
  TACR2 MUTATED TACR2 WILD-TYPE 
              2             270 
     TCGA-BA-4074      TCGA-BA-4075      TCGA-BA-4076      TCGA-BA-4077 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-BA-4078      TCGA-BA-5149      TCGA-BA-5151      TCGA-BA-5556 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-BA-6868      TCGA-BA-6869      TCGA-BA-6870      TCGA-BA-6871 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-BA-6872      TCGA-BA-6873      TCGA-BA-7269      TCGA-BA-A6DA 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-BA-A6DG      TCGA-BB-4225      TCGA-BB-4228      TCGA-BB-7871 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-BB-8596      TCGA-BB-A5HY      TCGA-BB-A6UM      TCGA-BB-A6UO 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CN-4727      TCGA-CN-4728      TCGA-CN-4730      TCGA-CN-4736 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CN-4738      TCGA-CN-4739      TCGA-CN-4741      TCGA-CN-4742 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CN-5358      TCGA-CN-5359      TCGA-CN-5360      TCGA-CN-5361 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CN-5363      TCGA-CN-5365      TCGA-CN-5366      TCGA-CN-5367 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CN-5370      TCGA-CN-6010      TCGA-CN-6011      TCGA-CN-6012 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CN-6017      TCGA-CN-6021      TCGA-CN-6023      TCGA-CN-6024 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CN-6989      TCGA-CN-6992      TCGA-CN-6994      TCGA-CN-6997 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CN-6998      TCGA-CN-A498      TCGA-CN-A49B      TCGA-CN-A49C 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CN-A63T      TCGA-CN-A63U      TCGA-CN-A63V      TCGA-CN-A641 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CN-A6UY      TCGA-CN-A6V3      TCGA-CN-A6V6      TCGA-CQ-5323 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CQ-5324      TCGA-CQ-5325      TCGA-CQ-5330      TCGA-CQ-5331 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CQ-5333      TCGA-CQ-6218      TCGA-CQ-6219      TCGA-CQ-6221 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CQ-6222      TCGA-CQ-6223      TCGA-CQ-6224      TCGA-CQ-6227 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CQ-6228      TCGA-CQ-7063      TCGA-CQ-7072      TCGA-CQ-A4C6 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CQ-A4C7      TCGA-CQ-A4C9      TCGA-CQ-A4CB      TCGA-CQ-A4CI 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CR-5247      TCGA-CR-5248      TCGA-CR-5250      TCGA-CR-6467 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CR-6471      TCGA-CR-6473      TCGA-CR-6474      TCGA-CR-6477 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CR-6478      TCGA-CR-6482      TCGA-CR-6487      TCGA-CR-6491 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CR-6492      TCGA-CR-6493      TCGA-CR-7364      TCGA-CR-7365 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CR-7367      TCGA-CR-7368      TCGA-CR-7369      TCGA-CR-7370 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CR-7371      TCGA-CR-7373      TCGA-CR-7374      TCGA-CR-7376 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CR-7377      TCGA-CR-7383      TCGA-CR-7385      TCGA-CR-7386 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CR-7388      TCGA-CR-7389      TCGA-CR-7390      TCGA-CR-7391 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CR-7392      TCGA-CR-7394      TCGA-CR-7395      TCGA-CR-7397 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CR-7399      TCGA-CR-7401      TCGA-CR-7402      TCGA-CV-5430 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CV-5431      TCGA-CV-5432      TCGA-CV-5435      TCGA-CV-5436 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CV-5440      TCGA-CV-5443      TCGA-CV-5966      TCGA-CV-5970 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CV-5976      TCGA-CV-6433      TCGA-CV-6436      TCGA-CV-6441 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CV-6934      TCGA-CV-6935      TCGA-CV-6936      TCGA-CV-6941 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CV-6943      TCGA-CV-6945      TCGA-CV-6952      TCGA-CV-6954 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CV-6960      TCGA-CV-6961      TCGA-CV-7091      TCGA-CV-7095 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CV-7097      TCGA-CV-7099      TCGA-CV-7100      TCGA-CV-7101 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CV-7102      TCGA-CV-7180      TCGA-CV-7183      TCGA-CV-7235 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CV-7242      TCGA-CV-7245      TCGA-CV-7248      TCGA-CV-7250 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CV-7254      TCGA-CV-7261      TCGA-CV-7406      TCGA-CV-7410 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CV-7418      TCGA-CV-7422      TCGA-CV-7424      TCGA-CV-7427 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CV-7430      TCGA-CV-7432      TCGA-CV-7433      TCGA-CV-7434 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CV-7435      TCGA-CV-7440      TCGA-CV-7446      TCGA-CV-7568 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CV-A45Q      TCGA-CV-A45Y      TCGA-CV-A45Z      TCGA-CV-A460 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CV-A461      TCGA-CV-A464      TCGA-CV-A468      TCGA-CV-A6JD 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CV-A6JE      TCGA-CV-A6JN      TCGA-CV-A6JO      TCGA-CV-A6JU 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CV-A6JY      TCGA-CV-A6JZ      TCGA-CV-A6K1      TCGA-CV-A6K2 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-CX-7086      TCGA-CX-7219      TCGA-D6-6516      TCGA-D6-6823 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-D6-6824      TCGA-D6-6825      TCGA-D6-6827      TCGA-D6-8568 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-D6-8569      TCGA-D6-A4Z9      TCGA-D6-A4ZB      TCGA-D6-A6EK 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-D6-A6EP      TCGA-D6-A74Q      TCGA-DQ-5625      TCGA-DQ-5629 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-DQ-5630      TCGA-DQ-5631      TCGA-DQ-7588      TCGA-DQ-7589 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-DQ-7590      TCGA-DQ-7591      TCGA-DQ-7592      TCGA-DQ-7593 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-DQ-7595      TCGA-F7-7848      TCGA-F7-8489      TCGA-F7-A50G 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-F7-A50I      TCGA-F7-A50J      TCGA-F7-A61S      TCGA-F7-A61V 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-F7-A61W      TCGA-F7-A620      TCGA-F7-A623      TCGA-H7-7774 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-H7-A6C4      TCGA-H7-A6C5      TCGA-H7-A76A      TCGA-HD-8634 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-HD-8635      TCGA-HD-A634      TCGA-HD-A6I0      TCGA-HL-7533 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-IQ-7631      TCGA-IQ-7632      TCGA-IQ-A61E      TCGA-IQ-A61G 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-KU-A66S      TCGA-KU-A6H7      TCGA-KU-A6H8      TCGA-MT-A51W 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-MT-A51X      TCGA-MT-A67D      TCGA-MZ-A6I9      TCGA-MZ-A7D7 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-P3-A6SX      TCGA-P3-A6T0      TCGA-P3-A6T4      TCGA-P3-A6T8 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-QK-A6IG      TCGA-QK-A6II      TCGA-QK-A6IJ      TCGA-RS-A6TP 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-TN-A7HI      TCGA-TN-A7HL      TCGA-UF-A718      TCGA-UF-A71B 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-UF-A71D      TCGA-UF-A7J9      TCGA-UF-A7JC      TCGA-UF-A7JD 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-UF-A7JF      TCGA-UF-A7JH      TCGA-UF-A7JJ      TCGA-UF-A7JS 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
     TCGA-WA-A7GZ      TCGA-WA-A7H4 
"TACR2 WILD-TYPE" "TACR2 WILD-TYPE" 
D64V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TACR2 MUTATED                                  0     0
  TACR2 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TACR2 MUTATED                           0     4
  TACR2 WILD-TYPE                        36   437
D64V12, multiclass
                                  clus
vv                                 TACR2 MUTATED TACR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              36
  WHITE                                        4             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"
D64V13, binary
                 cls
clus                0   1
  TACR2 MUTATED     0   4
  TACR2 WILD-TYPE  25 441
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TACR2 MUTATED      0    4
  TACR2 WILD-TYPE   25  441
                        clus
vv                       TACR2 MUTATED TACR2 WILD-TYPE
  HISPANIC OR LATINO                 0              25
  NOT HISPANIC OR LATINO             4             441
[1] 2 2
[1] FALSE
