[1] "ofn"        "-oTHNSC-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/HNSC-TP/19775211/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/19781934/transformed.cor.cli.txt"

nPatients in clinical file=528, in cluster file=522, common to both=522
[1]  82 522
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               70               452 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               70               452 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              121               401 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              121               401 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               97               425 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               97               425 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               74               448 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               74               448 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               81               441 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               81               441 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              254               268 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              254               268 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               41               481 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               41               481 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               37               485 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               37               485 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              201               321 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              201               321 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               68               454 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               68               454 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               83               439 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               83               439 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               63               459 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               63               459 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              183               339 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              183               339 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              129               393 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              129               393 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              155               367 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              155               367 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              310               212 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              310               212 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              102               420 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              102               420 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              139               383 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              139               383 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                40                482 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                40                482 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                34                488 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                34                488 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                66                456 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                66                456 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                71                451 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                71                451 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               148                374 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               148                374 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                89                433 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                89                433 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                57                465 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                57                465 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               151                371 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               151                371 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                72                450 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                72                450 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               107                415 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               107                415 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               107                415 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               107                415 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                67                455 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                67                455 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                87                435 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                87                435 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               123                399 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               123                399 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                53                469 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                53                469 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                56                466 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                56                466 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                78                444 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                78                444 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               190                332 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               190                332 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               201                321 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               201                321 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                35                487 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                35                487 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               112                410 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               112                410 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               53               469 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               53               469 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               95               427 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               95               427 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               58               464 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               58               464 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               39               483 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               39               483 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               33               489 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               33               489 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               46               476 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               46               476 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              297               225 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              297               225 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               61               461 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               61               461 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              194               328 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              194               328 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              151               371 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              151               371 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               51               471 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               51               471 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              164               358 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              164               358 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               68               454 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               68               454 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               68               454 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               68               454 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               29               493 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               29               493 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               40               482 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               40               482 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              187               335 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              187               335 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               30               492 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               30               492 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              186               336 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              186               336 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               87               435 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               87               435 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               156                366 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               156                366 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               113                409 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               113                409 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               141                381 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               141                381 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               172                350 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               172                350 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                37                485 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                37                485 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                33                489 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                33                489 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               167                355 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               167                355 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                58                464 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                58                464 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               103                419 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               103                419 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                63                459 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                63                459 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                81                441 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                81                441 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               107                415 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               107                415 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                34                488 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                34                488 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               104                418 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               104                418 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               211                311 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               211                311 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                98                424 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                98                424 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                86                436 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                86                436 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                47                475 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                47                475 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                28                494 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                28                494 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               184                338 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               184                338 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                75                447 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                75                447 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              134               388 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              134               388 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               83               439 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               83               439 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "NUMBER_PACK_YEARS_SMOKED"            
[16] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 522 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=201,	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=337,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=86,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 522 columns, 1 survival variables, and 13 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "RADIATION_THERAPY"             "HISTOLOGICAL_TYPE"            
 [9] "NUMBER_PACK_YEARS_SMOKED"      "YEAR_OF_TOBACCO_SMOKING_ONSET"
[11] "NUMBER_OF_LYMPH_NODES"         "RACE"                         
[13] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=60, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1  49 137 100 173 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   50   137   100   173 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  49 137 100 173 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   50   137   100   173 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
179  68 168   8 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
179  68 168   8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
179  68 168   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
179  68 168   8 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=86, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=59, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=19, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    32  38
  1P GAIN WILD-TYPE 271 180
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               70               451 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               38               180 
$`1P GAIN MUTATED`
TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A6DI 
       26.50        17.10        14.83        12.62         4.01        11.05 
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-CN-4727 TCGA-CN-4739 TCGA-CN-5359 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-A49A 
       51.29        45.83        12.39         6.74        32.22        17.29 
TCGA-CN-A6V6 TCGA-CQ-7067 TCGA-CR-6478 TCGA-CR-6482 TCGA-CR-7379 TCGA-CR-7388 
       20.88        16.73         6.02        11.34        34.06        27.06 
TCGA-CV-5431 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6933 
       17.16        76.50        80.12        86.83        60.49        90.12 
TCGA-CV-6937 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7255 
       20.52       111.16        18.81         1.84        77.16         2.10 
TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-A45R 
       18.41        35.54        22.85         0.07        34.09       180.16 
TCGA-CV-A45X TCGA-CV-A461 TCGA-CV-A6JE TCGA-CX-7082 TCGA-D6-A74Q TCGA-DQ-5625 
        6.51        67.86        35.34        10.42        11.11        37.25 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7596 TCGA-F7-8298 TCGA-H7-7774 TCGA-H7-A76A 
       30.94        14.04        41.59        32.71        13.38        20.94 
TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-KU-A66T TCGA-P3-A5Q5 TCGA-P3-A5Q6 
        5.29        13.84        15.48        18.15        29.92        15.78 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       36.82        47.01        18.97         6.51        14.76        12.20 
TCGA-T2-A6WZ TCGA-UF-A719 TCGA-UF-A71E TCGA-UF-A7JH 
       15.91        54.67        49.45        29.46 

$`1P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       23.74        42.35        57.93        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IF 
       68.48        15.52        21.17         3.55        41.85        29.42 
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-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
        5.69        14.47         7.82         2.27        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.60         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
       18.38        22.42        36.72        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 
       66.28        24.66        38.40        12.92         8.81        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       48.76        55.86        38.04         4.67        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       26.86        32.81        52.14        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       14.33        27.58        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
        8.58        71.31         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.57        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        48.00        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
       34.13         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       35.05        38.89         3.68        17.42        32.48        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       35.01        25.41        23.57        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 
        2.70        23.44        19.82        24.39        19.53        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       45.99        10.42        11.21         4.24        41.19        32.38 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       32.88        46.95        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
       38.76        70.13        64.87        53.52        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       43.10        77.56        44.48        11.61        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       39.52        34.52        36.99        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       10.22        11.64         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
        9.17        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        29.82        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58         7.10         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
       48.39       139.43       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 
       17.95       107.51        87.55        91.53        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       23.05        48.59         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 
       62.43         9.60         2.14         9.70         5.46         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       21.90        26.43        11.24       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       42.38        15.09        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       10.98         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
       64.83       126.15        12.66         7.99         9.01         5.26 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
       52.31        12.92        21.80        71.21        10.75       130.88 
TCGA-CV-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-7261 
       17.13        95.34         4.96        11.87        47.97        36.13 
TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       57.47        17.85       210.97        89.33         9.67         0.46 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
       25.08        25.94       100.57        14.89        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
       54.94         3.52        16.27        84.49        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
      153.86        16.64         6.38        22.19        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Y 
      169.38       159.65        35.47         1.05        45.96        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       48.20        60.43         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        5.98         6.38        29.79         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       18.84        34.36        51.12        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
       23.05         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN 
       25.32        17.72        12.36        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5630 
       24.95        13.94        12.10        12.79        58.45        33.86 
TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       18.02        46.32        46.45        20.45        37.58        40.24 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       40.04        39.12        37.18        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       31.13        18.94        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
       20.25        12.43        15.16        15.06        13.61        21.11 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
        4.27         3.65         6.90        34.75        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        37.71        11.84        37.41         0.07        33.57 
TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       13.68        19.04        13.35        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
        7.13        16.08        17.98        71.74        51.25        10.85 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       19.00        75.55         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 
        9.34        12.72        18.64        21.07        19.73         5.62 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       17.82        15.32         8.32        12.72        16.96         6.87 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ 
        7.10        32.45        13.71         3.12        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 
       20.35        64.80         2.83        49.51        48.03        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK 
       74.47        17.95        24.30        55.43        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-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 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.07              0.07 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           180.16            210.97 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            20.52             21.07 
[1] "0.1 - 180.2 (20.5)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.3"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  1P GAIN MUTATED         3        6         8        36         2         0
  1P GAIN WILD-TYPE      24       70        74       217        10         1
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 3                24
  STAGE II                6                70
  STAGE III               8                74
  STAGE IVA              36               217
  STAGE IVB               2                10
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1P GAIN MUTATED       3  17  14  23
  1P GAIN WILD-TYPE    47 120  86 150
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1               3                47
  T2                 17               120
  T3                 14                86
  T4                 23               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
  1P GAIN MUTATED    16  11  26   1
  1P GAIN WILD-TYPE 163  57 142   7
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              16               163
  N1              11                57
  N2              26               142
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    19   0
  1P GAIN WILD-TYPE 170   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     19    0
  1P GAIN WILD-TYPE  170    1
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              19               170
  1               0                 1
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    18  52
  1P GAIN WILD-TYPE 122 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     18   52
  1P GAIN WILD-TYPE  122  330
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              18               122
  MALE                52               330
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    15  45
  1P GAIN WILD-TYPE 136 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     15   45
  1P GAIN WILD-TYPE  136  238
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               15               136
  YES              45               238
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  1P GAIN MUTATED                                      65
  1P GAIN WILD-TYPE                                   446
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  1P GAIN MUTATED                                                             1
  1P GAIN WILD-TYPE                                                           0
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  1P GAIN MUTATED                                                     4
  1P GAIN WILD-TYPE                                                   6
D1V9, multiclass
                                                             clus
vv                                                            1P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    65
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       4
                                                             clus
vv                                                            1P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     446
  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"
D1V10, continuous
D1V11, continuous
D1V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     1
  1P GAIN WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                          13    54
  1P GAIN WILD-TYPE                        35   392
D1V13, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                     13                35
  WHITE                                         54               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"
D1V14, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     5  61
  1P GAIN WILD-TYPE  21 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      5   61
  1P GAIN WILD-TYPE   21  398
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                21
  NOT HISPANIC OR LATINO              61               398
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    63  58
  1Q GAIN WILD-TYPE 240 160
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              121               400 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               58               160 
$`1Q GAIN MUTATED`
TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6DI 
       17.10        14.83         3.55        12.62        41.85        11.05 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 
        9.14         4.41        66.28        24.66        71.05        20.52 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4739 TCGA-CN-5359 
       25.71        10.55        51.29        56.68        45.83        12.39 
TCGA-CN-5367 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6023 
       11.57        56.94        50.07        23.90         6.74        52.08 
TCGA-CN-6997 TCGA-CN-A49A TCGA-CN-A63U TCGA-CN-A6V6 TCGA-CQ-7064 TCGA-CQ-7067 
       32.48        17.29        31.69        20.88        64.87        16.73 
TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-6478 TCGA-CR-6482 TCGA-CR-7370 
       23.24        33.60        31.23         6.02        11.34         3.45 
TCGA-CR-7379 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5431 
       34.06        27.06        12.89        29.82       139.43        17.16 
TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5977 TCGA-CV-5978 
      108.95       107.51        76.50        80.12        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6940 
       43.23        90.12         9.70         5.46        20.52        26.43 
TCGA-CV-6941 TCGA-CV-6951 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 
       11.24        30.08         4.14       111.16        18.81         5.26 
TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7254 
        1.84        71.21        77.16        31.36        95.34        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7421 
        2.10        36.13        18.41        35.54        17.85         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45W 
       34.09       100.57        16.64        22.19       180.16        45.96 
TCGA-CV-A45X TCGA-CV-A461 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CX-7082 TCGA-CX-7086 
        6.51        67.86        35.34         6.38        10.42        18.84 
TCGA-D6-6827 TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-7589 
       18.67        13.94        11.11        37.25        30.94        46.32 
TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-A622 TCGA-H7-7774 TCGA-H7-A76A TCGA-HD-7754 
       41.59        32.71        11.80        13.38        20.94        25.74 
TCGA-HD-7917 TCGA-HL-7533 TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61O TCGA-IQ-A6SH 
       27.48        34.75        37.41         0.07        13.84        15.48 
TCGA-KU-A66T TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A6SW TCGA-P3-A6T5 TCGA-QK-A6VB 
       18.15        29.92        15.78        36.82        29.00        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-T2-A6WZ 
       19.73         6.51        14.76        12.20        15.32        15.91 
TCGA-T2-A6X0 TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JD 
        7.10        13.25        54.67        48.03        49.45        24.30 
TCGA-UF-A7JH 
       29.46 

$`1Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 
       26.50        23.74        42.35        57.93        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6873 TCGA-BA-A4IF 
       65.59        68.48        15.52        21.17         4.01        29.42 
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-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
        5.69        14.47         7.82         2.27        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 
       16.41         6.15       105.90         4.60        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7872 TCGA-BB-A5HZ 
       36.72        33.70        50.20        44.98        38.40        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
       12.92         8.81         6.28        12.69        48.76        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       38.04         4.67        12.89        26.86        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 
       57.11        12.99        20.55        14.33        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
       13.05        42.02        46.32         8.58        71.31         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       16.21        11.54        11.84        12.49         8.52        52.08 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       30.67        48.00        47.44        28.04        19.07        34.13 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        9.07         9.24        11.08        10.45        32.22        35.05 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       38.89         3.68        17.42        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W 
       23.57        29.72        21.21         7.40        22.32        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       24.39        19.53        48.20        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
        4.24        41.19        32.38        32.88        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        70.13        53.52 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       43.04        41.88        43.10        77.56        44.48        11.61 
TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 
       29.36        29.49        14.14        12.46        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-6480 TCGA-CR-6481 
       34.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
       47.18        39.16        47.34        40.93        35.84         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7380 
       24.95        29.23         0.99        31.96         9.17        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 
       26.17        17.13        32.78        47.01        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58         7.10         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 
       35.41        29.95        48.39       129.21        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       17.95        87.55        91.53        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
       86.83        48.59        54.74        21.07        62.43         9.60 
TCGA-CV-6934 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        2.14         4.73        21.90       140.78        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-7089 TCGA-CV-7090 
        7.13         8.42        28.34         2.50        64.83       126.15 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
       12.66         7.99         9.01        52.31        12.92        21.80 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 
       10.75       130.88         4.73        47.47        36.00        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7406 TCGA-CV-7410 
       18.97        17.13         4.96        11.87        57.47       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-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
       14.89        56.48       156.49        54.94         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-A45O 
       84.49        19.76         7.17       153.86         6.38        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45Y 
       21.01       169.38       159.65        35.47         1.05        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       48.20        60.43         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        5.98        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7219 
       23.47        19.92        22.52        10.42        10.55        34.36 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       16.14        11.44        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES 
       28.77         7.63        22.59        24.95        12.10        12.79 
TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 
       58.45        33.86        18.02        14.04        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8489 
       37.58        40.24        40.04        39.12        37.18        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
       17.85        20.25        12.43        15.16        15.06        13.61 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
       21.11         0.07        28.47        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       22.03        12.66        22.85         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        3.65         6.90        15.95        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-KU-A66S 
       11.84        33.57         5.29        13.68        19.04        13.35 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.27        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         6.25        15.42         7.13        16.08        17.98 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       71.74        51.25        10.85        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       18.97         2.04        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.21        23.15         7.30        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       18.64         5.62        17.82         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HL 
        6.87        32.45        13.71         3.12        13.55        20.35 
TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       64.80         2.83        49.51        44.65        74.47        17.95 
TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       55.43        18.05        13.94        20.75        22.36        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        17.03        20.55        14.56 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.07              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           180.16            210.97 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            23.90             20.48 
[1] "0.1 - 180.2 (23.9)" "0.1 - 211.0 (20.5)"
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  1Q GAIN MUTATED         5       14        15        62         4         0
  1Q GAIN WILD-TYPE      22       62        67       191         8         1
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 5                22
  STAGE II               14                62
  STAGE III              15                67
  STAGE IVA              62               191
  STAGE IVB               4                 8
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1Q GAIN MUTATED       6  32  19  45
  1Q GAIN WILD-TYPE    44 105  81 128
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1               6                44
  T2                 32               105
  T3                 19                81
  T4                 45               128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q GAIN MUTATED    31  15  43   3
  1Q GAIN WILD-TYPE 148  53 125   5
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              31               148
  N1              15                53
  N2              43               125
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    34   0
  1Q GAIN WILD-TYPE 155   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     34    0
  1Q GAIN WILD-TYPE  155    1
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              34               155
  1               0                 1
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    27  94
  1Q GAIN WILD-TYPE 113 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     27   94
  1Q GAIN WILD-TYPE  113  288
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              27               113
  MALE                94               288
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    26  73
  1Q GAIN WILD-TYPE 125 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     26   73
  1Q GAIN WILD-TYPE  125  210
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               26               125
  YES              73               210
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  1Q GAIN MUTATED                                     114
  1Q GAIN WILD-TYPE                                   397
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  1Q GAIN MUTATED                                                             1
  1Q GAIN WILD-TYPE                                                           0
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  1Q GAIN MUTATED                                                     6
  1Q GAIN WILD-TYPE                                                   4
D2V9, multiclass
                                                             clus
vv                                                            1Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   114
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       6
                                                             clus
vv                                                            1Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     397
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, continuous
D2V11, continuous
D2V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  0     0
  1Q GAIN WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                          21    95
  1Q GAIN WILD-TYPE                        27   351
D2V13, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                     21                27
  WHITE                                         95               351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     7 105
  1Q GAIN WILD-TYPE  19 354
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      7  105
  1Q GAIN WILD-TYPE   19  354
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                19
  NOT HISPANIC OR LATINO             105               354
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    55  42
  2P GAIN WILD-TYPE 248 176
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               97               424 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               42               176 
$`2P GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5555 TCGA-BA-A4IF TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7864 
        9.30        17.10        29.42        20.48        16.41        50.20 
TCGA-BB-8596 TCGA-CN-4727 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5374 
       71.05        51.29        13.05        46.32        12.39        56.94 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
       50.07        48.00        52.08        11.08        10.45        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A63T TCGA-CQ-5329 TCGA-CQ-5332 TCGA-CQ-6225 
       38.89         3.68         7.40        70.45        10.42        13.25 
TCGA-CQ-7072 TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7380 
       77.56        11.77        16.90        39.16        24.95        19.92 
TCGA-CR-7383 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5440 TCGA-CV-6933 
       17.13         5.13         5.95       139.43       107.51        90.12 
TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6950 TCGA-CV-6962 
       20.52        21.90        26.43        11.24        15.09         4.14 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7103 TCGA-CV-7178 TCGA-CV-7235 TCGA-CV-7242 
      126.15       111.16        52.31        71.21        77.16        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
       31.36        26.20        18.97        95.34        47.97        36.13 
TCGA-CV-7263 TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
       18.41        17.85        22.85         0.07        34.09       100.57 
TCGA-CV-7429 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45U TCGA-CV-A45X TCGA-CV-A45Z 
        3.52       153.86        16.64        35.47         6.51        48.20 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-8569 TCGA-D6-A4ZB 
       18.84        34.36        25.41        23.05        25.32        12.36 
TCGA-D6-A6EP TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-A620 TCGA-F7-A623 
       13.94        30.94        46.32        37.58        17.85        20.25 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A6SH 
       13.84         3.65         6.90        37.71        37.41        15.48 
TCGA-MZ-A7D7 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-AA3J 
       17.98        21.07        19.73         6.51        12.20        15.32 
TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JF 
       12.72        15.91         2.83        49.45        44.65        55.43 
TCGA-UF-A7JK 
       13.94 

$`2P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       23.74        42.35        57.93        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       68.48        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
        4.01        41.85        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-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       11.05        13.38         6.15       105.90         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 
        4.41        18.38        22.42        36.72        33.70        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY 
       66.28        24.66        38.40        20.52        25.71        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
       27.19        12.92         8.81         6.28        12.69        48.76 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       55.86        38.04         4.67        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       32.81        52.14        57.11        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
       45.83        27.58        73.61        42.02         8.58        71.31 
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-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
        8.52        52.08        30.67        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6992 
       19.07        34.13         6.74         9.07         9.24        35.05 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        32.48        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       17.29        29.72        21.21        31.69        22.32        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       24.39        20.88        19.53        48.20        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
        2.93        54.58        62.37        45.99        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
       41.19        32.38        32.88        46.95        56.58         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
       14.99        38.76        70.13        64.87        53.52        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       43.04        41.88        43.10        44.48        11.61        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       84.23        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-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        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       15.75         9.27        47.18        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.45         3.09        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       34.06        26.17        32.78        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       29.82        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 
        7.10        35.41        29.95        48.39        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 
      108.95        76.24        19.20        17.95        87.55        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 
       62.43         9.60         2.14         9.70         5.46         4.73 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 
      140.78        19.79        12.03        42.38        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        2.50        64.83        18.81        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 
        5.26         1.84        12.92        21.80        10.75       130.88 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 
        4.73        47.47        17.13         4.96        11.87         2.10 
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-7416 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       25.08        25.94        14.89        56.48       156.49        54.94 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-7440 
       16.27        84.49        19.76         7.17         6.38        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V 
       27.98        21.01       169.38       180.16       159.65         1.05 
TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       45.96        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        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.42        10.55        51.12        13.25 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
        9.60         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ 
       17.72        28.77         7.63        22.59        24.95        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        11.11        58.45        37.25        33.86        18.02 
TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       14.04        46.45        20.45        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A624 
       31.13        18.94        24.95         0.46        11.80        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 
       14.66        22.03        12.66        22.85         0.36         4.27 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61I 
       34.75        15.95        38.53        14.50        11.84         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A66S 
       33.57         5.29        13.68        13.84        19.04        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
        1.84        12.62         6.25        15.42         7.13        16.08 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        71.74        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z8 
        7.30        21.47         9.34        12.72        18.64         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
       14.76        17.82         8.32        16.96         6.87         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       32.45        13.71         3.12        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JC 
       64.80        54.67        49.51        48.03        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       24.30        29.46        18.05        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 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.07              0.07 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           153.86            210.97 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           21.900            20.815 
[1] "0.1 - 153.9 (21.9)" "0.1 - 211.0 (20.8)"
[1] "hr=" "1.1"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  2P GAIN MUTATED         5       15        16        49         3         0
  2P GAIN WILD-TYPE      22       61        66       204         9         1
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 5                22
  STAGE II               15                61
  STAGE III              16                66
  STAGE IVA              49               204
  STAGE IVB               3                 9
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2P GAIN MUTATED       8  23  22  38
  2P GAIN WILD-TYPE    42 114  78 135
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1               8                42
  T2                 23               114
  T3                 22                78
  T4                 38               135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2P GAIN MUTATED    38  10  34   2
  2P GAIN WILD-TYPE 141  58 134   6
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              38               141
  N1              10                58
  N2              34               134
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    32   0
  2P GAIN WILD-TYPE 157   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     32    0
  2P GAIN WILD-TYPE  157    1
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              32               157
  1               0                 1
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    17  80
  2P GAIN WILD-TYPE 123 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     17   80
  2P GAIN WILD-TYPE  123  302
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              17               123
  MALE                80               302
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    22  52
  2P GAIN WILD-TYPE 129 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     22   52
  2P GAIN WILD-TYPE  129  231
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               22               129
  YES              52               231
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  2P GAIN MUTATED                                      94
  2P GAIN WILD-TYPE                                   417
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  2P GAIN MUTATED                                                             0
  2P GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  2P GAIN MUTATED                                                     3
  2P GAIN WILD-TYPE                                                   7
D3V9, multiclass
                                                             clus
vv                                                            2P GAIN 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                       3
                                                             clus
vv                                                            2P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     417
  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"
D3V10, continuous
D3V11, continuous
D3V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  1     0
  2P GAIN WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                          13    81
  2P GAIN WILD-TYPE                        35   365
D3V13, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                     13                35
  WHITE                                         81               365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     4  85
  2P GAIN WILD-TYPE  22 374
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      4   85
  2P GAIN WILD-TYPE   22  374
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              85               374
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    41  33
  2Q GAIN WILD-TYPE 262 185
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               74               447 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               33               185 
$`2Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-A4IF TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7864 TCGA-BB-8596 
        9.30        29.42        20.48        16.41        50.20        71.05 
TCGA-CN-4727 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5374 TCGA-CN-6012 
       51.29        13.05        46.32        12.39        56.94        48.00 
TCGA-CN-6024 TCGA-CN-6994 TCGA-CN-A63T TCGA-CQ-5329 TCGA-CQ-5332 TCGA-CQ-6224 
       11.08        38.89         7.40        70.45        10.42        56.58 
TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7072 TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-7365 
       13.25        14.99        77.56        11.77        16.90        39.16 
TCGA-CR-7383 TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-6940 TCGA-CV-6941 
       17.13       139.43       108.95       107.51        26.43        11.24 
TCGA-CV-6950 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7103 TCGA-CV-7235 TCGA-CV-7242 
       15.09         4.14       111.16        52.31        77.16        36.00 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 
       26.20        18.97        95.34        47.97        36.13        18.41 
TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7429 TCGA-CV-7435 
       22.85         0.07        34.09       100.57         3.52       153.86 
TCGA-CV-A45X TCGA-CV-A45Z TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-8569 
        6.51        48.20        18.84        34.36        23.05        25.32 
TCGA-D6-A4ZB TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-A623 
       12.36        30.94        14.04        46.32        37.58        20.25 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-MT-A67D TCGA-P3-A6T5 
        3.65         6.90        37.71        37.41         1.84        29.00 
TCGA-QK-A6VB TCGA-QK-A8ZA TCGA-T2-A6WZ TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       21.07        12.20        15.91        54.67         2.83        49.51 
TCGA-UF-A7J9 TCGA-UF-A7JF 
       44.65        55.43 

$`2Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
       12.62         4.01        41.85        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-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
        2.27        11.05        13.38         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HU 
       44.98        66.28        24.66        38.40        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-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       48.76        55.86        38.04         4.67        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       26.86        32.81        52.14        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 
       14.33        45.83        27.58        73.61        42.02         8.58 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       71.31         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 
       12.49         8.52        52.08        50.07        30.67        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
       47.44        28.04        19.07        34.13         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 
        9.24        52.08        10.45        32.22        35.05         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        32.48        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       17.29        29.72        21.21        31.69        22.32        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       24.39        20.88        19.53        48.20        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
        2.93        54.58        62.37        45.99        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6229 
       41.19        32.38        32.88        46.95         4.24        38.76 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
       70.13        64.87        53.52        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        44.48        11.61        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
       29.49        14.14        12.46        31.23        84.23        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-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        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-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       19.92        26.17        32.78        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       29.82        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         5.13         5.95        35.41        29.95        48.39 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 
       17.16       129.21        76.24        19.20        17.95        87.55 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 
        5.46        20.52         4.73        21.90       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       12.03        42.38        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 
       10.98         7.13         8.42        28.34         2.50        64.83 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      126.15        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
        1.84        12.92        21.80        71.21        10.75       130.88 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 
        4.73        47.47        31.36        17.13         4.96        11.87 
TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
        2.10        57.47        35.54        17.85       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7425 
        9.67         0.46        25.08        25.94        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
      156.49        54.94        16.27        84.49        19.76         7.17 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       16.64         6.38        22.19        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Y 
      180.16       159.65        35.47         1.05        45.96        88.87 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       60.43        67.86         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.42        10.55        51.12        13.25        25.41         9.60 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 
        2.53        16.14        11.44        18.67        24.95        17.72 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       28.77         7.63        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        11.11        58.45        37.25        33.86        18.02 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       46.45        20.45        40.24        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       37.18        32.71        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 
       18.94        24.95         0.46        17.85        11.80        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G 
        4.27        34.75        15.95        38.53        14.50        11.84 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
        0.07        33.57         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       15.48        13.35        18.15        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
        7.96        30.05        12.62         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
       16.08        17.98        29.92        15.78        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       10.85        36.82        47.01        19.00        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        2.04        12.99        16.01        13.15        21.07        21.21 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       23.15         7.30        21.47         9.34        12.72        18.64 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J 
       19.73         6.51         5.62        14.76        17.82        15.32 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
        8.32        12.72        16.96         6.87         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       13.71         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
       48.03        49.45        74.47        17.95        24.30        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       18.05        13.94        20.75        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.07              0.07 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           153.86            210.97 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           27.715            20.520 
[1] "0.1 - 153.9 (27.7)" "0.1 - 211.0 (20.5)"
[1] "hr=" "1.1"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  2Q GAIN MUTATED         2       13        11        37         1         0
  2Q GAIN WILD-TYPE      25       63        71       216        11         1
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 2                25
  STAGE II               13                63
  STAGE III              11                71
  STAGE IVA              37               216
  STAGE IVB               1                11
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2Q GAIN MUTATED       6  20  14  27
  2Q GAIN WILD-TYPE    44 117  86 146
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1               6                44
  T2                 20               117
  T3                 14                86
  T4                 27               146
[1] 4 2
[1] 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
  2Q GAIN MUTATED    32   5  24   1
  2Q GAIN WILD-TYPE 147  63 144   7
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              32               147
  N1               5                63
  N2              24               144
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    22   0
  2Q GAIN WILD-TYPE 167   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     22    0
  2Q GAIN WILD-TYPE  167    1
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              22               167
  1               0                 1
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    14  60
  2Q GAIN WILD-TYPE 126 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     14   60
  2Q GAIN WILD-TYPE  126  322
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              14               126
  MALE                60               322
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    18  40
  2Q GAIN WILD-TYPE 133 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     18   40
  2Q GAIN WILD-TYPE  133  243
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               18               133
  YES              40               243
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  2Q GAIN MUTATED                                      74
  2Q GAIN WILD-TYPE                                   437
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  2Q GAIN MUTATED                                                             0
  2Q GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  2Q GAIN MUTATED                                                     0
  2Q GAIN WILD-TYPE                                                  10
D4V9, multiclass
                                                             clus
vv                                                            2Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    74
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            2Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     437
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, continuous
D4V11, continuous
D4V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  1     0
  2Q GAIN WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                           8    64
  2Q GAIN WILD-TYPE                        40   382
D4V13, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      8                40
  WHITE                                         64               382
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     4  64
  2Q GAIN WILD-TYPE  22 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4   64
  2Q GAIN WILD-TYPE   22  395
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              64               395
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    48  33
  3P GAIN WILD-TYPE 255 185
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               81               440 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               33               185 
$`3P GAIN MUTATED`
TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5153 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 
       37.28         9.07        57.93        20.48        68.48        15.52 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6DD TCGA-BB-4223 TCGA-BB-4225 TCGA-CN-4723 
        4.01        29.42         5.69       105.90         4.60        55.86 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 
       26.86        32.81        23.90         6.74         9.07        52.08 
TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A6V1 TCGA-CN-A6V7 
       10.45        38.89        23.57        21.21        19.82        19.53 
TCGA-CQ-5323 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6474 
       48.20        46.95        13.25        58.42        50.01        18.54 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-7365 TCGA-CR-7368 
       11.64         7.69        12.46        15.75        39.16        40.93 
TCGA-CR-7389 TCGA-CR-7397 TCGA-CV-5431 TCGA-CV-5442 TCGA-CV-5977 TCGA-CV-6433 
       12.89         7.10        17.16        76.50        60.49        21.07 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-7097 TCGA-CV-7103 TCGA-CV-7178 TCGA-CV-7236 
       21.90        26.43        12.66        52.31        71.21         4.73 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7421 
       47.47        31.36        36.13        35.54        17.85         0.07 
TCGA-CV-7437 TCGA-D6-A6EM TCGA-DQ-5624 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8489 
       16.64         7.63        58.45        39.12        41.59        21.63 
TCGA-F7-A623 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A634 TCGA-IQ-A61E 
       20.25        27.48        22.03        12.66         4.27        37.71 
TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6SX 
        6.25         7.13        16.08        17.98        15.78        47.01 
TCGA-P3-A6T5 TCGA-P3-A6T8 TCGA-QK-A6IJ TCGA-QK-A8Z8 TCGA-RS-A6TO TCGA-T2-A6X0 
       29.00        13.15        12.72         5.62        12.72         7.10 
TCGA-TN-A7HJ TCGA-UF-A71D TCGA-UF-A7JA 
       13.25        48.03        74.47 

$`3P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 
        3.35        15.19         9.30        13.64        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 
       42.35        17.10        23.84        65.59        21.17        14.83 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        3.55        12.62        41.85        28.11        20.45        30.18 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       27.95        11.54         7.10        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 
       11.05        13.38        20.48        16.41         6.15         9.14 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.41        18.38        22.42        36.72        33.70        50.20 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       44.98        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-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
       12.69        48.76        38.04         4.67        51.29        56.68 
TCGA-CN-4729 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       12.89        52.14        57.11        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       45.83        27.58        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
        8.58        12.39        71.31         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.84        11.57        12.49         8.52        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       50.07        30.67        48.00        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 
       34.13         9.24        11.08        32.22        35.05         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A 
       17.42        32.48        11.74        35.01        25.41        17.29 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       29.72         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V3 TCGA-CN-A6V6 
        4.41        12.07         2.70        23.44        24.39        20.88 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       45.99        10.42        11.21         4.24        41.19        32.38 
TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       32.88        56.58         4.24        14.99        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
       64.87        53.52        16.73        43.04        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       77.56        44.48        11.61        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.49        14.14        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
       54.67        37.87        26.27        39.52        34.52        36.99 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6491 
       16.90         6.02        11.90        10.22        11.34        22.78 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        9.27        47.18        47.34        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       29.82        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-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-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-5971 
       87.55        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6436 
       86.83        48.59         7.07        43.23        54.74        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-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
        4.73        11.24       140.78        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       15.09        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
        7.13         8.42        28.34         2.50         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      126.15       111.16        18.81         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1.84        12.92        21.80        10.75       130.88        77.16 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       36.00        26.20        18.97        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7410 
       11.87        47.97         2.10        18.41        57.47       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-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       34.09       100.57        14.89        56.48       156.49        54.94 
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-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
        6.38        22.19        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       48.20        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ 
       10.42        10.42        10.55        18.84        34.36        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       28.77        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       11.11        37.25        30.94        33.86        18.02        14.04 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       46.32        46.45        20.45        37.58        40.24        40.04 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       37.18        32.71        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 
       24.95         0.46        17.85        11.80        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       15.16        15.06        13.61        21.11        20.94         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8635 
       28.47        25.74        21.93        27.48        14.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
        0.36        13.84         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 
       38.53        14.50        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S 
        5.29        13.68        13.84        19.04        15.48        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
        1.84        12.62        15.42        29.92        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       10.85        36.82        19.00        75.55        18.97         2.04 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       12.99        16.01        21.07        21.21        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
       21.47         9.34        18.64        21.07        19.73         6.51 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP 
       14.76        12.20        17.82        15.32         8.32        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
        6.87        15.91        32.45        13.71         3.12        13.55 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       20.35        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       44.65        17.95        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       13.94        20.75        22.36        32.65         2.96        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.07              0.07 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           105.90            210.97 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            21.07             20.91 
[1] "0.1 - 105.9 (21.1)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1"  
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  3P GAIN MUTATED         3       11        12        38         1         1
  3P GAIN WILD-TYPE      24       65        70       215        11         0
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 3                24
  STAGE II               11                65
  STAGE III              12                70
  STAGE IVA              38               215
  STAGE IVB               1                11
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  3P GAIN MUTATED       7  25  10  25
  3P GAIN WILD-TYPE    43 112  90 148
D5V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1               7                43
  T2                 25               112
  T3                 10                90
  T4                 25               148
[1] 4 2
[1] 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
  3P GAIN MUTATED    21  14  27   1
  3P GAIN WILD-TYPE 158  54 141   7
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              21               158
  N1              14                54
  N2              27               141
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    21   1
  3P GAIN WILD-TYPE 168   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     21    1
  3P GAIN WILD-TYPE  168    0
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              21               168
  1               1                 0
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    23  58
  3P GAIN WILD-TYPE 117 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     23   58
  3P GAIN WILD-TYPE  117  324
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              23               117
  MALE                58               324
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    24  40
  3P GAIN WILD-TYPE 127 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     24   40
  3P GAIN WILD-TYPE  127  243
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               24               127
  YES              40               243
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  3P GAIN MUTATED                                      80
  3P GAIN WILD-TYPE                                   431
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  3P GAIN MUTATED                                                             0
  3P GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  3P GAIN MUTATED                                                     1
  3P GAIN WILD-TYPE                                                   9
D5V9, multiclass
                                                             clus
vv                                                            3P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    80
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            3P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     431
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, continuous
D5V11, continuous
D5V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  0     1
  3P GAIN WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           6    72
  3P GAIN WILD-TYPE                        42   374
D5V13, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      6                42
  WHITE                                         72               374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     4  72
  3P GAIN WILD-TYPE  22 387
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4   72
  3P GAIN WILD-TYPE   22  387
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              72               387
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   141 112
  3Q GAIN WILD-TYPE 162 106
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              253               268 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              112               106 
$`3Q GAIN MUTATED`
TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5557 
       37.28         9.07        26.50        23.74        57.93        20.48 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       68.48        15.52        14.83        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DD TCGA-BA-A6DI TCGA-BA-A8YP 
       29.42        20.45        27.95         5.69        11.05        16.41 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7871 
      105.90         4.60         4.41        33.70        50.20        24.66 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A6UM 
       38.40        71.05        20.52        25.71        10.55        12.92 
TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
        6.28        55.86        38.04         4.67        51.29        56.68 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4739 
       12.89        26.86        32.81        12.99        20.55        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       27.58        73.61        13.05        46.32         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       71.31         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6019 
       52.08        56.94        48.00        23.90        47.44        34.13 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        6.74         9.07        52.08        11.08        10.45        32.22 
TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C 
       38.89        11.74        35.01        23.57        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
        7.40        19.82        24.39        20.88        19.53        48.20 
TCGA-CQ-5329 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-6229 
       70.45        32.38        46.95        13.25        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       64.87        16.73        41.88        77.56        44.48        23.24 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-6467 TCGA-CR-6470 
       29.49        14.14        84.23        37.87        58.42        50.01 
TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       18.54         6.02        11.90        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
       22.78        15.75        39.16        40.93        35.84         3.09 
TCGA-CR-7372 TCGA-CR-7377 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       24.95         9.17        32.78        47.01        27.06        12.89 
TCGA-CR-7397 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        7.10        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5973 
       19.20        17.95       107.51        76.50        80.12        86.83 
TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 
       60.49        54.74        21.07        90.12         9.70         5.46 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6954 
       21.90        26.43        12.03        42.38        30.08        65.82 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 
        4.14        64.83       126.15       111.16        12.66         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7236 
        1.84        52.31        12.92        71.21        10.75         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-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       95.34        47.97        36.13        18.41        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 
       17.85       210.97         0.46        22.85        25.08         0.07 
TCGA-CV-7424 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45R TCGA-CV-A45U 
       14.89         7.17       153.86        16.64       180.16        35.47 
TCGA-CV-A45W TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A465 TCGA-CV-A6JZ 
       45.96        48.20        60.43        67.86         7.07        23.47 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A74Q 
       18.84        34.36        25.32        12.36         7.63        11.11 
TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7595 
       58.45        33.86        18.02        46.32        37.58        39.12 
TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       41.59        32.71        21.63        20.25         3.02        31.13 
TCGA-F7-A61V TCGA-F7-A623 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-8224 
       24.95        20.25        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-A61E TCGA-IQ-A61G 
       22.03        12.66         4.27        34.75        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K TCGA-KU-A66T TCGA-MT-A67G TCGA-MZ-A5BI 
       37.41        33.57         5.29        18.15         6.25         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF 
       16.08        17.98        29.92        15.78        71.74        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 
       36.82        47.01        18.97         2.04        29.00        16.01 
TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IJ TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-RS-A6TO 
       13.15        21.21        12.72         5.62        14.76        12.72 
TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
       16.96        15.91         7.10        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A71E 
       13.25        20.35        54.67         2.83        48.03        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK 
       44.65        74.47        24.30        55.43        29.46        13.94 
TCGA-UF-A7JO 
       20.75 

$`3Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5555 
        3.35        15.19         9.30        13.64        42.35        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       23.84        65.59        21.17         3.55        28.11        30.18 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ 
       11.54         7.10        14.47         7.82         2.27        13.38 
TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
       20.48         6.15         9.14        18.38        22.42        36.72 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 
       44.98        66.28        27.19         8.81        12.69        48.76 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-5355 TCGA-CN-5369 TCGA-CN-5370 
       52.14        57.11        14.33        42.02        12.49         8.52 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6022 TCGA-CN-6992 
       50.07        30.67        28.04        19.07         9.24        35.05 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A63U 
        3.68        17.42        32.48        25.41        17.29        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5330 
       23.44        52.37        21.50         2.93        54.58        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
       45.99        10.42        11.21         4.24        41.19        32.88 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 
       56.58         4.24        70.13        53.52        43.04        43.10 
TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 
       11.61        29.36        33.60        12.46        31.23        11.77 
TCGA-CR-5248 TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 
       54.67        26.27        39.52        34.52        36.99        16.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7370 
       10.22        11.34         9.27        47.18        47.34         3.45 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
       29.23         0.99        31.96        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       17.13        29.82        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5434 TCGA-CV-5435 
       30.58         5.13         5.95        35.41       108.95        76.24 
TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 
       87.55        91.53        17.92        13.35        23.05        48.59 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6937 
        7.07        43.23        62.43         9.60         2.14        20.52 
TCGA-CV-6938 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6952 
        4.73        11.24       140.78        19.79        15.09         6.08 
TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       53.95        10.98         7.13         8.42        28.34         2.50 
TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7177 TCGA-CV-7183 TCGA-CV-7235 
       18.81         7.99         9.01        21.80       130.88        77.16 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7418 
        4.96        11.87         2.10        89.33         9.67        25.94 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 
       34.09       100.57        56.48       156.49        54.94         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
       16.27        84.49        19.76         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y 
       21.01       169.38       159.65         1.05         6.51        88.87 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
        0.76        56.61        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-A6K0 
       29.79         6.48        28.01         3.62        21.24        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.42        10.55        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EO 
       18.67        24.95        17.72        28.77        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-7588 
       13.94        12.10        12.79        37.25        30.94        14.04 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-F7-7848 TCGA-F7-A61S 
       46.45        20.45        40.24        40.04        37.18        18.94 
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-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       15.06        13.61        21.11        20.94         0.07        28.47 
TCGA-HD-7832 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 
       27.48        22.85         0.36        13.84         3.65         6.90 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61I TCGA-IQ-A61L TCGA-IQ-A61O 
       15.95        38.53        14.50         0.07        13.68        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       19.04        15.48        13.35        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-P3-A5QE 
        7.96        30.05         1.84        12.62        15.42        51.25 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG 
       19.00        75.55        12.99        21.07        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
       21.47         9.34        18.64        21.07        19.73         6.51 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6WX TCGA-T2-A6X2 
       12.20        17.82        15.32         8.32         6.87        32.45 
TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A7JC TCGA-UF-A7JJ TCGA-UF-A7JS TCGA-UF-A7JT 
       64.80        49.51        17.95        18.05        22.36        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        17.03        20.55        14.56 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.07              0.07 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           210.97            169.38 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            23.74             19.02 
[1] "0.1 - 211.0 (23.7)" "0.1 - 169.4 (19.0)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  3Q GAIN MUTATED        10       37        39       128         6         1
  3Q GAIN WILD-TYPE      17       39        43       125         6         0
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                10                17
  STAGE II               37                39
  STAGE III              39                43
  STAGE IVA             128               125
  STAGE IVB               6                 6
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  3Q GAIN MUTATED      22 69 49 85
  3Q GAIN WILD-TYPE    28 68 51 88
D6V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1              22                28
  T2                 69                68
  T3                 49                51
  T4                 85                88
[1] 4 2
[1] 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
  3Q GAIN MUTATED    72  36  95   6
  3Q GAIN WILD-TYPE 107  32  73   2
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              72               107
  N1              36                32
  N2              95                73
  N3               6                 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"
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    88   1
  3Q GAIN WILD-TYPE 101   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     88    1
  3Q GAIN WILD-TYPE  101    0
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              88               101
  1               1                 0
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    58 196
  3Q GAIN WILD-TYPE  82 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     58  196
  3Q GAIN WILD-TYPE   82  186
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              58                82
  MALE               196               186
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    67 140
  3Q GAIN WILD-TYPE  84 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     67  140
  3Q GAIN WILD-TYPE   84  143
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               67                84
  YES             140               143
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  3Q GAIN MUTATED                                     249
  3Q GAIN WILD-TYPE                                   262
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  3Q GAIN MUTATED                                                             0
  3Q GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  3Q GAIN MUTATED                                                     5
  3Q GAIN WILD-TYPE                                                   5
D6V9, multiclass
                                                             clus
vv                                                            3Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   249
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       5
                                                             clus
vv                                                            3Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     262
  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"
D6V10, continuous
D6V11, continuous
D6V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  1     5
  3Q GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                          23   214
  3Q GAIN WILD-TYPE                        25   232
D6V13, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          5                 6
  BLACK OR AFRICAN AMERICAN                     23                25
  WHITE                                        214               232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V14, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    13 218
  3Q GAIN WILD-TYPE  13 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     13  218
  3Q GAIN WILD-TYPE   13  241
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  13                13
  NOT HISPANIC OR LATINO             218               241
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    21  20
  4P GAIN WILD-TYPE 282 198
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               41               480 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               20               198 
$`4P GAIN MUTATED`
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6DI TCGA-BB-4225 TCGA-CN-4727 
       12.62         4.01        41.85        11.05         4.60        51.29 
TCGA-CN-4737 TCGA-CN-4740 TCGA-CQ-6224 TCGA-CQ-7069 TCGA-CR-5247 TCGA-CR-7389 
       20.55        27.58        56.58        41.88        11.77        12.89 
TCGA-CV-5430 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6939 
      139.43        86.83        48.59        60.49        54.74        21.90 
TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7090 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7255 
       12.03        65.82       126.15         1.84        10.75         2.10 
TCGA-CV-7263 TCGA-CV-7416 TCGA-CV-7424 TCGA-CV-7433 TCGA-CV-A45W TCGA-DQ-5625 
       18.41        25.08        14.89        19.76        45.96        37.25 
TCGA-DQ-7592 TCGA-F7-A623 TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-MT-A67D TCGA-MZ-A5BI 
       37.58        20.25        13.68        15.48         1.84         7.13 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-UF-A7JK 
        2.04        29.00        18.64        14.76        13.94 

$`4P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       20.48        65.59        68.48        15.52        21.17        14.83 
TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
        3.55        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-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.41        18.38        22.42        36.72        33.70        50.20 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       44.98        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-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
       12.69        48.76        55.86        38.04         4.67        56.68 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       12.89        26.86        32.81        52.14        57.11        12.99 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       14.33        45.83        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
        8.58        12.39        71.31         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.84        11.57        12.49         8.52        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        34.13         6.74         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       11.08        10.45        32.22        35.05        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        32.48        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       17.29        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       19.82        24.39        20.88        19.53        48.20        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 
       10.42        11.21         4.24        41.19        32.38        32.88 
TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       46.95        13.25         4.24        14.99        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 
       64.87        53.52        16.73        43.04        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-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-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       47.18        39.16        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.09        24.95        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       27.06        29.82        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58         7.10         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-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        87.55        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 
       17.92        13.35        23.05         7.07        43.23        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
       20.52         4.73        26.43        11.24       140.78        19.79 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 
       42.38        15.09        30.08         6.08        53.95        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-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      111.16        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 
       52.31        12.92        21.80        71.21       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-7261 
       17.13        95.34         4.96        11.87        47.97        36.13 
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-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
        0.46        22.85        25.94         0.07        34.09       100.57 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       56.48       156.49        54.94         3.52        16.27        84.49 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
        7.17       153.86        16.64         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       21.01       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       56.61         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
       19.92        22.52        10.42        10.42        10.55        18.84 
TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       34.36        51.12        13.25        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
        2.53        16.14        11.44        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 
       13.94        12.10        12.79        11.11        58.45        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
       33.86        18.02        14.04        46.32        46.45        20.45 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       40.24        40.04        39.12        41.59        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       21.63        20.25         3.02        31.13        18.94        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
        0.46        17.85        11.80        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       15.06        13.61        21.11        20.94         0.07        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       25.74        21.93        27.48        27.48        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O 
       11.84        37.41         0.07        33.57         5.29        13.84 
TCGA-IQ-A6SG TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       19.04        13.35        18.15        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 
        7.96        30.05        12.62         6.25        15.42        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       17.98        29.92        15.78        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T6 
       36.82        47.01        19.00        75.55        18.97        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       16.01        13.15        21.07        21.21        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
       21.47         9.34        12.72        21.07        19.73         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
        5.62        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       16.96         6.87        15.91         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        3.12        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        49.51        48.03        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JO 
       17.95        24.30        55.43        29.46        18.05        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 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             1.84              0.07 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           139.43            210.97 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            19.76             21.07 
[1] "1.8 - 139.4 (19.8)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.2"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  4P GAIN MUTATED         0        8         4        21         0         0
  4P GAIN WILD-TYPE      27       68        78       232        12         1
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 0                27
  STAGE II                8                68
  STAGE III               4                78
  STAGE IVA              21               232
  STAGE IVB               0                12
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4P GAIN MUTATED       1  13   4  15
  4P GAIN WILD-TYPE    49 124  96 158
D7V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1               1                49
  T2                 13               124
  T3                  4                96
  T4                 15               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
  4P GAIN MUTATED     8   5  14   0
  4P GAIN WILD-TYPE 171  63 154   8
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               8               171
  N1               5                63
  N2              14               154
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    11   0
  4P GAIN WILD-TYPE 178   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     11    0
  4P GAIN WILD-TYPE  178    1
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              11               178
  1               0                 1
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    10  31
  4P GAIN WILD-TYPE 130 351
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     10   31
  4P GAIN WILD-TYPE  130  351
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              10               130
  MALE                31               351
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    12  19
  4P GAIN WILD-TYPE 139 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     12   19
  4P GAIN WILD-TYPE  139  264
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               12               139
  YES              19               264
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  4P GAIN MUTATED                                      41
  4P GAIN WILD-TYPE                                   470
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  4P GAIN MUTATED                                                             0
  4P GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  4P GAIN MUTATED                                                     0
  4P GAIN WILD-TYPE                                                  10
D7V9, multiclass
                                                             clus
vv                                                            4P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    41
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            4P GAIN 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                        10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, continuous
D7V11, continuous
D7V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  1     1
  4P GAIN WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           7    31
  4P GAIN WILD-TYPE                        41   415
D7V13, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      7                41
  WHITE                                         31               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"
D7V14, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4  32
  4P GAIN WILD-TYPE  22 427
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4   32
  4P GAIN WILD-TYPE   22  427
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              32               427
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    19  18
  4Q GAIN WILD-TYPE 284 200
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               37               484 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               18               200 
$`4Q GAIN MUTATED`
TCGA-BA-6872 TCGA-BB-4225 TCGA-BB-A5HZ TCGA-CN-4727 TCGA-CN-4740 TCGA-CN-5363 
       12.62         4.60        27.19        51.29        27.58         8.32 
TCGA-CQ-7069 TCGA-CR-5247 TCGA-CR-6491 TCGA-CR-7389 TCGA-CV-5436 TCGA-CV-5977 
       41.88        11.77        22.78        12.89        19.20        60.49 
TCGA-CV-6939 TCGA-CV-6945 TCGA-CV-7090 TCGA-CV-7102 TCGA-CV-7242 TCGA-CV-7245 
       21.90        12.03       126.15         1.84        36.00        26.20 
TCGA-CV-7263 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7433 TCGA-CV-A45W TCGA-CV-A45X 
       18.41        22.85        25.08        19.76        45.96         6.51 
TCGA-D6-6826 TCGA-DQ-5625 TCGA-F7-A623 TCGA-HD-7753 TCGA-IQ-A61L TCGA-MT-A67D 
       11.44        37.25        20.25        28.47        13.68         1.84 
TCGA-MZ-A5BI TCGA-P3-A6SW TCGA-P3-A6T4 TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z9 
        7.13        36.82         2.04        18.64        19.73        14.76 
TCGA-UF-A7J9 
       44.65 

$`4Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       20.48        65.59        68.48        15.52        21.17        14.83 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
        3.55         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        27.95        11.54         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
        7.82         2.27        11.05        13.38        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
        6.15       105.90         9.14         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
       36.72        33.70        50.20        44.98        66.28        24.66 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A6UM 
       38.40        71.05        20.52        25.71        10.55        12.92 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
        8.81         6.28        12.69        48.76        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        4.67        56.68        12.89        26.86        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 
       57.11        12.99        20.55        14.33        45.83        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        42.02        46.32         8.58        12.39        71.31 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       16.21        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
       47.44        28.04        19.07        34.13         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        9.24        52.08        11.08        10.45        32.22        35.05 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 
       38.89         3.68        17.42        32.48        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       25.41        23.57        17.29        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
        2.70        23.44        19.82        24.39        20.88        19.53 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.38        32.88        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
       14.99        38.76        70.13        64.87        53.52        16.73 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       43.04        43.10        77.56        44.48        11.61        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-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-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6492 TCGA-CR-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-7390 TCGA-CR-7391 TCGA-CR-7392 
       32.78        47.01        27.06        29.82        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58         7.10         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
      108.95        76.24        17.95       107.51        87.55        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       48.59         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-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 
        4.73        26.43        11.24       140.78        19.79        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-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      111.16        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
       52.31        12.92        21.80        71.21        10.75       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7248 
       77.16         4.73        47.47        31.36        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-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-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 
        0.46        25.94         0.07        34.09       100.57        14.89 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       56.48       156.49        54.94         3.52        16.27        84.49 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
        7.17       153.86        16.64         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       21.01       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
        7.07        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
       22.52        10.42        10.42        10.55        18.84        34.36 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6827 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-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       28.77         7.63        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-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        46.32        46.45        20.45        37.58        40.24 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       40.04        39.12        41.59        37.18        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       17.85        11.80        12.43        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 
       13.61        21.11        20.94         0.07        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       27.48        27.48        14.66        22.03        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
        0.36        13.84         4.27         3.65         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
        0.07        33.57         5.29        13.84        19.04        15.48 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        19.27        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       30.05        12.62         6.25        15.42        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SX 
       29.92        15.78        71.74        51.25        10.85        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       19.00        75.55        18.97        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA 
        9.34        12.72        21.07         6.51         5.62        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       17.82        15.32         8.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
       15.91         7.10        32.45        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.25        20.35        64.80        54.67         2.83        49.51 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       48.03        49.45        74.47        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       29.46        18.05        13.94        20.75        22.36        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        17.03        20.55        14.56 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             1.84              0.07 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           126.15            210.97 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            19.76             21.04 
[1] "1.8 - 126.2 (19.8)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1.4"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  4Q GAIN MUTATED         1        8         0        20         2         0
  4Q GAIN WILD-TYPE      26       68        82       233        10         1
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 1                26
  STAGE II                8                68
  STAGE III               0                82
  STAGE IVA              20               233
  STAGE IVB               2                10
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4Q GAIN MUTATED       2   9   4  16
  4Q GAIN WILD-TYPE    48 128  96 157
D8V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1               2                48
  T2                  9               128
  T3                  4                96
  T4                 16               157
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4Q GAIN MUTATED    10   3  12   2
  4Q GAIN WILD-TYPE 169  65 156   6
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              10               169
  N1               3                65
  N2              12               156
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    14   0
  4Q GAIN WILD-TYPE 175   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     14    0
  4Q GAIN WILD-TYPE  175    1
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              14               175
  1               0                 1
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     9  28
  4Q GAIN WILD-TYPE 131 354
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      9   28
  4Q GAIN WILD-TYPE  131  354
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               9               131
  MALE                28               354
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    10  16
  4Q GAIN WILD-TYPE 141 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     10   16
  4Q GAIN WILD-TYPE  141  267
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               10               141
  YES              16               267
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  4Q GAIN MUTATED                                      36
  4Q GAIN WILD-TYPE                                   475
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  4Q GAIN MUTATED                                                             0
  4Q GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  4Q GAIN MUTATED                                                     1
  4Q GAIN WILD-TYPE                                                   9
D8V9, multiclass
                                                             clus
vv                                                            4Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    36
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            4Q GAIN 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                         9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, continuous
D8V11, continuous
D8V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     0
  4Q GAIN WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           8    28
  4Q GAIN WILD-TYPE                        40   418
D8V13, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      8                40
  WHITE                                         28               418
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     4  29
  4Q GAIN WILD-TYPE  22 430
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4   29
  4Q GAIN WILD-TYPE   22  430
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              29               430
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   116  84
  5P GAIN WILD-TYPE 187 134
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              200               321 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               84               134 
$`5P GAIN MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-5556 
        3.35        15.19         9.30         9.07        17.10        23.84 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       65.59        68.48        15.52        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A6D8 TCGA-BA-A6DB 
        4.01        41.85        29.42        28.11        27.95         7.10 
TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4227 
       14.47        11.05        20.48         6.15       105.90         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 
       18.38        22.42        50.20        66.28        71.05        20.52 
TCGA-BB-A5HU TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 
       25.71         6.28        55.86        51.29        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4742 
       32.81        12.99        20.55        14.33        45.83        13.05 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6019 
       12.39         8.32        11.84        50.07        30.67        34.13 
TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A498 
        6.74        52.08        35.05        38.89        32.48        25.41 
TCGA-CN-A49B TCGA-CN-A63W TCGA-CN-A6UY TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5330 
       29.72        12.39        23.44        24.39        20.88        62.37 
TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7072 
       32.88        56.58        13.25        64.87        16.73        77.56 
TCGA-CQ-A4CD TCGA-CR-5243 TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
       33.60        84.23        58.42        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-7365 TCGA-CR-7367 
       16.90        11.64        12.46        15.75        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7389 
       40.93        35.84        34.06        19.92        17.13        12.89 
TCGA-CR-7392 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5435 
       46.85         5.13         5.95        48.39        17.16        76.24 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       17.95       107.51        76.50        80.12        17.92        13.35 
TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6945 
        7.07         9.60         5.46        20.52        11.24        12.03 
TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
       65.82         7.13         8.42         2.50       126.15       111.16 
TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
       18.81         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7409 TCGA-CV-7416 
       71.21        10.75        77.16        26.20        17.85        25.08 
TCGA-CV-7421 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7437 TCGA-CV-A45R TCGA-CV-A45U 
        0.07        14.89         3.52        16.64       180.16        35.47 
TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A6JE TCGA-CX-7086 
        6.51        48.20         0.76         7.07        35.34        18.84 
TCGA-D6-8568 TCGA-D6-8569 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 
       24.95        25.32        30.94        33.86        18.02        46.32 
TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A620 
       46.45        37.58        41.59        31.13        18.94        17.85 
TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
       15.06        20.94        28.47        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-A61E 
       14.66        22.85         3.65        34.75        15.95        37.71 
TCGA-IQ-A61J TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T 
       33.57        13.84        19.04        15.48        13.35        18.15 
TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A7BN TCGA-MZ-A5BI 
       19.27        14.37         7.96         1.84        15.42         7.13 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
       17.98        15.78        71.74        36.82        47.01        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       18.97         2.04        12.99        13.15        21.07        21.21 
TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
        7.30        12.72        19.73         5.62        14.76        12.20 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A71A 
        8.32        12.72        15.91        13.55        13.25         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JK TCGA-UF-A7JS 
       49.51        48.03        74.47        55.43        13.94        22.36 
TCGA-UP-A6WW TCGA-WA-A7GZ 
       17.03        20.55 

$`5P GAIN WILD-TYPE`
TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64        37.28        26.50        23.74        42.35        57.93 
TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DD 
       20.48         3.55        20.45        30.18        11.54         5.69 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4225 
        7.82         2.27        13.38        16.41         9.14         4.60 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HY 
       36.72        33.70        44.98        24.66        38.40        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 
       27.19        12.92         8.81        12.69        48.76        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-4741 
        4.67        56.68        52.14        57.11        27.58        73.61 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 
       42.02        46.32         8.58        71.31        16.21        11.54 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 
       11.57        12.49         8.52        52.08        56.94        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6022 
       23.90        47.44        28.04        19.07         9.07         9.24 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       11.08        10.45        32.22         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       35.01        23.57        17.29        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6V1 
       22.32        16.57         4.41        12.07         2.70        19.82 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       19.53        48.20        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       70.45        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       32.38        46.95         4.24        14.99        38.76        70.13 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       53.52        43.04        41.88        43.10        44.48        11.61 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       23.24        29.36        29.49        14.14        12.46        31.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6472 
       11.77        54.67        37.87        26.27        50.01        34.52 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 
        6.02        11.90        10.22        11.34         7.69        22.78 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        9.27        47.18         3.45         3.09        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
        0.99        31.96         9.17        26.17        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       27.06        29.82        30.02        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
        7.10        35.41        29.95       139.43       129.21       108.95 
TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       19.20        87.55        91.53        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 
       60.49        43.23        54.74        21.07        62.43        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6942 
        2.14         9.70         4.73        21.90        26.43       140.78 
TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       19.79        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6955 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7097 TCGA-CV-7099 
       10.98        28.34         4.14        64.83        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
        9.01       130.88         4.73        47.47        36.00        31.36 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       18.97        17.13        95.34         4.96        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 
        2.10        36.13        18.41        57.47        35.54       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7422 
       89.33         9.67         0.46        22.85        25.94        34.09 
TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
      100.57        56.48       156.49        54.94        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
       19.76         7.17       153.86         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Y 
       21.01       169.38       159.65         1.05        45.96        88.87 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM 
       60.43        67.86        56.61        15.25         5.98         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 
       19.92        22.52        10.42        10.42        10.55        34.36 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       16.14        11.44        18.67        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        7.63        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7593 
       11.11        58.45        37.25        14.04        20.45        40.24 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       40.04        39.12        37.18        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
        3.02        24.95         0.46        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7754 
       13.38        15.16        13.61        21.11         0.07        25.74 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
       22.03        12.66         0.36        13.84         4.27         6.90 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61K 
       38.53        14.50        11.84        37.41         0.07         5.29 
TCGA-IQ-A61L TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
       13.68        10.75        30.05        12.62         6.25        16.08 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6T0 TCGA-P3-A6T5 TCGA-P3-A6T7 
       29.92        51.25        10.85        19.00        29.00        16.01 
TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 
       23.15        21.47         9.34        18.64        21.07         6.51 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
       17.82        15.32        16.96         6.87         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71E 
       13.71         3.12        20.35        64.80        54.67        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JO 
       44.65        17.95        24.30        29.46        18.05        20.75 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-WA-A7H4 
       32.65         2.96        14.56 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.07              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           180.16            210.97 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           19.825            21.500 
[1] "0.1 - 180.2 (19.8)" "0.1 - 211.0 (21.5)"
[1] "hr=" "1"  
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  5P GAIN MUTATED         7       21        35       100         5         1
  5P GAIN WILD-TYPE      20       55        47       153         7         0
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 7                20
  STAGE II               21                55
  STAGE III              35                47
  STAGE IVA             100               153
  STAGE IVB               5                 7
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5P GAIN MUTATED      16  51  40  68
  5P GAIN WILD-TYPE    34  86  60 105
D9V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1              16                34
  T2                 51                86
  T3                 40                60
  T4                 68               105
[1] 4 2
[1] 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
  5P GAIN MUTATED    53  32  71   4
  5P GAIN WILD-TYPE 126  36  97   4
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              53               126
  N1              32                36
  N2              71                97
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    70   1
  5P GAIN WILD-TYPE 119   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     70    1
  5P GAIN WILD-TYPE  119    0
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              70               119
  1               1                 0
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    47 154
  5P GAIN WILD-TYPE  93 228
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     47  154
  5P GAIN WILD-TYPE   93  228
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              47                93
  MALE               154               228
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    52 122
  5P GAIN WILD-TYPE  99 161
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     52  122
  5P GAIN WILD-TYPE   99  161
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               52                99
  YES             122               161
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  5P GAIN MUTATED                                     198
  5P GAIN WILD-TYPE                                   313
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  5P GAIN MUTATED                                                             1
  5P GAIN WILD-TYPE                                                           0
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  5P GAIN MUTATED                                                     2
  5P GAIN WILD-TYPE                                                   8
D9V9, multiclass
                                                             clus
vv                                                            5P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   198
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            5P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     313
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, continuous
D9V11, continuous
D9V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  1     3
  5P GAIN WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                          24   168
  5P GAIN WILD-TYPE                        24   278
D9V13, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                     24                24
  WHITE                                        168               278
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    15 173
  5P GAIN WILD-TYPE  11 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     15  173
  5P GAIN WILD-TYPE   11  286
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                  15                11
  NOT HISPANIC OR LATINO             173               286
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    40  28
  5Q GAIN WILD-TYPE 263 190
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               68               453 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               28               190 
$`5Q GAIN MUTATED`
TCGA-BA-4074 TCGA-BA-5149 TCGA-BA-5556 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-A4IF 
       15.19        26.50        23.84        21.17        14.83        29.42 
TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4223 TCGA-BB-7861 TCGA-BB-7864 TCGA-BB-A5HU 
       11.05        20.48       105.90        22.42        50.20        25.71 
TCGA-CN-4738 TCGA-CN-5363 TCGA-CN-6011 TCGA-CN-6023 TCGA-CN-6997 TCGA-CN-A49B 
       14.33         8.32        30.67        52.08        32.48        29.72 
TCGA-CN-A6UY TCGA-CN-A6V3 TCGA-CQ-6224 TCGA-CQ-7067 TCGA-CR-5243 TCGA-CR-6471 
       23.44        24.39        56.58        16.73        84.23        39.52 
TCGA-CR-6473 TCGA-CR-6484 TCGA-CR-7389 TCGA-CR-7399 TCGA-CV-5431 TCGA-CV-5439 
       36.99        11.64        12.89         5.95        17.16        17.95 
TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-6441 TCGA-CV-6936 TCGA-CV-6945 TCGA-CV-6954 
       76.50        80.12         9.60         5.46        12.03        65.82 
TCGA-CV-6956 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7416 TCGA-CV-A45U 
        7.13         1.84        77.16        26.20        25.08        35.47 
TCGA-CV-A463 TCGA-D6-8569 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-F7-A50J 
        0.76        25.32        30.94        33.86        46.45        31.13 
TCGA-F7-A61S TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-A61O 
       18.94        21.93        27.48        22.85         3.65        13.84 
TCGA-MT-A51W TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6T2 
       14.37         7.13        17.98        15.78        71.74        75.55 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A6IG TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-TN-A7HJ 
        2.04        13.15         7.30        12.20         8.32        13.25 
TCGA-UF-A7JS TCGA-WA-A7GZ 
       22.36        20.55 

$`5Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 
        3.35         9.30        13.64        37.28         9.07        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       42.35        57.93        17.10        20.48        65.59        68.48 
TCGA-BA-6868 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG 
       15.52         3.55        12.62         4.01        41.85        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-A6DJ TCGA-BA-A8YP TCGA-BB-4217 
       14.47         7.82         2.27        13.38        16.41         6.15 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 
        9.14         4.60         4.41        18.38        36.72        33.70 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       44.98        66.28        24.66        38.40        71.05        20.52 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       10.55        27.19        12.92         8.81         6.28        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
       48.76        55.86        38.04         4.67        51.29        56.68 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       12.89        26.86        32.81        52.14        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       20.55        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 
       46.32         8.58        12.39        71.31        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.84        11.57        12.49         8.52        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       50.07        48.00        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 
       34.13         6.74         9.07         9.24        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       32.22        35.05        38.89         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T 
       35.01        25.41        23.57        17.29        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
        2.70        19.82        20.88        19.53        48.20        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 
       10.42        11.21         4.24        41.19        32.38        32.88 
TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       46.95        13.25         4.24        14.99        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       64.87        53.52        43.04        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-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-6472 TCGA-CR-6474 TCGA-CR-6477 
       26.27        58.42        50.01        34.52        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-7365 TCGA-CR-7367 
       22.78        15.75         9.27        47.18        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       40.93        35.84         3.45         3.09        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
        0.99        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 
       17.13        32.78        47.01        27.06        29.82        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58         7.10         5.13 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
       35.41        29.95        48.39       139.43       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 
       76.24        19.20       107.51        87.55        91.53        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-6933 TCGA-CV-6934 
       43.23        54.74        21.07        62.43        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        9.70        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
      140.78        19.79        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       53.95        10.98         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-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        9.01         5.26        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
       10.75       130.88         4.73        47.47        36.00        31.36 
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-7418 
      210.97        89.33         9.67         0.46        22.85        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-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
       54.94         3.52        16.27        84.49        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
      153.86        16.64         6.38        22.19        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      169.38       180.16       159.65         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 
       88.87        48.20        60.43        67.86        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ 
       10.42        10.42        10.55        18.84        34.36        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       11.44        18.67        24.95        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        7.63        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       11.11        58.45        37.25        18.02        14.04        46.32 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45        37.58        40.24        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V 
       37.18        32.71        21.63        20.25         3.02        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
        0.46        17.85        11.80        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       15.16        15.06        13.61        21.11        20.94         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
       28.47        25.74        27.48        14.66        22.03        12.66 
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 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S 
       33.57         5.29        13.68        19.04        15.48        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       18.15        19.27        10.75         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
       12.62         6.25        15.42        16.08        29.92        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T5 
       10.85        36.82        47.01        19.00        18.97        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH 
       12.99        16.01        21.07        21.21        23.15        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        18.64        21.07        19.73         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP 
        5.62        14.76        17.82        15.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        6.87        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.55        20.35        64.80        54.67         2.83        49.51 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       48.03        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT 
       55.43        29.46        18.05        13.94        20.75        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
        2.96        17.03        14.56 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.76              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           105.90            210.97 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           22.145            20.750 
[1] "0.8 - 105.9 (22.1)" "0.1 - 211.0 (20.8)"
[1] "hr=" "1"  
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  5Q GAIN MUTATED         3        3        10        38         1         0
  5Q GAIN WILD-TYPE      24       73        72       215        11         1
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 3                24
  STAGE II                3                73
  STAGE III              10                72
  STAGE IVA              38               215
  STAGE IVB               1                11
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5Q GAIN MUTATED       6  13  18  21
  5Q GAIN WILD-TYPE    44 124  82 152
D10V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1               6                44
  T2                 13               124
  T3                 18                82
  T4                 21               152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5Q GAIN MUTATED    16   9  29   1
  5Q GAIN WILD-TYPE 163  59 139   7
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              16               163
  N1               9                59
  N2              29               139
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    21   0
  5Q GAIN WILD-TYPE 168   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     21    0
  5Q GAIN WILD-TYPE  168    1
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              21               168
  1               0                 1
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    13  55
  5Q GAIN WILD-TYPE 127 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     13   55
  5Q GAIN WILD-TYPE  127  327
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              13               127
  MALE                55               327
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    13  46
  5Q GAIN WILD-TYPE 138 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     13   46
  5Q GAIN WILD-TYPE  138  237
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               13               138
  YES              46               237
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  5Q GAIN MUTATED                                      67
  5Q GAIN WILD-TYPE                                   444
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  5Q GAIN MUTATED                                                             1
  5Q GAIN WILD-TYPE                                                           0
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  5Q GAIN MUTATED                                                     0
  5Q GAIN WILD-TYPE                                                  10
D10V9, multiclass
                                                             clus
vv                                                            5Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    67
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            5Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     444
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, continuous
D10V11, continuous
D10V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     1
  5Q GAIN WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           8    58
  5Q GAIN WILD-TYPE                        40   388
D10V13, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      8                40
  WHITE                                         58               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"
D10V14, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     7  58
  5Q GAIN WILD-TYPE  19 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7   58
  5Q GAIN WILD-TYPE   19  401
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                19
  NOT HISPANIC OR LATINO              58               401
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    46  36
  6P GAIN WILD-TYPE 257 182
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               82               439 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               36               182 
$`6P GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A4II TCGA-BA-A6DI 
        9.30        17.10        14.83         4.01        30.18        11.05 
TCGA-BB-4224 TCGA-BB-7870 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-5356 
        9.14        66.28        10.55         6.28        55.86        46.32 
TCGA-CN-5363 TCGA-CN-5367 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 
        8.32        11.57         6.74         9.24        52.08        32.22 
TCGA-CN-A49A TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V6 TCGA-CQ-5329 
       17.29        31.69        12.39        12.07        20.88        70.45 
TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CQ-A4CE 
       45.99         4.24        32.38        16.73        11.61        29.49 
TCGA-CR-5247 TCGA-CR-6487 TCGA-CR-7368 TCGA-CR-7389 TCGA-CR-7402 TCGA-CV-5430 
       11.77         7.69        40.93        12.89        29.95       139.43 
TCGA-CV-5442 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6954 
       76.50        60.49        54.74        90.12        20.52        65.82 
TCGA-CV-6959 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7255 TCGA-CV-7407 
        8.42        77.16        31.36        95.34         2.10        35.54 
TCGA-CV-7415 TCGA-CV-7440 TCGA-CV-A45U TCGA-CV-A6JE TCGA-CV-A6JU TCGA-D6-A6EP 
       22.85        22.19        35.47        35.34         3.62        13.94 
TCGA-DQ-5625 TCGA-F7-A50I TCGA-H7-8502 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 
       37.25         3.02        15.06        28.47        21.93        27.48 
TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-KU-A66T TCGA-MT-A51W 
        6.90        37.71        13.68        15.48        18.15        14.37 
TCGA-MT-A67D TCGA-MZ-A5BI TCGA-P3-A6SW TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-QK-A6IG 
        1.84         7.13        36.82        18.97         2.04         7.30 
TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-RS-A6TO TCGA-TN-A7HJ 
       21.07         6.51        14.76        12.20        12.72        13.25 
TCGA-UF-A719 TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JK 
       54.67        24.30        29.46        13.94 

$`6P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       23.74        42.35        57.93        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 
       68.48        15.52        21.17         3.55        12.62        41.85 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       29.42        28.11        20.45        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
        5.69        14.47         7.82         2.27        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
       16.41         6.15       105.90         4.60         4.41        18.38 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 
       22.42        36.72        33.70        50.20        44.98        24.66 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM 
       38.40        71.05        20.52        25.71        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
        8.81        12.69        48.76        38.04         4.67        51.29 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       56.68        12.89        26.86        32.81        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5364 
       13.05        42.02         8.58        12.39        71.31        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.54        11.84        12.49         8.52        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
       19.07        34.13         9.07        11.08        10.45        35.05 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 
       38.89         3.68        17.42        32.48        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V 
       25.41        23.57        29.72        21.21         7.40        22.32 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
       16.57         4.41         2.70        23.44        19.82        24.39 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       19.53        48.20        52.37        21.50         2.93        54.58 
TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
       62.37        10.42        11.21        41.19        32.88        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       56.58        13.25         4.24        14.99        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       64.87        53.52        43.04        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH 
       44.48        23.24        29.36        33.60        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       31.23        84.23        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-6488 
        6.02        11.90        10.22        11.34        11.64        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       22.78        15.75         9.27        47.18        39.16        47.34 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       32.78        47.01        27.06        29.82        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58         7.10         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       35.41        48.39        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 
       19.20        17.95       107.51        87.55        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 
       17.92        13.35        23.05        86.83        48.59         7.07 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
       43.23        21.07        62.43         9.60         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
        5.46         4.73        21.90        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       53.95        10.98         7.13        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-7236 TCGA-CV-7238 TCGA-CV-7242 
       71.21        10.75       130.88         4.73        47.47        36.00 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       26.20        18.97        17.13         4.96        11.87        47.97 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       36.13        18.41        57.47        17.85       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        9.67         0.46        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 
      100.57        14.89        56.48       156.49        54.94         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-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
        6.38        27.98        21.01       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-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ 
        6.38        29.79         6.48        28.01        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
       19.92        22.52        10.42        10.42        10.55        18.84 
TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       34.36        51.12        13.25        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
        2.53        16.14        11.44        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-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        46.32        46.45        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       40.24        40.04        39.12        41.59        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       21.63        20.25        31.13        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       17.85        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 
       13.61        21.11        20.94         0.07        25.74        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65        34.75        15.95        38.53        14.50 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O 
       11.84        37.41         0.07        33.57         5.29        13.84 
TCGA-IQ-A6SG TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A 
       19.04        13.35        19.27        10.75         7.96        30.05 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
       12.62         6.25        15.42        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T0 
       15.78        71.74        51.25        10.85        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       75.55        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.21        23.15        21.47         9.34        12.72        18.64 
TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP 
       19.73         5.62        17.82        15.32         8.32        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        6.87        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D 
       13.55        20.35        64.80         2.83        49.51        48.03 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JJ 
       49.45        44.65        74.47        17.95        55.43        18.05 
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 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             1.84              0.07 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           139.43            210.97 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            17.72             21.11 
[1] "1.8 - 139.4 (17.7)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.2"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  6P GAIN MUTATED         4       12        14        39         4         0
  6P GAIN WILD-TYPE      23       64        68       214         8         1
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 4                23
  STAGE II               12                64
  STAGE III              14                68
  STAGE IVA              39               214
  STAGE IVB               4                 8
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6P GAIN MUTATED       4  23  17  31
  6P GAIN WILD-TYPE    46 114  83 142
D11V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1               4                46
  T2                 23               114
  T3                 17                83
  T4                 31               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
  6P GAIN MUTATED    30  12  27   2
  6P GAIN WILD-TYPE 149  56 141   6
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              30               149
  N1              12                56
  N2              27               141
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    33   0
  6P GAIN WILD-TYPE 156   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     33    0
  6P GAIN WILD-TYPE  156    1
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              33               156
  1               0                 1
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    19  64
  6P GAIN WILD-TYPE 121 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     19   64
  6P GAIN WILD-TYPE  121  318
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              19               121
  MALE                64               318
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    26  45
  6P GAIN WILD-TYPE 125 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     26   45
  6P GAIN WILD-TYPE  125  238
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               26               125
  YES              45               238
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  6P GAIN MUTATED                                      81
  6P GAIN WILD-TYPE                                   430
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  6P GAIN MUTATED                                                             0
  6P GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  6P GAIN MUTATED                                                     2
  6P GAIN WILD-TYPE                                                   8
D11V9, multiclass
                                                             clus
vv                                                            6P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    81
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            6P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     430
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, continuous
D11V11, continuous
D11V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0     1
  6P GAIN WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                          15    62
  6P GAIN WILD-TYPE                        33   384
D11V13, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                     15                33
  WHITE                                         62               384
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V14, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     4  71
  6P GAIN WILD-TYPE  22 388
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4   71
  6P GAIN WILD-TYPE   22  388
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              71               388
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    34  28
  6Q GAIN WILD-TYPE 269 190
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               62               459 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               28               190 
$`6Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-6873 TCGA-BA-A4II TCGA-BB-7870 TCGA-BB-A5HU TCGA-C9-A47Z 
        9.30         4.01        30.18        66.28        25.71         6.28 
TCGA-CN-4723 TCGA-CN-5356 TCGA-CN-5363 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-A49A 
       55.86        46.32         8.32         6.74         9.24        17.29 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A6V6 TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-6220 
       31.69        12.39        20.88        45.99         4.24        32.38 
TCGA-CQ-7067 TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-7380 TCGA-CR-7389 TCGA-CV-5430 
       16.73        29.49        11.77        19.92        12.89       139.43 
TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6959 
       76.50        86.83        60.49        54.74        90.12         8.42 
TCGA-CV-6962 TCGA-CV-7255 TCGA-CV-7415 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45R 
        4.14         2.10        22.85         7.17        22.19       180.16 
TCGA-CV-A465 TCGA-CV-A6JM TCGA-CX-7219 TCGA-D6-A6EP TCGA-DQ-5625 TCGA-F7-A50I 
        7.07         6.38        34.36        13.94        37.25         3.02 
TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-IQ-A61L 
       28.47        21.93        27.48         6.90        37.71        13.68 
TCGA-IQ-A6SH TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67D TCGA-MZ-A5BI TCGA-P3-A5Q6 
       15.48        18.15        14.37         1.84         7.13        15.78 
TCGA-P3-A6T4 TCGA-QK-A6IG TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-RS-A6TO 
        2.04         7.30        21.07         6.51        12.20        12.72 
TCGA-UF-A719 TCGA-UF-A71E 
       54.67        49.45 

$`6Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 
       12.62        41.85        29.42        28.11        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       33.70        50.20        44.98        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 
       20.52        10.55        27.19        12.92         8.81        12.69 
TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       48.76        38.04         4.67        51.29        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       26.86        32.81        52.14        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
        8.58        12.39        71.31        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.57        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        48.00        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
       34.13         9.07        52.08        11.08        10.45        32.22 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       35.05        38.89         3.68        17.42        32.48        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       35.01        25.41        23.57        29.72        21.21         7.40 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       22.32        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       19.82        24.39        19.53        48.20        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 
        2.93        54.58        70.45        62.37        10.42        11.21 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       41.19        32.88        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
       14.99        38.76        70.13        64.87        53.52        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       29.36        33.60        14.14        12.46        31.23        84.23 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       34.52        36.99        18.54        16.90         6.02        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       15.75         9.27        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
       31.96         9.17        34.06        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       47.01        27.06        29.82        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58         7.10         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       29.95        48.39        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 
       19.20        17.95       107.51        87.55        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
       17.92        13.35        23.05        48.59         7.07        43.23 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       21.07        62.43         9.60         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 
       53.95        65.82        10.98         7.13        28.34         2.50 
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-7261 TCGA-CV-7263 TCGA-CV-7406 
        4.96        11.87        47.97        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-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-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       56.48       156.49        54.94         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P 
       19.76       153.86        16.64         6.38        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      169.38       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-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
       15.25         5.98        35.34        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       22.59        24.95        12.10        12.79        11.11        58.45 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       30.94        33.86        18.02        14.04        46.32        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45        37.58        40.24        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S 
       37.18        32.71        21.63        20.25        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       24.95         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
        0.07        25.74        27.48        14.66        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 
       22.85         0.36        13.84         4.27         3.65        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       15.95        38.53        14.50        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A66S TCGA-KU-A6H7 
       33.57         5.29        13.84        19.04        13.35        19.27 
TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
       10.75         7.96        30.05        12.62         6.25        15.42 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       16.08        17.98        29.92        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 
       36.82        47.01        19.00        75.55        18.97        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z8 
       21.47         9.34        12.72        18.64        19.73         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX 
       14.76        17.82        15.32         8.32        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
       15.91         7.10        32.45        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D 
       13.25        20.35        64.80         2.83        49.51        48.03 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       18.05        13.94        20.75        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             1.84              0.07 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           180.16            210.97 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            17.01             21.11 
[1] "1.8 - 180.2 (17.0)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.2"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  6Q GAIN MUTATED         3        8        15        27         3         0
  6Q GAIN WILD-TYPE      24       68        67       226         9         1
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 3                24
  STAGE II                8                68
  STAGE III              15                67
  STAGE IVA              27               226
  STAGE IVB               3                 9
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6Q GAIN MUTATED       3  18  12  25
  6Q GAIN WILD-TYPE    47 119  88 148
D12V4, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1               3                47
  T2                 18               119
  T3                 12                88
  T4                 25               148
[1] 4 2
[1] 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
  6Q GAIN MUTATED    26  12  16   1
  6Q GAIN WILD-TYPE 153  56 152   7
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              26               153
  N1              12                56
  N2              16               152
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    22   0
  6Q GAIN WILD-TYPE 167   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     22    0
  6Q GAIN WILD-TYPE  167    1
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              22               167
  1               0                 1
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    15  48
  6Q GAIN WILD-TYPE 125 334
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     15   48
  6Q GAIN WILD-TYPE  125  334
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              15               125
  MALE                48               334
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    24  32
  6Q GAIN WILD-TYPE 127 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     24   32
  6Q GAIN WILD-TYPE  127  251
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               24               127
  YES              32               251
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  6Q GAIN MUTATED                                      61
  6Q GAIN WILD-TYPE                                   450
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  6Q GAIN MUTATED                                                             0
  6Q GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  6Q GAIN MUTATED                                                     2
  6Q GAIN WILD-TYPE                                                   8
D12V9, multiclass
                                                             clus
vv                                                            6Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    61
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            6Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     450
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, continuous
D12V11, continuous
D12V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     1
  6Q GAIN WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                          10    49
  6Q GAIN WILD-TYPE                        38   397
D12V13, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                     10                38
  WHITE                                         49               397
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     7  51
  6Q GAIN WILD-TYPE  19 408
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7   51
  6Q GAIN WILD-TYPE   19  408
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                19
  NOT HISPANIC OR LATINO              51               408
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    84  98
  7P GAIN WILD-TYPE 219 120
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              182               339 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               98               120 
$`7P GAIN MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-6870 
       15.19         9.30        13.64        26.50        17.10        14.83 
TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4224 TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-8596 
       11.05        20.48         9.14        33.70        66.28        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4722 TCGA-CN-4729 TCGA-CN-4730 
       20.52        10.55         6.28        48.76        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-5358 
       32.81        20.55        14.33        45.83        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-6011 
       12.39         8.32        11.54        11.84        11.57        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       48.00        23.90         6.74         9.24        52.08        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-A49A TCGA-CN-A63T 
       10.45        32.22         3.68        32.48        17.29         7.40 
TCGA-CN-A63V TCGA-CN-A641 TCGA-CQ-5329 TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-6225 
       22.32        12.07        70.45         4.24        32.38        13.25 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       16.73        43.04        41.88        77.56        11.61        23.24 
TCGA-CQ-A4CH TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-7364 
       12.46        18.54        16.90         6.02        11.64        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7382 
       39.16        47.34         3.45         9.17        19.92        26.17 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7398 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       12.89        29.82         5.13       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5978 
      108.95        17.95       107.51        76.50        80.12         7.07 
TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6945 TCGA-CV-6950 
       90.12         9.70         5.46        26.43        12.03        15.09 
TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7091 
       30.08        53.95        65.82         4.14       126.15       111.16 
TCGA-CV-7101 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7236 
        5.26        21.80        71.21        10.75        77.16         4.73 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7255 
       31.36        26.20        18.97        17.13        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7416 TCGA-CV-7422 
       36.13        18.41        35.54        17.85        25.08        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 
      100.57        14.89        56.48       153.86        16.64        22.19 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A463 TCGA-CV-A6JM 
       35.47         1.05         6.51        48.20         0.76         6.38 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JZ TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        6.48        28.01        23.47        18.84        34.36        25.41 
TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EM 
       23.05        11.44        18.67        25.32        28.77         7.63 
TCGA-D6-A6EP TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       13.94        37.25        30.94        18.02        14.04        46.32 
TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A622 TCGA-H7-A6C5 
       37.58        32.71         3.02        18.94        11.80        21.11 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-8634 TCGA-HD-A633 
        0.07        28.47        21.93        27.48        12.66        13.84 
TCGA-IQ-7631 TCGA-IQ-A61H TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
       38.53        37.41         5.29        13.84        19.04        15.48 
TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67G TCGA-MZ-A7D7 
       18.15        14.37         7.96        30.05         6.25        17.98 
TCGA-P3-A5Q6 TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T8 
       15.78        47.01        18.97         2.04        12.99        13.15 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-RS-A6TO TCGA-T2-A6WZ 
        7.30         9.34        19.73         6.51        12.72        15.91 
TCGA-T2-A6X2 TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       32.45         3.12        13.25        49.45        44.65        74.47 
TCGA-UF-A7JK TCGA-WA-A7GZ 
       13.94        20.55 

$`7P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
        3.35        37.28         9.07        23.74        42.35        57.93 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
       23.84        20.48        65.59        68.48        15.52        21.17 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG 
        3.55        12.62         4.01        41.85        29.42        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-A6DJ TCGA-BA-A8YP TCGA-BB-4217 
       14.47         7.82         2.27        13.38        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
      105.90         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HU TCGA-BB-A5HZ 
       50.20        44.98        24.66        38.40        25.71        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
       12.92         8.81        12.69        55.86        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4740 
       51.29        56.68        52.14        57.11        12.99        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5369 
       73.61        13.05        42.02        71.31        16.21        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6017 
        8.52        52.08        56.94        50.07        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
       19.07        34.13         9.07        35.05        38.89        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C 
       11.74        35.01        25.41        23.57        29.72        21.21 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY 
       31.69        12.39        16.57         4.41         2.70        23.44 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       19.82        24.39        20.88        19.53        48.20        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
       21.50         2.93        54.58        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
       11.21        41.19        32.88        46.95        56.58         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7071 
       14.99        38.76        70.13        64.87        53.52        43.10 
TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI 
       44.48        29.36        33.60        29.49        14.14        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-6480 TCGA-CR-6481 
       50.01        39.52        34.52        36.99        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.34         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       40.93        35.84         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       31.96        34.06        17.13        32.78        47.01        27.06 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58         7.10 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5435 TCGA-CV-5436 
        5.95        35.41        29.95        48.39        76.24        19.20 
TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       87.55        91.53        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       48.59        60.49        43.23        54.74        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 
        9.60         2.14        20.52         4.73        21.90        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6952 TCGA-CV-6955 TCGA-CV-6956 
      140.78        19.79        42.38         6.08        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7095 TCGA-CV-7097 
        8.42        28.34         2.50        64.83        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7183 
        7.99         9.01         1.84        52.31        12.92       130.88 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7406 
       47.47        36.00        95.34         4.96        11.87        57.47 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 
      210.97        89.33         9.67         0.46        22.85        25.94 
TCGA-CV-7421 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
        0.07       156.49        54.94         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       19.76         7.17         6.38        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 
      180.16       159.65        45.96        88.87        60.43        67.86 
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-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
        3.62        21.24        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
       10.55        51.12        13.25         9.60         2.53        16.14 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ 
       24.95        17.72        12.36        22.59        24.95        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 
       12.79        11.11        58.45        33.86        46.45        20.45 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
       40.24        40.04        39.12        41.59        37.18        21.63 
TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
       20.25        31.13        24.95         0.46        17.85        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A 
       12.43        13.38        15.16        15.06        13.61        20.94 
TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 
       25.74        27.48        14.66        22.03        22.85         0.36 
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-A61I TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S 
       37.71        11.84         0.07        33.57        13.68        13.35 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI 
       19.27        10.75         1.84        12.62        15.42         7.13 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       16.08        29.92        71.74        51.25        10.85        36.82 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 
       19.00        75.55        29.00        16.01        21.07        21.21 
TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z8 
       23.15        21.47        12.72        18.64        21.07         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP 
       14.76        12.20        17.82        15.32         8.32        16.96 
TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 
        6.87         7.10        13.71        13.55        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JC TCGA-UF-A7JD 
       54.67         2.83        49.51        48.03        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       55.43        29.46        18.05        20.75        22.36        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
        2.96        17.03        14.56 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.07              0.07 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           153.86            210.97 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           18.755            21.630 
[1] "0.1 - 153.9 (18.8)" "0.1 - 211.0 (21.6)"
[1] "hr=" "1.7"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  7P GAIN MUTATED         9       29        30        92         6         0
  7P GAIN WILD-TYPE      18       47        52       161         6         1
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 9                18
  STAGE II               29                47
  STAGE III              30                52
  STAGE IVA              92               161
  STAGE IVB               6                 6
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7P GAIN MUTATED      13  50  40  66
  7P GAIN WILD-TYPE    37  87  60 107
D13V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1              13                37
  T2                 50                87
  T3                 40                60
  T4                 66               107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7P GAIN MUTATED    64  23  61   4
  7P GAIN WILD-TYPE 115  45 107   4
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              64               115
  N1              23                45
  N2              61               107
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    61   0
  7P GAIN WILD-TYPE 128   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     61    0
  7P GAIN WILD-TYPE  128    1
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              61               128
  1               0                 1
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    47 136
  7P GAIN WILD-TYPE  93 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     47  136
  7P GAIN WILD-TYPE   93  246
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              47                93
  MALE               136               246
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    54  89
  7P GAIN WILD-TYPE  97 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     54   89
  7P GAIN WILD-TYPE   97  194
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               54                97
  YES              89               194
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  7P GAIN MUTATED                                     180
  7P GAIN WILD-TYPE                                   331
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  7P GAIN MUTATED                                                             1
  7P GAIN WILD-TYPE                                                           0
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  7P GAIN MUTATED                                                     2
  7P GAIN WILD-TYPE                                                   8
D13V9, multiclass
                                                             clus
vv                                                            7P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   180
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            7P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     331
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, continuous
D13V11, continuous
D13V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  1     4
  7P GAIN WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                          22   152
  7P GAIN WILD-TYPE                        26   294
D13V13, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          4                 7
  BLACK OR AFRICAN AMERICAN                     22                26
  WHITE                                        152               294
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V14, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     9 164
  7P GAIN WILD-TYPE  17 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      9  164
  7P GAIN WILD-TYPE   17  295
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                17
  NOT HISPANIC OR LATINO             164               295
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    61  67
  7Q GAIN WILD-TYPE 242 151
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              128               393 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               67               151 
$`7Q GAIN MUTATED`
TCGA-BA-6870 TCGA-BA-A6DI TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 
       14.83        11.05        33.70        66.28        71.05        20.52 
TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4722 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4738 
       10.55         6.28        48.76        51.29        12.89        14.33 
TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
       45.83        46.32         8.58        71.31         8.32        11.54 
TCGA-CN-5367 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6024 
       11.57        48.00        23.90         6.74        52.08        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-A49A TCGA-CN-A63T 
       10.45        32.22         3.68        32.48        17.29         7.40 
TCGA-CN-A63V TCGA-CN-A641 TCGA-CQ-6225 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 
       22.32        12.07        13.25        16.73        41.88        77.56 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CR-6478 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7389 
       11.61        23.24         6.02        39.16         3.45        12.89 
TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       29.82       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5978 TCGA-CV-6933 TCGA-CV-6935 
       17.95       107.51        76.50         7.07        90.12         9.70 
TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6962 TCGA-CV-7090 
       11.24        12.03        15.09        30.08         4.14       126.15 
TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7235 TCGA-CV-7245 
      111.16         5.26        21.80        71.21        77.16        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 
       18.97        17.13        47.97        36.13        18.41        35.54 
TCGA-CV-7416 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7435 TCGA-CV-7437 
       25.08        34.09        14.89        56.48       153.86        16.64 
TCGA-CV-A45V TCGA-CV-A45Z TCGA-CV-A463 TCGA-CV-A6JM TCGA-CV-A6JZ TCGA-CX-7086 
        1.05        48.20         0.76         6.38        23.47        18.84 
TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EM 
       25.41        11.44        18.67        25.32        28.77         7.63 
TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 
       13.94        11.11        37.25        30.94        18.02        14.04 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A61S TCGA-HD-7753 
       46.32        37.58        32.71         3.02        18.94        28.47 
TCGA-HD-7831 TCGA-HD-7917 TCGA-IQ-7631 TCGA-IQ-A61H TCGA-IQ-A61K TCGA-IQ-A61O 
       21.93        27.48        38.53        37.41         5.29        13.84 
TCGA-IQ-A6SH TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       15.48        14.37        30.05         6.25        17.98        15.78 
TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-QK-A6II TCGA-QK-A8Z7 TCGA-QK-AA3J 
       47.01         2.04        12.99         9.34         6.51        15.32 
TCGA-RS-A6TO TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A7J9 
       12.72         3.12        13.25        54.67         2.83        44.65 
TCGA-UF-A7JA TCGA-WA-A7GZ 
       74.47        20.55 

$`7Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 
       20.48        65.59        68.48        15.52        21.17         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        27.95        11.54         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
        7.82         2.27        13.38        20.48        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HU 
       36.72        50.20        44.98        24.66        38.40        25.71 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 
       27.19        12.92         8.81        12.69        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        4.67        56.68        26.86        32.81        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       12.99        20.55        27.58        73.61        13.05        42.02 
TCGA-CN-5359 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       12.39        16.21        11.84        12.49         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       56.94        50.07        30.67        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
       34.13         9.07         9.24        35.05        38.89        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C 
       11.74        35.01        25.41        23.57        29.72        21.21 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY 
       31.69        12.39        16.57         4.41         2.70        23.44 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       19.82        24.39        20.88        19.53        48.20        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 
       10.42        11.21         4.24        41.19        32.38        32.88 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       46.95        56.58         4.24        14.99        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB 
       64.87        53.52        43.04        43.10        44.48        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       39.52        34.52        36.99        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       15.75         9.27        47.18        47.34        40.93        35.84 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-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-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       27.06        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         5.13         5.95        35.41        29.95        48.39 
TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       19.20        87.55        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-6934 TCGA-CV-6936 TCGA-CV-6937 
       21.07        62.43         9.60         2.14         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 
        4.73        21.90        26.43       140.78        19.79        42.38 
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-7089 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       28.34         2.50        64.83        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7180 TCGA-CV-7183 
        9.01         1.84        52.31        12.92        10.75       130.88 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7252 
        4.73        47.47        36.00        31.36        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       11.87         2.10        57.47        17.85       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7423 
        9.67         0.46        22.85        25.94         0.07       100.57 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
      156.49        54.94         3.52        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
        7.17         6.38        22.19        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      180.16       159.65        35.47        45.96         6.51        88.87 
TCGA-CV-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-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
       35.34        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 
       19.92        22.52        10.42        10.42        10.55        34.36 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       51.12        13.25         9.60        23.05         2.53        16.14 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ 
       24.95        17.72        12.36        22.59        24.95        12.10 
TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 
       12.79        58.45        33.86        46.45        20.45        40.24 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       40.04        39.12        41.59        37.18        21.63        20.25 
TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       31.13        24.95         0.46        17.85        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
       12.43        13.38        15.16        15.06        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       20.94         0.07        25.74        27.48        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        6.90        34.75        15.95        14.50        37.71        11.84 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-KU-A66S TCGA-KU-A66T 
        0.07        33.57        13.68        19.04        13.35        18.15 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN 
       19.27        10.75         7.96         1.84        12.62        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
        7.13        16.08        29.92        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T7 
       36.82        19.00        75.55        18.97        29.00        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       12.72        18.64        21.07        19.73         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       12.20        17.82         8.32        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 
        7.10        32.45        13.71        13.55        20.35        64.80 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.51        48.03        49.45        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       29.46        18.05        13.94        20.75        22.36        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
        2.96        17.03        14.56 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.76              0.07 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           153.86            210.97 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            18.89             21.07 
[1] "0.8 - 153.9 (18.9)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.3"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  7Q GAIN MUTATED         9       20        21        62         4         0
  7Q GAIN WILD-TYPE      18       56        61       191         8         1
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 9                18
  STAGE II               20                56
  STAGE III              21                61
  STAGE IVA              62               191
  STAGE IVB               4                 8
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7Q GAIN MUTATED      11  32  27  47
  7Q GAIN WILD-TYPE    39 105  73 126
D14V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1              11                39
  T2                 32               105
  T3                 27                73
  T4                 47               126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7Q GAIN MUTATED    48  15  39   3
  7Q GAIN WILD-TYPE 131  53 129   5
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              48               131
  N1              15                53
  N2              39               129
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    41   0
  7Q GAIN WILD-TYPE 148   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     41    0
  7Q GAIN WILD-TYPE  148    1
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              41               148
  1               0                 1
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    33  96
  7Q GAIN WILD-TYPE 107 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     33   96
  7Q GAIN WILD-TYPE  107  286
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              33               107
  MALE                96               286
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    36  64
  7Q GAIN WILD-TYPE 115 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     36   64
  7Q GAIN WILD-TYPE  115  219
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               36               115
  YES              64               219
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  7Q GAIN MUTATED                                     126
  7Q GAIN WILD-TYPE                                   385
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  7Q GAIN MUTATED                                                             1
  7Q GAIN WILD-TYPE                                                           0
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  7Q GAIN MUTATED                                                     2
  7Q GAIN WILD-TYPE                                                   8
D14V9, multiclass
                                                             clus
vv                                                            7Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   126
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            7Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     385
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, continuous
D14V11, continuous
D14V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  1     2
  7Q GAIN WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                          16   106
  7Q GAIN WILD-TYPE                        32   340
D14V13, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                     16                32
  WHITE                                        106               340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V14, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     8 112
  7Q GAIN WILD-TYPE  18 347
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      8  112
  7Q GAIN WILD-TYPE   18  347
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   8                18
  NOT HISPANIC OR LATINO             112               347
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    94  61
  8P GAIN WILD-TYPE 209 157
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              155               366 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               61               157 
$`8P GAIN MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 
        3.35         9.30        17.10        20.48        68.48        15.52 
TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DG TCGA-BA-A6DL 
        3.55        28.11        20.45        30.18         2.27        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7861 
       16.41         6.15       105.90         9.14         4.60        22.42 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4722 
       50.20        66.28        38.40        71.05        20.52        48.76 
TCGA-CN-4723 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       55.86        12.89        32.81        14.33        45.83        27.58 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6012 
       42.02        46.32        12.39        11.84        50.07        48.00 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A499 
        9.24        11.08        38.89         3.68        11.74        23.57 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5330 
        7.40        31.69        22.32        52.37        21.50        62.37 
TCGA-CQ-6224 TCGA-CQ-7068 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI 
       56.58        43.04        23.24        29.49        14.14        31.23 
TCGA-CR-5243 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6482 
       84.23        58.42        50.01        16.90         6.02        11.34 
TCGA-CR-6487 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7376 
        7.69         9.27        39.16        47.34         3.45        31.96 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7389 TCGA-CV-5430 TCGA-CV-5431 
       34.06        26.17        17.13        12.89       139.43        17.16 
TCGA-CV-5435 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5976 TCGA-CV-5977 
       76.24       107.51        76.50        80.12        48.59        60.49 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       54.74        21.07         2.14         5.46        20.52         4.73 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6953 TCGA-CV-7091 TCGA-CV-7095 
       19.79        12.03        42.38        53.95       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7180 TCGA-CV-7243 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7263 
       12.66        10.75        31.36        11.87        47.97        18.41 
TCGA-CV-7409 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T 
       17.85        14.89        54.94        21.01       180.16       159.65 
TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6K0 
        6.51        48.20        67.86        15.25        35.34        19.92 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-8568 TCGA-D6-A6EK TCGA-D6-A6EN 
       18.84        25.41        23.05        24.95        28.77        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5629 TCGA-DQ-7588 TCGA-F7-7848 
       24.95        13.94        12.10        30.94        14.04        37.18 
TCGA-F7-8489 TCGA-F7-A61S TCGA-F7-A624 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7831 
       21.63        18.94        12.43        13.61        20.94        21.93 
TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A634 TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W 
       27.48        22.03         4.27        13.84        13.35        14.37 
TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5QE TCGA-P3-A6T3 
        1.84         6.25         7.13        17.98        51.25        18.97 
TCGA-P3-A6T5 TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T3-A92M 
       29.00         7.30        12.72        12.72         6.87        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-UF-A719 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF 
        3.12        13.55        54.67        74.47        17.95        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       29.46        18.05        13.94        20.75        22.36 

$`8P GAIN WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
       15.19        13.64        37.28         9.07        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 
       42.35        57.93        23.84        65.59        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA 
       12.62         4.01        41.85        29.42        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DI TCGA-BA-A6DJ 
        7.10         5.69        14.47         7.82        11.05        13.38 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7871 
        4.41        18.38        36.72        33.70        44.98        24.66 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       25.71        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 
       12.69        38.04         4.67        51.29        56.68        26.86 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4741 TCGA-CN-4742 
       52.14        57.11        12.99        20.55        73.61        13.05 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 
        8.58        71.31         8.32        16.21        11.54        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 
       12.49         8.52        52.08        56.94        30.67        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
       47.44        28.04        19.07        34.13         6.74         9.07 
TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 
       52.08        10.45        32.22        35.05        17.42        32.48 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63W 
       35.01        25.41        17.29        29.72        21.21        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5326 TCGA-CQ-5327 
       24.39        20.88        19.53        48.20         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       70.45        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       32.38        32.88        46.95        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 
       38.76        70.13        64.87        53.52        16.73        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        77.56        44.48        11.61        29.36        33.60 
TCGA-CQ-A4CH TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6471 
       12.46        11.77        54.67        37.87        26.27        39.52 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 
       34.52        36.99        18.54        11.90        10.22        11.64 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 
       12.46        22.78        15.75        47.18        40.93        35.84 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7380 
        3.09        24.95        29.23         0.99         9.17        19.92 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       32.78        47.01        27.06        29.82        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58         7.10         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 
       35.41        29.95        48.39       129.21       108.95        19.20 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       17.95        87.55        91.53        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       86.83         7.07        43.23        62.43         9.60        90.12 
TCGA-CV-6935 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6950 
        9.70        21.90        26.43        11.24       140.78        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
       30.08         6.08        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-7099 
       28.34         2.50         4.14        64.83       126.15         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-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       71.21       130.88        77.16         4.73        47.47        36.00 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7255 
       26.20        18.97        17.13        95.34         4.96         2.10 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       36.13        57.47        35.54       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        0.46        22.85        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
      100.57        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-A45O TCGA-CV-A45Q TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Y 
       27.98       169.38        35.47         1.05        45.96        88.87 
TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A6JD TCGA-CV-A6JM 
       60.43         0.76        56.61         7.07         5.98         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-CX-A4AQ 
       22.52        10.42        10.42        10.55        34.36        51.12 
TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
       13.25         9.60         2.53        16.14        11.44        18.67 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6ES TCGA-D6-A74Q 
       25.32        17.72        12.36         7.63        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 
       58.45        37.25        33.86        18.02        46.32        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45        37.58        40.24        40.04        39.12        41.59 
TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W 
       32.71        20.25         3.02        31.13        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       17.85        11.80        20.25        13.38        15.16        15.06 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8224 
       21.11         0.07        28.47        25.74        27.48        14.66 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 
       12.66        22.85         0.36        13.84         3.65         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
       34.75        15.95        38.53        14.50        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SG 
       37.41         0.07        33.57         5.29        13.68        19.04 
TCGA-IQ-A6SH TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A 
       15.48        18.15        19.27        10.75         7.96        30.05 
TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
       12.62        15.42        16.08        29.92        15.78        71.74 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
       10.85        36.82        47.01        19.00        75.55         2.04 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
       21.47         9.34        18.64        21.07        19.73         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         8.32 
TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HJ TCGA-TN-A7HL 
       16.96        15.91         7.10        32.45        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       64.80         2.83        49.51        48.03        49.45        44.65 
TCGA-UF-A7JD TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       24.30        32.65         2.96        17.03        20.55        14.56 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             1.84              0.07 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           180.16            210.97 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           21.010            20.715 
[1] "1.8 - 180.2 (21.0)" "0.1 - 211.0 (20.7)"
[1] "hr=" "1.2"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  8P GAIN MUTATED         9       23        27        73         3         0
  8P GAIN WILD-TYPE      18       53        55       180         9         1
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 9                18
  STAGE II               23                53
  STAGE III              27                55
  STAGE IVA              73               180
  STAGE IVB               3                 9
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  8P GAIN MUTATED      18  47  25  47
  8P GAIN WILD-TYPE    32  90  75 126
D15V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1              18                32
  T2                 47                90
  T3                 25                75
  T4                 47               126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8P GAIN MUTATED    49  26  50   3
  8P GAIN WILD-TYPE 130  42 118   5
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              49               130
  N1              26                42
  N2              50               118
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    59   0
  8P GAIN WILD-TYPE 130   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     59    0
  8P GAIN WILD-TYPE  130    1
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              59               130
  1               0                 1
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    32 123
  8P GAIN WILD-TYPE 108 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     32  123
  8P GAIN WILD-TYPE  108  259
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              32               108
  MALE               123               259
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    49  83
  8P GAIN WILD-TYPE 102 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     49   83
  8P GAIN WILD-TYPE  102  200
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               49               102
  YES              83               200
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  8P GAIN MUTATED                                     149
  8P GAIN WILD-TYPE                                   362
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  8P GAIN MUTATED                                                             1
  8P GAIN WILD-TYPE                                                           0
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  8P GAIN MUTATED                                                     5
  8P GAIN WILD-TYPE                                                   5
D15V9, multiclass
                                                             clus
vv                                                            8P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   149
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       5
                                                             clus
vv                                                            8P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     362
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  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"
D15V10, continuous
D15V11, continuous
D15V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     2
  8P GAIN WILD-TYPE                                2     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                          19   126
  8P GAIN WILD-TYPE                        29   320
D15V13, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                     19                29
  WHITE                                        126               320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     8 133
  8P GAIN WILD-TYPE  18 326
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      8  133
  8P GAIN WILD-TYPE   18  326
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   8                18
  NOT HISPANIC OR LATINO             133               326
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   175 135
  8Q GAIN WILD-TYPE 128  83
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              310               211 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              135                83 
$`8Q GAIN MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5555 
        3.35         9.30        37.28        26.50        42.35        17.10 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 
       20.48        65.59        68.48        15.52        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
       12.62         4.01        41.85        28.11        20.45        30.18 
TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP 
       11.54         5.69         2.27        11.05        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15       105.90         9.14         4.60         4.41        18.38 
TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 
       22.42        33.70        50.20        66.28        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
       20.52        10.55        27.19         6.28        12.69        48.76 
TCGA-CN-4723 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 
       55.86        56.68        12.89        32.81        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       14.33        45.83        27.58        13.05        42.02        46.32 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 
        8.32        16.21        11.54        11.84         8.52        52.08 
TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
       48.00         6.74         9.24        11.08        10.45        35.05 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
       38.89         3.68        17.42        11.74        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       17.29        29.72         7.40        31.69        22.32        12.39 
TCGA-CN-A640 TCGA-CN-A642 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 
        4.41         2.70        52.37        21.50         2.93        70.45 
TCGA-CQ-5330 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
       62.37         4.24        41.19        56.58         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7072 
       38.76        53.52        16.73        43.04        41.88        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG 
       44.48        11.61        23.24        29.36        29.49        14.14 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6473 
       31.23        84.23        11.77        58.42        50.01        36.99 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       16.90         6.02        11.34        11.64         7.69        12.46 
TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 
        9.27        39.16        47.34        35.84         3.45        24.95 
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-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 
       47.01        27.06        12.89         7.10         5.95        35.41 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 
      139.43        17.16       129.21        76.24        19.20       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5976 TCGA-CV-5977 
       87.55        76.50        80.12        17.92        48.59        60.49 
TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6936 
        7.07        54.74        21.07        62.43         2.14         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
       20.52         4.73        26.43        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        8.42         4.14        64.83       126.15       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
       12.66         1.84        12.92        71.21        10.75       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
       77.16         4.73        47.47        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 
       17.13        11.87        47.97         2.10        18.41        35.54 
TCGA-CV-7409 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7424 
       17.85         0.46        25.08         0.07       100.57        14.89 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45P 
      156.49        54.94         7.17        16.64         6.38        21.01 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
      180.16       159.65        35.47         6.51        88.87        48.20 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6JM 
       67.86        56.61         7.07        15.25        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CX-7082 TCGA-CX-7086 
       29.79         6.48        23.47        19.92        10.42        18.84 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8568 
       34.36        25.41         9.60        23.05        11.44        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EO 
       25.32        17.72        12.36        28.77        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
       13.94        12.10        12.79        58.45        37.25        30.94 
TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 
       33.86        14.04        46.32        37.58        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A620 TCGA-F7-A624 
       21.63         3.02        31.13        18.94        17.85        12.43 
TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
       15.16        13.61        20.94        21.93        27.48        27.48 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-A61E 
       22.03        12.66        22.85         4.27        34.75        37.71 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A66S TCGA-KU-A66T 
        5.29        13.68        13.84        19.04        13.35        18.15 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       14.37         7.96         1.84         6.25        15.42         7.13 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6T3 TCGA-P3-A6T5 
       17.98        15.78        71.74        51.25        18.97        29.00 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.07        21.21         7.30        21.47         9.34        12.72 
TCGA-QK-A6VC TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6WZ 
       19.73        17.82         8.32        12.72         6.87        15.91 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 
       32.45        13.71         3.12        13.55        13.25        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       54.67         2.83        49.45        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-WA-A7H4 
       22.36        32.65         2.96        14.56 

$`8Q GAIN WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5556 
       15.19        13.64         9.07        23.74        57.93        23.84 
TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DF 
       21.17        29.42        27.95         7.10        14.47         7.82 
TCGA-BA-A6DJ TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-A5HU TCGA-BB-A6UM 
       13.38        36.72        44.98        24.66        25.71        12.92 
TCGA-BB-A6UO TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4733 
        8.81        38.04         4.67        51.29        26.86        52.14 
TCGA-CN-4735 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5367 
       57.11        73.61         8.58        12.39        71.31        11.57 
TCGA-CN-5369 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
       12.49        56.94        50.07        30.67        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6989 
       28.04        19.07        34.13         9.07        52.08        32.22 
TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A49C TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6UY 
       32.48        35.01        21.21        16.57        12.07        23.44 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5327 
       19.82        24.39        20.88        19.53        48.20        54.58 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 
       45.99        10.42        11.21        32.38        32.88        46.95 
TCGA-CQ-6225 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7071 TCGA-CQ-A4CD TCGA-CQ-A4CH 
       13.25        70.13        64.87        43.10        33.60        12.46 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6474 
       54.67        37.87        26.27        39.52        34.52        18.54 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 
       11.90        10.22        22.78        15.75        47.18        40.93 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7390 TCGA-CR-7391 
        3.09        29.23         0.99        32.78        29.82        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7402 
       46.85        32.65        44.25        30.58         5.13        29.95 
TCGA-CR-7404 TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 
       48.39       108.95        17.95        91.53        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6939 
       86.83        43.23         9.60        90.12         9.70        21.90 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7099 
       65.82        10.98         7.13        28.34         2.50         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7242 TCGA-CV-7250 
        9.01         5.26        52.31        21.80        36.00        95.34 
TCGA-CV-7252 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
        4.96        36.13        57.47       210.97        89.33         9.67 
TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7429 TCGA-CV-7430 
       22.85        25.94        34.09        56.48         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
       84.49        19.76       153.86        22.19        27.98       169.38 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A6JD TCGA-CV-A6JT 
        1.05        45.96        60.43         0.76         5.98        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ 
        3.62        21.24        22.52        10.42        10.55        51.12 
TCGA-D6-6515 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-A6EM TCGA-D6-A74Q 
       13.25         2.53        16.14        18.67         7.63        11.11 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       18.02        46.45        20.45        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-A50G TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A623 
       41.59        20.25        24.95         0.46        11.80        20.25 
TCGA-H7-7774 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.38        15.06        21.11         0.07        28.47        25.74 
TCGA-HD-8224 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 
       14.66         0.36        13.84         3.65         6.90        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       38.53        14.50        11.84        37.41         0.07        33.57 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-MZ-A6I9 
       15.48        19.27        10.75        30.05        12.62        16.08 
TCGA-P3-A5Q5 TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       29.92        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A6IF TCGA-QK-A6V9 
        2.04        12.99        16.01        13.15        23.15        18.64 
TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J 
       21.07         6.51         5.62        14.76        12.20        15.32 
TCGA-RS-A6TP TCGA-T2-A6X0 TCGA-TN-A7HL TCGA-UF-A71B TCGA-UF-A71D TCGA-UP-A6WW 
       16.96         7.10        20.35        49.51        48.03        17.03 
TCGA-WA-A7GZ 
       20.55 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.07              0.07 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           180.16            210.97 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           20.465            21.900 
[1] "0.1 - 180.2 (20.5)" "0.1 - 211.0 (21.9)"
[1] "hr=" "1.1"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  8Q GAIN MUTATED        17       43        54       149        10         0
  8Q GAIN WILD-TYPE      10       33        28       104         2         1
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                17                10
  STAGE II               43                33
  STAGE III              54                28
  STAGE IVA             149               104
  STAGE IVB              10                 2
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  8Q GAIN MUTATED      32  77  64 103
  8Q GAIN WILD-TYPE    18  60  36  70
D16V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1              32                18
  T2                 77                60
  T3                 64                36
  T4                103                70
[1] 4 2
[1] 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
  8Q GAIN MUTATED   102  42 103   7
  8Q GAIN WILD-TYPE  77  26  65   1
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             102                77
  N1              42                26
  N2             103                65
  N3               7                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   116   0
  8Q GAIN WILD-TYPE  73   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    116    0
  8Q GAIN WILD-TYPE   73    1
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             116                73
  1               0                 1
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    86 224
  8Q GAIN WILD-TYPE  54 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     86  224
  8Q GAIN WILD-TYPE   54  158
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              86                54
  MALE               224               158
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   101 158
  8Q GAIN WILD-TYPE  50 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    101  158
  8Q GAIN WILD-TYPE   50  125
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              101                50
  YES             158               125
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  8Q GAIN MUTATED                                     303
  8Q GAIN WILD-TYPE                                   208
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  8Q GAIN MUTATED                                                             1
  8Q GAIN WILD-TYPE                                                           0
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  8Q GAIN MUTATED                                                     6
  8Q GAIN WILD-TYPE                                                   4
D16V9, multiclass
                                                             clus
vv                                                            8Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   303
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       6
                                                             clus
vv                                                            8Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     208
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, continuous
D16V11, continuous
D16V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  2     7
  8Q GAIN WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                          31   257
  8Q GAIN WILD-TYPE                        17   189
D16V13, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          7                 4
  BLACK OR AFRICAN AMERICAN                     31                17
  WHITE                                        257               189
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    18 266
  8Q GAIN WILD-TYPE   8 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     18  266
  8Q GAIN WILD-TYPE    8  193
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  18                 8
  NOT HISPANIC OR LATINO             266               193
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    55  47
  9P GAIN WILD-TYPE 248 171
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              102               419 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               47               171 
$`9P GAIN MUTATED`
TCGA-BA-5149 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A6DA 
       26.50        23.84        20.48        68.48         4.01        11.54 
TCGA-BA-A6DJ TCGA-BB-7870 TCGA-BB-A5HZ TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 
       13.38        66.28        27.19        42.02        12.39         8.32 
TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6995 
        8.52        50.07        30.67        52.08        38.89         3.68 
TCGA-CN-6996 TCGA-CN-A499 TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CQ-5329 
       17.42        23.57         4.41         2.70        20.88        70.45 
TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C6 
       62.37        46.95        38.76        70.13        43.04        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4CD TCGA-CR-6467 TCGA-CR-6487 TCGA-CR-7370 TCGA-CR-7371 
       11.61        33.60        58.42         7.69         3.45         3.09 
TCGA-CR-7373 TCGA-CR-7395 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5966 
       29.23        30.58       107.51        87.55        76.50        17.92 
TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 
       60.49        21.07        62.43         4.73        21.90        11.24 
TCGA-CV-6952 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7099 TCGA-CV-7235 TCGA-CV-7238 
        6.08         4.14        64.83         7.99        77.16        47.47 
TCGA-CV-7247 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7425 
       18.97        47.97        36.13        35.54        17.85        56.48 
TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-A45Q TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A468 
      156.49         3.52       169.38         0.76         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JZ TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-A6EM 
        5.98         6.48        23.47        34.36        25.41         7.63 
TCGA-D6-A6EN TCGA-D6-A6EQ TCGA-DQ-5625 TCGA-F7-A61S TCGA-F7-A622 TCGA-H7-7774 
       22.59        12.10        37.25        18.94        11.80        13.38 
TCGA-H7-8502 TCGA-HD-7917 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-A61K 
       15.06        27.48         4.27         6.90        34.75         5.29 
TCGA-IQ-A61L TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A6SW 
       13.68        14.37        30.05        12.62         6.25        36.82 
TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A6IG TCGA-QK-A8Z9 TCGA-RS-A6TO 
       75.55        29.00        16.01         7.30        14.76        12.72 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T3-A92N TCGA-TN-A7HI TCGA-UF-A7J9 TCGA-UF-A7JT 
        6.87        15.91         3.12        13.55        44.65        32.65 

$`9P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6868 
       23.74        42.35        57.93        17.10        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
       21.17        14.83         3.55        12.62        41.85        29.42 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD 
       28.11        20.45        30.18        27.95         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP 
       14.47         7.82         2.27        11.05        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15       105.90         9.14         4.60         4.41        18.38 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 
       22.42        36.72        33.70        50.20        44.98        24.66 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A6UM 
       38.40        71.05        20.52        25.71        10.55        12.92 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
        8.81         6.28        12.69        48.76        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
        4.67        51.29        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       52.14        57.11        12.99        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 
       27.58        73.61        13.05        46.32         8.58        71.31 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 
       16.21        11.54        11.84        11.57        12.49        52.08 
TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       56.94        48.00        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 
       34.13         6.74         9.07         9.24        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       32.22        35.05        32.48        11.74        35.01        25.41 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       17.29        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
       12.39        16.57        12.07        23.44        19.82        24.39 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       19.53        48.20        52.37        21.50         2.93        54.58 
TCGA-CQ-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-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 
       32.88        56.58        13.25         4.24        14.99        64.87 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 
       53.52        16.73        41.88        43.10        77.56        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       29.36        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 
       11.77        54.67        37.87        26.27        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-6488 TCGA-CR-6491 TCGA-CR-6492 
       10.22        11.34        11.64        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       24.95         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       26.17        17.13        32.78        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 
       29.82        30.02        46.85        32.65        44.25         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-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       91.53        80.12        13.35        23.05        86.83        48.59 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
        7.07        43.23        54.74         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 
        9.70         5.46        20.52        26.43       140.78        19.79 
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-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
       10.98         7.13         8.42        28.34         2.50       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-7236 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        4.73        36.00        31.36        26.20        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7410 
        4.96        11.87         2.10        18.41        57.47       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-7428 TCGA-CV-7430 
        0.07        34.09       100.57        14.89        54.94        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-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       22.19        27.98        21.01       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-A464 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JT 
       67.86        56.61        35.34         6.38        29.79        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
        3.62        21.24        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 
       10.55        18.84        51.12        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-A6EO TCGA-D6-A6EP TCGA-D6-A6ES 
       17.72        12.36        28.77        24.95        13.94        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       11.11        58.45        30.94        33.86        18.02        14.04 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       46.32        46.45        20.45        37.58        40.24        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       39.12        41.59        37.18        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
        3.02        31.13        24.95         0.46        17.85        20.25 
TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       12.43        15.16        13.61        21.11        20.94         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 
       12.66        22.85         0.36        13.84         3.65        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T 
       33.57        13.84        19.04        15.48        13.35        18.15 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A7BN TCGA-MZ-A5BI 
       19.27        10.75         7.96         1.84        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
       16.08        17.98        29.92        15.78        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 
       10.85        47.01        19.00        18.97         2.04        12.99 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
       13.15        21.07        21.21        23.15        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        18.64        21.07        19.73         6.51         5.62 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6X0 
       12.20        17.82        15.32         8.32        16.96         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       32.45        13.71        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC 
        2.83        49.51        48.03        49.45        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36         2.96        17.03        20.55        14.56 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.76              0.07 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           169.38            210.97 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           20.975            20.940 
[1] "0.8 - 169.4 (21.0)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1.1"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  9P GAIN MUTATED         5       19        14        52         4         0
  9P GAIN WILD-TYPE      22       57        68       201         8         1
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 5                22
  STAGE II               19                57
  STAGE III              14                68
  STAGE IVA              52               201
  STAGE IVB               4                 8
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9P GAIN MUTATED       7  27  22  39
  9P GAIN WILD-TYPE    43 110  78 134
D17V4, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1               7                43
  T2                 27               110
  T3                 22                78
  T4                 39               134
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9P GAIN MUTATED    36  13  33   4
  9P GAIN WILD-TYPE 143  55 135   4
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              36               143
  N1              13                55
  N2              33               135
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    37   0
  9P GAIN WILD-TYPE 152   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     37    0
  9P GAIN WILD-TYPE  152    1
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              37               152
  1               0                 1
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    37  65
  9P GAIN WILD-TYPE 103 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     37   65
  9P GAIN WILD-TYPE  103  317
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              37               103
  MALE                65               317
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    33  54
  9P GAIN WILD-TYPE 118 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     33   54
  9P GAIN WILD-TYPE  118  229
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               33               118
  YES              54               229
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  9P GAIN MUTATED                                     101
  9P GAIN WILD-TYPE                                   410
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  9P GAIN MUTATED                                                             0
  9P GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  9P GAIN MUTATED                                                     1
  9P GAIN WILD-TYPE                                                   9
D17V9, multiclass
                                                             clus
vv                                                            9P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   101
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            9P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     410
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, continuous
D17V11, continuous
D17V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     2
  9P GAIN WILD-TYPE                                2     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           6    92
  9P GAIN WILD-TYPE                        42   354
D17V13, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      6                42
  WHITE                                         92               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V14, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     7  91
  9P GAIN WILD-TYPE  19 368
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      7   91
  9P GAIN WILD-TYPE   19  368
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                19
  NOT HISPANIC OR LATINO              91               368
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    72  66
  9Q GAIN WILD-TYPE 231 152
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              138               383 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               66               152 
$`9Q GAIN MUTATED`
TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6873 
       26.50        17.10        23.84        20.48        68.48         4.01 
TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DJ TCGA-BB-4224 TCGA-BB-7864 TCGA-BB-7870 
       11.54         5.69        13.38         9.14        50.20        66.28 
TCGA-BB-A5HZ TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4741 TCGA-CN-5355 
       27.19        55.86        51.29        56.68        73.61        42.02 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6021 
       12.39         8.32        11.57        50.07        30.67         9.07 
TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A499 TCGA-CN-A49A 
       52.08        38.89         3.68        17.42        23.57        17.29 
TCGA-CN-A63T TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5323 
        7.40         4.41         2.70        24.39        20.88        48.20 
TCGA-CQ-5325 TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7063 
       21.50        62.37        46.95        13.25        38.76        70.13 
TCGA-CQ-7068 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-6467 
       43.04        44.48        11.61        33.60        14.14        58.42 
TCGA-CR-6477 TCGA-CR-7368 TCGA-CR-7373 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7389 
       16.90        40.93        29.23        34.06        19.92        12.89 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 
      129.21       108.95        17.95       107.51        76.50        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6938 
       17.92        13.35        60.49        21.07        62.43         4.73 
TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6952 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7099 
       21.90        11.24         6.08         4.14        64.83         7.99 
TCGA-CV-7100 TCGA-CV-7177 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7245 
        9.01        21.80        77.16         4.73        47.47        26.20 
TCGA-CV-7247 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7415 
       18.97        36.13        18.41        35.54        17.85        22.85 
TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7434 
       34.09        56.48       156.49         3.52        84.49         7.17 
TCGA-CV-A45Q TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A468 
      169.38        48.20        67.86         0.76         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JZ TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6516 TCGA-D6-8569 
        5.98        23.47        34.36        51.12        25.41        25.32 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5625 TCGA-F7-A61S 
        7.63        22.59        12.10        11.11        37.25        18.94 
TCGA-F7-A622 TCGA-H7-7774 TCGA-H7-8502 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8314 
       11.80        13.38        15.06        27.48        27.48        22.03 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-A61L TCGA-MT-A51W TCGA-MT-A67A 
        4.27         6.90        15.95        13.68        14.37        30.05 
TCGA-MT-A67G TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A64Z 
        6.25        36.82        75.55        29.00        16.01        21.07 
TCGA-QK-A6IG TCGA-QK-A8Z9 TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T3-A92N 
        7.30        14.76        12.72         6.87        15.91         3.12 
TCGA-TN-A7HI TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JS TCGA-UF-A7JT 
       13.55        49.45        44.65        74.47        22.36        32.65 

$`9Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
       23.74        42.35        57.93        65.59        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG 
       14.83         3.55        12.62        41.85        29.42        28.11 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DF 
       20.45        30.18        27.95         7.10        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
        2.27        11.05        20.48        16.41         6.15       105.90 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU 
       44.98        24.66        38.40        71.05        20.52        25.71 
TCGA-BB-A5HY TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
       10.55        12.92         8.81         6.28        12.69        48.76 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       38.04         4.67        12.89        26.86        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       57.11        12.99        20.55        14.33        45.83        27.58 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 
       13.05        46.32         8.58        71.31        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 
       11.84        12.49         8.52        52.08        56.94        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       23.90        47.44        28.04        19.07        34.13         6.74 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 
        9.24        11.08        10.45        32.22        35.05        32.48 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U 
       11.74        35.01        25.41        29.72        21.21        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V1 
       22.32        12.39        16.57        12.07        23.44        19.82 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 
       19.53        52.37         2.93        54.58        70.45        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 
       10.42        11.21         4.24        41.19        32.38        32.88 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
       56.58         4.24        14.99        64.87        53.52        16.73 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE 
       41.88        43.10        77.56        23.24        29.36        29.49 
TCGA-CQ-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-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
       26.27        50.01        39.52        34.52        36.99        18.54 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        6.02        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       12.46        22.78        15.75         9.27        47.18        39.16 
TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 
       47.34        35.84         3.45         3.09        24.95         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       31.96         9.17        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       27.06        29.82        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58         7.10         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 
       48.39       139.43        17.16        76.24        19.20        87.55 
TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
       91.53        23.05        86.83        48.59         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       54.74         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       20.52        26.43       140.78        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       15.09        30.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        8.42        28.34         2.50       126.15       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7178 
       12.66         5.26         1.84        52.31        12.92        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 
       10.75       130.88        36.00        31.36        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7410 
        4.96        11.87        47.97         2.10        57.47       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
       89.33         9.67         0.46        25.08        25.94         0.07 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7435 
      100.57        14.89        54.94        16.27        19.76       153.86 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R 
       16.64         6.38        22.19        27.98        21.01       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A460 TCGA-CV-A464 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       60.43        56.61        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
       28.01         3.62        21.24        19.92        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 
       10.42        10.55        18.84        13.25         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 
        2.53        16.14        11.44        18.67        24.95        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5624 
       12.36        28.77        24.95        13.94        12.79        58.45 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       30.94        33.86        18.02        14.04        46.32        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45        37.58        40.24        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       37.18        32.71        21.63        20.25         3.02        31.13 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-8501 
       24.95         0.46        17.85        20.25        12.43        15.16 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.61        21.11        20.94         0.07        28.47        25.74 
TCGA-HD-7831 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       21.93        14.66        12.66        22.85         0.36        13.84 
TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        3.65        34.75        38.53        14.50        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG 
       37.41         0.07        33.57         5.29        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X 
       15.48        13.35        18.15        19.27        10.75         7.96 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
        1.84        12.62        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SX 
       29.92        15.78        71.74        51.25        10.85        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A652 
       19.00        18.97         2.04        12.99        13.15        21.21 
TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
       23.15        21.47         9.34        12.72        18.64        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       19.73         6.51         5.62        12.20        17.82        15.32 
TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HJ 
        8.32        16.96         7.10        32.45        13.71        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D 
       20.35        64.80        54.67         2.83        49.51        48.03 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75         2.96        17.03        20.55        14.56 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.76              0.07 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           169.38            210.97 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           21.965            20.520 
[1] "0.8 - 169.4 (22.0)" "0.1 - 211.0 (20.5)"
[1] "hr=" "1.1"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  9Q GAIN MUTATED         6       23        17        77         6         0
  9Q GAIN WILD-TYPE      21       53        65       176         6         1
D18V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 6                21
  STAGE II               23                53
  STAGE III              17                65
  STAGE IVA              77               176
  STAGE IVB               6                 6
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9Q GAIN MUTATED      10  34  27  59
  9Q GAIN WILD-TYPE    40 103  73 114
D18V4, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1              10                40
  T2                 34               103
  T3                 27                73
  T4                 59               114
[1] 4 2
[1] 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
  9Q GAIN MUTATED    51  18  46   4
  9Q GAIN WILD-TYPE 128  50 122   4
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              51               128
  N1              18                50
  N2              46               122
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    47   0
  9Q GAIN WILD-TYPE 142   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     47    0
  9Q GAIN WILD-TYPE  142    1
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              47               142
  1               0                 1
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    41  98
  9Q GAIN WILD-TYPE  99 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     41   98
  9Q GAIN WILD-TYPE   99  284
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              41                99
  MALE                98               284
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    39  78
  9Q GAIN WILD-TYPE 112 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     39   78
  9Q GAIN WILD-TYPE  112  205
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               39               112
  YES              78               205
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  9Q GAIN MUTATED                                     136
  9Q GAIN WILD-TYPE                                   375
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  9Q GAIN MUTATED                                                             0
  9Q GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  9Q GAIN MUTATED                                                     3
  9Q GAIN WILD-TYPE                                                   7
D18V9, multiclass
                                                             clus
vv                                                            9Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   136
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       3
                                                             clus
vv                                                            9Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     375
  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"
D18V10, continuous
D18V11, continuous
D18V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     2
  9Q GAIN WILD-TYPE                                2     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                          12   122
  9Q GAIN WILD-TYPE                        36   324
D18V13, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                     12                36
  WHITE                                        122               324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    10 119
  9Q GAIN WILD-TYPE  16 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     10  119
  9Q GAIN WILD-TYPE   16  340
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  10                16
  NOT HISPANIC OR LATINO             119               340
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    27  13
  10P GAIN WILD-TYPE 276 205
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                40                481 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                13                205 
$`10P GAIN MUTATED`
TCGA-BA-5151 TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-A6DL TCGA-BB-7861 
       23.74        17.10        21.17        12.62        20.48        22.42 
TCGA-BB-A5HZ TCGA-CN-4727 TCGA-CN-5356 TCGA-CN-6013 TCGA-CN-6994 TCGA-CN-A63T 
       27.19        51.29        46.32        23.90        38.89         7.40 
TCGA-CQ-7067 TCGA-CR-5247 TCGA-CR-6488 TCGA-CR-7399 TCGA-CV-5441 TCGA-CV-6003 
       16.73        11.77        12.46         5.95        87.55        54.74 
TCGA-CV-6934 TCGA-CV-6937 TCGA-CV-7091 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7421 
        2.14        20.52       111.16        95.34        47.97         0.07 
TCGA-CV-7435 TCGA-CV-A45Z TCGA-CV-A6JM TCGA-CV-A6JY TCGA-DQ-7589 TCGA-F7-7848 
      153.86        48.20         6.38        21.24        46.32        37.18 
TCGA-HD-7917 TCGA-HD-A6HZ TCGA-IQ-A6SG TCGA-P3-A5QE TCGA-QK-A6IG TCGA-QK-A6VB 
       27.48         3.65        19.04        51.25         7.30        21.07 
TCGA-QK-A6VC TCGA-T2-A6WZ TCGA-TN-A7HI TCGA-UF-A71D 
       19.73        15.91        13.55        48.03 

$`10P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       26.50        42.35        57.93        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 
       68.48        15.52        14.83         3.55         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
       29.42        28.11        20.45        30.18        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       13.38        16.41         6.15       105.90         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
        4.41        18.38        36.72        33.70        50.20        44.98 
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-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
       10.55        12.92         8.81         6.28        12.69        48.76 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       55.86        38.04         4.67        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       32.81        52.14        57.11        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
       45.83        27.58        73.61        13.05        42.02         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       12.39        71.31         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.57        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       30.67        48.00        47.44        28.04        19.07        34.13 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       32.22        35.05         3.68        17.42        32.48        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
        2.70        23.44        19.82        24.39        20.88        19.53 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.38        32.88        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
       14.99        38.76        70.13        64.87        53.52        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-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-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 
       11.90        10.22        11.34        11.64         7.69        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       15.75         9.27        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        29.82        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58         7.10         5.13 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 
      108.95        76.24        19.20        17.95       107.51        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
       48.59        60.49         7.07        43.23        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 
        9.60        90.12         9.70         5.46         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       140.78        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       15.09        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
        7.13         8.42        28.34         2.50         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      126.15        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-7418 
       89.33         9.67         0.46        22.85        25.08        25.94 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       34.09       100.57        14.89        56.48       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 
        3.52        16.27        84.49        19.76         7.17        16.64 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
        6.38        22.19        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A460 TCGA-CV-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-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        5.98        35.34        29.79         6.48        28.01         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-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       18.84        34.36        51.12        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
       23.05         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN 
       25.32        17.72        12.36        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        13.94        12.10        12.79        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 
       37.25        30.94        33.86        18.02        14.04        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45        37.58        40.24        40.04        39.12        41.59 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       24.95         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
        0.07        28.47        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       22.03        12.66        22.85         0.36        13.84         4.27 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        37.41         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.84        15.48        13.35        18.15        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       71.74        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-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.07        21.21        23.15        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       18.64         6.51         5.62        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
       15.32         8.32        12.72        16.96         6.87         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       32.45        13.71         3.12        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-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 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.07               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            153.86             210.97 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            21.205             20.750 
[1] "0.1 - 153.9 (21.2)" "0.1 - 211.0 (20.8)"
[1] "hr=" "1.4"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  10P GAIN MUTATED         2        5         8        19         0         0
  10P GAIN WILD-TYPE      25       71        74       234        12         1
D19V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  2                 25
  STAGE II                 5                 71
  STAGE III                8                 74
  STAGE IVA               19                234
  STAGE IVB                0                 12
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10P GAIN MUTATED       5   9   9  13
  10P GAIN WILD-TYPE    45 128  91 160
D19V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1                5                 45
  T2                   9                128
  T3                   9                 91
  T4                  13                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
  10P GAIN MUTATED    18   8   9   0
  10P GAIN WILD-TYPE 161  60 159   8
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               18                161
  N1                8                 60
  N2                9                159
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    12   0
  10P GAIN WILD-TYPE 177   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     12    0
  10P GAIN WILD-TYPE  177    1
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               12                177
  1                0                  1
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    10  30
  10P GAIN WILD-TYPE 130 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     10   30
  10P GAIN WILD-TYPE  130  352
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               10                130
  MALE                 30                352
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    12  21
  10P GAIN WILD-TYPE 139 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     12   21
  10P GAIN WILD-TYPE  139  262
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                12                139
  YES               21                262
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  10P GAIN MUTATED                                      39
  10P GAIN WILD-TYPE                                   472
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  10P GAIN MUTATED                                                             0
  10P GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  10P GAIN MUTATED                                                     1
  10P GAIN WILD-TYPE                                                   9
D19V9, multiclass
                                                             clus
vv                                                            10P GAIN 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                        1
                                                             clus
vv                                                            10P GAIN 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                          9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, continuous
D19V11, continuous
D19V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0     0
  10P GAIN WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           3    37
  10P GAIN WILD-TYPE                        45   409
D19V13, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       3                 45
  WHITE                                          37                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"
D19V14, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     1  38
  10P GAIN WILD-TYPE  25 421
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1   38
  10P GAIN WILD-TYPE   25  421
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               38                421
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    22  12
  10Q GAIN WILD-TYPE 281 206
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                34                487 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                206 
$`10Q GAIN MUTATED`
TCGA-BA-5151 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A6DL TCGA-BB-A5HY TCGA-BB-A5HZ 
       23.74        12.62         4.01        20.48        10.55        27.19 
TCGA-CN-4727 TCGA-CN-6013 TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-A63T TCGA-CQ-5329 
       51.29        23.90        52.08        38.89         7.40        70.45 
TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CR-7390 TCGA-CR-7399 TCGA-CV-5441 TCGA-CV-5966 
       16.73        11.61        29.82         5.95        87.55        17.92 
TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6937 TCGA-CV-7091 TCGA-CV-7435 TCGA-CV-A6JY 
       54.74         9.60        20.52       111.16       153.86        21.24 
TCGA-D6-6825 TCGA-DQ-5629 TCGA-F7-A620 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-A6HZ 
       16.14        30.94        17.85        21.93        27.48         3.65 
TCGA-P3-A5Q6 TCGA-QK-A6IG TCGA-TN-A7HI TCGA-UF-A71D 
       15.78         7.30        13.55        48.03 

$`10Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       26.50        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
       41.85        29.42        28.11        20.45        30.18        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       11.05        13.38        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       50.20        44.98        66.28        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       20.52        25.71        12.92         8.81         6.28        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       48.76        55.86        38.04         4.67        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       26.86        32.81        52.14        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 
       46.32         8.58        12.39        71.31         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 
       56.94        50.07        30.67        48.00        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 
       19.07        34.13         6.74         9.07         9.24        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       10.45        32.22        35.05         3.68        17.42        32.48 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
       21.21        31.69        22.32        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        23.44        19.82        24.39        20.88 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       19.53        48.20        52.37        21.50         2.93        54.58 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.38        32.88        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
       14.99        38.76        70.13        64.87        53.52        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
       39.52        34.52        36.99        18.54        16.90         6.02 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       22.78        15.75         9.27        47.18        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       40.93        35.84         3.45         3.09        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
        0.99        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 
       17.13        32.78        47.01        27.06        12.89        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58         7.10         5.13 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 
      108.95        76.24        19.20        17.95       107.51        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       91.53        80.12        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-6933 
       60.49         7.07        43.23        21.07        62.43        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-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       140.78        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        8.42        28.34         2.50         4.14        64.83       126.15 
TCGA-CV-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-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
      156.49        54.94         3.52        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
        7.17        16.64         6.38        22.19        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
      169.38       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       56.61         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 
       29.79         6.48        28.01         3.62        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
       22.52        10.42        10.42        10.55        18.84        34.36 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       28.77         7.63        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        11.11        58.45        37.25        33.86        18.02 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       14.04        46.32        46.45        20.45        37.58        40.24 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       40.04        39.12        41.59        37.18        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         0.46 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.61        21.11        20.94         0.07        28.47        25.74 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
       27.48        14.66        22.03        12.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         6.90        34.75        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        37.71        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S 
        5.29        13.68        13.84        19.04        15.48        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
        1.84        12.62         6.25        15.42         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       17.98        29.92        71.74        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       21.47         9.34        12.72        18.64        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
        6.51         5.62        14.76        12.20        17.82        15.32 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
        8.32        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       32.45        13.71         3.12        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-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 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              3.65               0.07 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            153.86             210.97 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             20.88              20.94 
[1] "3.6 - 153.9 (20.9)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1.3"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  10Q GAIN MUTATED         3        3         6        19         0         0
  10Q GAIN WILD-TYPE      24       73        76       234        12         1
D20V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  3                 24
  STAGE II                 3                 73
  STAGE III                6                 76
  STAGE IVA               19                234
  STAGE IVB                0                 12
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10Q GAIN MUTATED       4   8   8  12
  10Q GAIN WILD-TYPE    46 129  92 161
D20V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T0+T1                4                 46
  T2                   8                129
  T3                   8                 92
  T4                  12                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
  10Q GAIN MUTATED    14   7  11   0
  10Q GAIN WILD-TYPE 165  61 157   8
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               14                165
  N1                7                 61
  N2               11                157
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    12   0
  10Q GAIN WILD-TYPE 177   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     12    0
  10Q GAIN WILD-TYPE  177    1
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               12                177
  1                0                  1
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     8  26
  10Q GAIN WILD-TYPE 132 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      8   26
  10Q GAIN WILD-TYPE  132  356
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                8                132
  MALE                 26                356
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    11  17
  10Q GAIN WILD-TYPE 140 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     11   17
  10Q GAIN WILD-TYPE  140  266
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                11                140
  YES               17                266
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  10Q GAIN MUTATED                                      34
  10Q GAIN WILD-TYPE                                   477
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  10Q GAIN MUTATED                                                             0
  10Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  10Q GAIN MUTATED                                                     0
  10Q GAIN WILD-TYPE                                                  10
D20V9, multiclass
                                                             clus
vv                                                            10Q GAIN 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                        0
                                                             clus
vv                                                            10Q GAIN 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                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, continuous
D20V11, continuous
D20V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     0
  10Q GAIN WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           0    34
  10Q GAIN WILD-TYPE                        48   412
D20V13, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 48
  WHITE                                          34                412
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V14, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2  31
  10Q GAIN WILD-TYPE  24 428
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   31
  10Q GAIN WILD-TYPE   24  428
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 24
  NOT HISPANIC OR LATINO               31                428
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    38  28
  11P GAIN WILD-TYPE 265 190
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                66                455 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                28                190 
$`11P GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5556 TCGA-BA-6868 TCGA-BA-A8YP TCGA-BB-4225 TCGA-BB-7861 
        9.30        23.84        15.52        16.41         4.60        22.42 
TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4742 TCGA-CN-5355 
       10.55         6.28        20.55        14.33        13.05        42.02 
TCGA-CN-5367 TCGA-CN-6997 TCGA-CQ-5323 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-7063 
       11.57        32.48        48.20        11.21         4.24        70.13 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CE TCGA-CQ-A4CG 
       53.52        41.88        44.48        11.61        29.49        14.14 
TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7382 TCGA-CV-6003 TCGA-CV-6433 
       11.64        39.16        47.34        26.17        54.74        21.07 
TCGA-CV-6937 TCGA-CV-6950 TCGA-CV-6959 TCGA-CV-7247 TCGA-CV-7254 TCGA-CV-7255 
       20.52        15.09         8.42        18.97        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7409 TCGA-CV-7416 TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CX-7086 
       36.13        17.85        25.08        21.24        23.47        18.84 
TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6516 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A6EP 
       34.36        51.12        25.41        18.67        25.32        13.94 
TCGA-DQ-7588 TCGA-F7-A50J TCGA-F7-A622 TCGA-HD-7229 TCGA-IQ-7630 TCGA-IQ-A61K 
       14.04        31.13        11.80         0.07        15.95         5.29 
TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-P3-A5QA TCGA-P3-A6T2 TCGA-P3-A6T3 
       13.68        19.04        15.48        71.74        75.55        18.97 
TCGA-P3-A6T5 TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-T2-A6WX TCGA-UF-A7JC 
       29.00         7.30        12.72        21.07         6.87        17.95 

$`11P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 
       23.74        42.35        57.93        17.10        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
       68.48        21.17        14.83         3.55        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
       41.85        29.42        28.11        20.45        30.18        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       11.05        13.38        20.48         6.15       105.90         9.14 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
        4.41        18.38        36.72        33.70        50.20        44.98 
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-A480 TCGA-CN-4722 TCGA-CN-4723 
       27.19        12.92         8.81        12.69        48.76        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       38.04         4.67        51.29        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4739 TCGA-CN-4740 
       32.81        52.14        57.11        12.99        45.83        27.58 
TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
       73.61        46.32         8.58        12.39        71.31         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       16.21        11.54        11.84        12.49         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       56.94        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       28.04        19.07        34.13         6.74         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
       52.08        11.08        10.45        32.22        35.05        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       17.29        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
       19.82        24.39        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       41.19        32.38        32.88        46.95        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7068 
        4.24        14.99        38.76        64.87        16.73        43.04 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH 
       43.10        77.56        23.24        29.36        33.60        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-6487 
       16.90         6.02        11.90        10.22        11.34         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 
       12.46        22.78        15.75         9.27        47.18        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-7383 TCGA-CR-7385 
       31.96         9.17        34.06        19.92        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        29.82        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58         7.10         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      108.95        76.24        19.20        17.95       107.51        87.55 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6436 
       86.83        48.59        60.49         7.07        43.23        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 
        9.60        90.12         2.14         9.70         5.46         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       21.90        26.43        11.24       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       42.38        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        7.13        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-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7263 
       26.20        17.13        95.34         4.96        11.87        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-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 
       22.85        25.94         0.07        34.09       100.57        14.89 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       56.48       156.49        54.94         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-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        21.01       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
        1.05        45.96         6.51        88.87        48.20        60.43 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       67.86         0.76        56.61         7.07        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       35.34         6.38        29.79         6.48        28.01         3.62 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6515 
       19.92        22.52        10.42        10.42        10.55        13.25 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 
        9.60        23.05         2.53        16.14        11.44        24.95 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
       12.10        12.79        11.11        58.45        37.25        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       33.86        18.02        46.32        46.45        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       40.24        40.04        39.12        41.59        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       21.63        20.25         3.02        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       17.85        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       13.61        21.11        20.94        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       27.48        27.48        14.66        22.03        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
        0.36        13.84         4.27         3.65         6.90        34.75 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       33.57        13.84        13.35        18.15        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T4 
       51.25        10.85        36.82        47.01        19.00         2.04 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       21.47         9.34        18.64        19.73         6.51         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
       16.96        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD 
       49.51        48.03        49.45        44.65        74.47        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       32.65         2.96        17.03        20.55        14.56 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.07               0.07 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             75.55             210.97 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             18.97              21.17 
[1] "0.1 - 75.5 (19.0)"  "0.1 - 211.0 (21.2)"
[1] "hr=" "1.2"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  11P GAIN MUTATED         5       13        16        26         2         0
  11P GAIN WILD-TYPE      22       63        66       227        10         1
D21V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  5                 22
  STAGE II                13                 63
  STAGE III               16                 66
  STAGE IVA               26                227
  STAGE IVB                2                 10
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11P GAIN MUTATED       6  21  18  17
  11P GAIN WILD-TYPE    44 116  82 156
D21V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1                6                 44
  T2                  21                116
  T3                  18                 82
  T4                  17                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
  11P GAIN MUTATED    31   9  15   2
  11P GAIN WILD-TYPE 148  59 153   6
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               31                148
  N1                9                 59
  N2               15                153
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    33   0
  11P GAIN WILD-TYPE 156   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     33    0
  11P GAIN WILD-TYPE  156    1
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               33                156
  1                0                  1
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    19  47
  11P GAIN WILD-TYPE 121 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     19   47
  11P GAIN WILD-TYPE  121  335
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               19                121
  MALE                 47                335
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    22  34
  11P GAIN WILD-TYPE 129 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     22   34
  11P GAIN WILD-TYPE  129  249
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                22                129
  YES               34                249
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  11P GAIN MUTATED                                      66
  11P GAIN WILD-TYPE                                   445
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  11P GAIN MUTATED                                                             0
  11P GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  11P GAIN MUTATED                                                     0
  11P GAIN WILD-TYPE                                                  10
D21V9, multiclass
                                                             clus
vv                                                            11P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     66
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            11P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      445
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V10, continuous
D21V11, continuous
D21V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     4
  11P GAIN WILD-TYPE                                2     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           8    52
  11P GAIN WILD-TYPE                        40   394
D21V13, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           4                  7
  BLACK OR AFRICAN AMERICAN                       8                 40
  WHITE                                          52                394
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V14, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     3  60
  11P GAIN WILD-TYPE  23 399
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3   60
  11P GAIN WILD-TYPE   23  399
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               60                399
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    42  29
  11Q GAIN WILD-TYPE 261 189
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                71                450 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                189 
$`11Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4225 
        9.30        23.84        65.59        20.48        16.41         4.60 
TCGA-BB-7861 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5367 
       22.42        32.81        20.55        13.05        42.02        11.57 
TCGA-CN-6018 TCGA-CN-6997 TCGA-CN-A63U TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6225 
       19.07        32.48        31.69        11.21         4.24        13.25 
TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4CE 
       70.13        53.52        41.88        77.56        11.61        29.49 
TCGA-CQ-A4CG TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7372 TCGA-CR-7383 
       14.14        11.64        39.16        47.34        24.95        17.13 
TCGA-CV-6003 TCGA-CV-6937 TCGA-CV-6950 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-7235 
       54.74        20.52        15.09         8.42        28.34        77.16 
TCGA-CV-7248 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7440 
       17.13         2.10        36.13        25.08       100.57        22.19 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6826 
       21.24        23.47        18.84        34.36        25.41        11.44 
TCGA-D6-6827 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-DQ-5631 TCGA-F7-A50J TCGA-F7-A622 
       18.67        12.36        13.94        18.02        31.13        11.80 
TCGA-HD-7229 TCGA-HD-7831 TCGA-IQ-7630 TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SG 
        0.07        21.93        15.95         5.29        13.68        19.04 
TCGA-IQ-A6SH TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-QK-A6IJ 
       15.48        15.78        71.74        18.97        29.00        12.72 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A7JC TCGA-UF-A7JJ 
       64.80        54.67        48.03        17.95        18.05 

$`11Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19        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-5559 
       23.74        42.35        57.93        17.10        20.48        68.48 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
       15.52        21.17        14.83         3.55        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
       41.85        29.42        28.11        20.45        30.18        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 
       11.05        13.38         6.15       105.90         9.14         4.41 
TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
       18.38        36.72        33.70        50.20        44.98        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-4722 
       27.19        12.92         8.81         6.28        12.69        48.76 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       55.86        38.04         4.67        51.29        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 
       26.86        52.14        57.11        12.99        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       27.58        73.61        46.32         8.58        12.39        71.31 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 
        8.32        16.21        11.54        11.84        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       47.44        28.04        34.13         6.74         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
       52.08        11.08        10.45        32.22        35.05        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W 
       17.29        29.72        21.21         7.40        22.32        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       24.39        20.88        19.53        48.20        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
       41.19        32.38        32.88        46.95        56.58         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 
       14.99        38.76        64.87        16.73        43.04        43.10 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CQ-A4CI 
       44.48        23.24        29.36        33.60        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-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-7368 TCGA-CR-7369 
       22.78        15.75         9.27        47.18        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.45         3.09        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       34.06        19.92        26.17        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        29.82        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58         7.10         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        87.55        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-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-6938 TCGA-CV-6939 
       90.12         2.14         9.70         5.46         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       140.78        19.79        12.03        42.38 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-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-7236 
       12.92        21.80        71.21        10.75       130.88         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 
       47.47        36.00        31.36        26.20        18.97        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
        4.96        11.87        47.97        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-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
       25.94         0.07        34.09        14.89        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
       54.94         3.52        16.27        84.49        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
      153.86        16.64         6.38        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
        7.07        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        6.48        28.01         3.62        19.92        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 
       10.42        10.55        51.12        13.25         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK 
        2.53        16.14        24.95        25.32        17.72        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        22.59        24.95        12.10        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 
       58.45        37.25        30.94        33.86        14.04        46.32 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       46.45        20.45        37.58        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 
       18.94        24.95         0.46        17.85        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11        20.94 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        27.48        27.48        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        6.90        34.75        38.53        14.50        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
       37.41         0.07        33.57        13.84        13.35        18.15 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.27        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         6.25        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       29.92        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       75.55         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-A6V9 
       21.21        23.15         7.30        21.47         9.34        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        19.73         6.51         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       17.82        15.32         8.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
       15.91         7.10        32.45        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
       13.25        20.35         2.83        49.51        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO 
       74.47        24.30        55.43        29.46        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 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.07               0.07 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            100.57             210.97 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             20.48              21.07 
[1] "0.1 - 100.6 (20.5)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1"  
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  11Q GAIN MUTATED         6       14        16        30         1         0
  11Q GAIN WILD-TYPE      21       62        66       223        11         1
D22V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  6                 21
  STAGE II                14                 62
  STAGE III               16                 66
  STAGE IVA               30                223
  STAGE IVB                1                 11
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11Q GAIN MUTATED       8  19  19  22
  11Q GAIN WILD-TYPE    42 118  81 151
D22V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1                8                 42
  T2                  19                118
  T3                  19                 81
  T4                  22                151
[1] 4 2
[1] 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
  11Q GAIN MUTATED    36   7  18   1
  11Q GAIN WILD-TYPE 143  61 150   7
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               36                143
  N1                7                 61
  N2               18                150
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    33   0
  11Q GAIN WILD-TYPE 156   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     33    0
  11Q GAIN WILD-TYPE  156    1
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               33                156
  1                0                  1
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    23  48
  11Q GAIN WILD-TYPE 117 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     23   48
  11Q GAIN WILD-TYPE  117  334
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               23                117
  MALE                 48                334
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    25  34
  11Q GAIN WILD-TYPE 126 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     25   34
  11Q GAIN WILD-TYPE  126  249
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                25                126
  YES               34                249
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  11Q GAIN MUTATED                                      71
  11Q GAIN WILD-TYPE                                   440
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  11Q GAIN MUTATED                                                             0
  11Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  11Q GAIN MUTATED                                                     0
  11Q GAIN WILD-TYPE                                                  10
D22V9, multiclass
                                                             clus
vv                                                            11Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     71
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            11Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      440
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, continuous
D22V11, continuous
D22V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     2
  11Q GAIN WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           8    57
  11Q GAIN WILD-TYPE                        40   389
D22V13, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       8                 40
  WHITE                                          57                389
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     3  60
  11Q GAIN WILD-TYPE  23 399
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3   60
  11Q GAIN WILD-TYPE   23  399
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               60                399
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    87  61
  12P GAIN WILD-TYPE 216 157
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               148                373 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                61                157 
$`12P GAIN MUTATED`
TCGA-4P-AA8J TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A4IH 
        3.35        17.10        68.48         3.55        29.42        20.45 
TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       11.05        20.48        16.41       105.90         9.14         4.60 
TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4728 
       36.72        66.28        10.55         6.28        38.04        56.68 
TCGA-CN-4729 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-5359 
       12.89        20.55        14.33        45.83        46.32        12.39 
TCGA-CN-5366 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
       11.84        48.00        19.07        52.08        11.08        10.45 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       38.89         3.68        35.01        23.57        17.29        29.72 
TCGA-CN-A63T TCGA-CN-A6V6 TCGA-CQ-5329 TCGA-CQ-5332 TCGA-CQ-6220 TCGA-CQ-6224 
        7.40        20.88        70.45        10.42        32.38        56.58 
TCGA-CQ-7067 TCGA-CQ-A4CE TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6487 
       16.73        29.49        84.23        11.77        58.42         7.69 
TCGA-CR-6488 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7379 TCGA-CR-7383 
       12.46        47.18        39.16        24.95        34.06        17.13 
TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 
       29.82         7.10         5.13         5.95       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6933 
      129.21       108.95       107.51         7.07        54.74        90.12 
TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6959 TCGA-CV-6962 
       20.52        26.43        11.24        12.03         8.42         4.14 
TCGA-CV-7091 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7242 TCGA-CV-7243 
      111.16         1.84        52.31        21.80        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7407 
       26.20        18.97        17.13        47.97        36.13        35.54 
TCGA-CV-7409 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7435 
       17.85        25.08        25.94         0.07        34.09       153.86 
TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45Z 
       16.64        22.19       180.16        35.47        45.96        48.20 
TCGA-CV-A6JM TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6823 
        6.38        18.84        34.36        13.25        25.41        23.05 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 
       11.11        58.45        30.94        14.04        46.32        20.45 
TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A624 TCGA-H7-7774 
       37.58        37.18        31.13        18.94        12.43        13.38 
TCGA-H7-8501 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-A6HZ 
       15.16        28.47        25.74        21.93        27.48         3.65 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       19.04        15.48        18.15        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6T2 TCGA-P3-A6T3 
        1.84         6.25        17.98        15.78        75.55        18.97 
TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6VB TCGA-QK-A8Z9 
        2.04        21.07        23.15         7.30        21.07        14.76 
TCGA-QK-A8ZA TCGA-RS-A6TO TCGA-T3-A92N TCGA-TN-A7HI TCGA-UF-A71A TCGA-UF-A71B 
       12.20        12.72         3.12        13.55         2.83        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JH 
       49.45        44.65        17.95        29.46 

$`12P GAIN WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       23.74        42.35        57.93        23.84        20.48        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       15.52        21.17        14.83        12.62         4.01        41.85 
TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       28.11        30.18        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4227 
       14.47         7.82         2.27        13.38         6.15         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 
       18.38        22.42        33.70        50.20        44.98        24.66 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM 
       38.40        71.05        20.52        25.71        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 
        8.81        12.69        48.76        55.86         4.67        51.29 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4740 
       26.86        32.81        52.14        57.11        12.99        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
       73.61        13.05        42.02         8.58        71.31         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       16.21        11.54        11.57        12.49         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       56.94        50.07        30.67        23.90        47.44        28.04 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6989 TCGA-CN-6992 
       34.13         6.74         9.07         9.24        32.22        35.05 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49C TCGA-CN-A63U 
       17.42        32.48        11.74        25.41        21.21        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       23.44        19.82        24.39        19.53        48.20        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
       21.50         2.93        54.58        62.37        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 
        4.24        41.19        32.88        46.95        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
       14.99        38.76        70.13        64.87        53.52        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5248 
       29.36        33.60        14.14        12.46        31.23        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-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 
       11.64        22.78        15.75         9.27        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
       35.84         3.45         3.09        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        9.17        19.92        26.17        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       12.89        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       35.41        29.95        48.39        76.24        19.20        17.95 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       87.55        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6433 
       23.05        86.83        48.59        60.49        43.23        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 
       62.43         9.60         2.14         9.70         5.46         4.73 
TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
       21.90       140.78        19.79        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 
        6.08        53.95        65.82        10.98         7.13        28.34 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        2.50        64.83       126.15        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
        9.01         5.26        12.92        71.21        10.75       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       77.16         4.73        47.47        95.34         4.96        11.87 
TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
        2.10        18.41        57.47       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
        0.46        22.85       100.57        14.89        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
       54.94         3.52        16.27        84.49        19.76         7.17 
TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V 
        6.38        27.98        21.01       169.38       159.65         1.05 
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-A6JN TCGA-CV-A6JO 
        7.07        15.25         5.98        35.34        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6517 TCGA-D6-6824 
       10.42        10.42        10.55        51.12         9.60         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       16.14        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       12.36        28.77         7.63        22.59        24.95        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 
       12.10        12.79        37.25        33.86        18.02        46.45 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
       40.24        40.04        39.12        41.59        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       20.25         3.02        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       20.25        15.06        13.61        21.11        20.94         0.07 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
       27.48        14.66        22.03        12.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         6.90        34.75        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        37.71        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 
        5.29        13.68        13.84        13.35        19.27        10.75 
TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA 
       12.62        15.42         7.13        16.08        29.92        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T5 
       51.25        10.85        36.82        47.01        19.00        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6II 
       12.99        16.01        13.15        21.21        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB 
       12.72        18.64        19.73         6.51         5.62        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       15.32         8.32        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       32.45        13.71        13.25        20.35        64.80        54.67 
TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK 
       48.03        74.47        24.30        55.43        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.07               0.07 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            180.16             210.97 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            20.715             21.010 
[1] "0.1 - 180.2 (20.7)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  12P GAIN MUTATED         9       20        25        73         4         0
  12P GAIN WILD-TYPE      18       56        57       180         8         1
D23V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  9                 18
  STAGE II                20                 56
  STAGE III               25                 57
  STAGE IVA               73                180
  STAGE IVB                4                  8
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12P GAIN MUTATED      14  42  30  47
  12P GAIN WILD-TYPE    36  95  70 126
D23V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1               14                 36
  T2                  42                 95
  T3                  30                 70
  T4                  47                126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12P GAIN MUTATED    54  19  48   3
  12P GAIN WILD-TYPE 125  49 120   5
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               54                125
  N1               19                 49
  N2               48                120
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    50   0
  12P GAIN WILD-TYPE 139   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     50    0
  12P GAIN WILD-TYPE  139    1
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               50                139
  1                0                  1
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    34 114
  12P GAIN WILD-TYPE 106 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     34  114
  12P GAIN WILD-TYPE  106  268
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               34                106
  MALE                114                268
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    43  80
  12P GAIN WILD-TYPE 108 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     43   80
  12P GAIN WILD-TYPE  108  203
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                43                108
  YES               80                203
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  12P GAIN MUTATED                                     146
  12P GAIN WILD-TYPE                                   365
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  12P GAIN MUTATED                                                             0
  12P GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  12P GAIN MUTATED                                                     2
  12P GAIN WILD-TYPE                                                   8
D23V9, multiclass
                                                             clus
vv                                                            12P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    146
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            12P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      365
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, continuous
D23V11, continuous
D23V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  1     1
  12P GAIN WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                          18   125
  12P GAIN WILD-TYPE                        30   321
D23V13, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                      18                 30
  WHITE                                         125                321
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V14, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     6 133
  12P GAIN WILD-TYPE  20 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      6  133
  12P GAIN WILD-TYPE   20  326
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 20
  NOT HISPANIC OR LATINO              133                326
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    53  36
  12Q GAIN WILD-TYPE 250 182
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                89                432 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                36                182 
$`12Q GAIN MUTATED`
TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A6DL TCGA-BB-4223 TCGA-BB-4225 
       68.48         3.55        29.42        20.48       105.90         4.60 
TCGA-BB-7870 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4728 
       66.28        10.55         6.28        38.04        51.29        56.68 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-6010 TCGA-CN-6012 
       20.55        45.83        46.32        12.39        50.07        48.00 
TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49A 
       52.08        10.45         3.68        35.01        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A6V6 TCGA-CQ-5332 TCGA-CQ-6220 TCGA-CQ-6224 
       29.72         7.40        20.88        10.42        32.38        56.58 
TCGA-CQ-7067 TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-7365 TCGA-CR-7379 
       16.73        29.49        11.77        58.42        39.16        34.06 
TCGA-CR-7383 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-6940 
       17.13         5.95       139.43        17.16       108.95        26.43 
TCGA-CV-6941 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7102 TCGA-CV-7242 TCGA-CV-7243 
       11.24         8.42         4.14         1.84        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 
       26.20        18.97        17.13        25.08         0.07        34.09 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45Z TCGA-D6-6515 TCGA-D6-6516 
      153.86        22.19       180.16        48.20        13.25        25.41 
TCGA-D6-6823 TCGA-D6-A74Q TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-F7-A50J 
       23.05        11.11        14.04        46.32        20.45        31.13 
TCGA-F7-A61S TCGA-F7-A624 TCGA-H7-7774 TCGA-HD-7753 TCGA-HD-A6HZ TCGA-IQ-A6SH 
       18.94        12.43        13.38        28.47         3.65        15.48 
TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-P3-A6T4 
       18.15        14.37        30.05         1.84         6.25         2.04 
TCGA-QK-A6IF TCGA-QK-A6VB TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-RS-A6TO TCGA-T3-A92N 
       23.15        21.07        14.76        12.20        12.72         3.12 
TCGA-TN-A7HI TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC 
       13.55         2.83        49.45        44.65        17.95 

$`12Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       20.48        65.59        15.52        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
        4.01        41.85        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-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 
       11.05        13.38        16.41         6.15         9.14         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
       18.38        22.42        36.72        33.70        50.20        44.98 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HZ 
       24.66        38.40        71.05        20.52        25.71        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 
       12.92         8.81        12.69        48.76        55.86         4.67 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       12.89        26.86        32.81        52.14        57.11        12.99 
TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
       14.33        27.58        73.61        13.05        42.02         8.58 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       71.31         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 
       12.49         8.52        52.08        56.94        30.67        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
       47.44        28.04        19.07        34.13         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
        9.24        11.08        32.22        35.05        38.89        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V 
       32.48        11.74        25.41        21.21        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       19.82        24.39        19.53        48.20        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
        2.93        54.58        70.45        62.37        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 
        4.24        41.19        32.88        46.95        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
       14.99        38.76        70.13        64.87        53.52        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       29.36        33.60        14.14        12.46        31.23        84.23 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
       54.67        37.87        26.27        50.01        39.52        34.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
       36.99        18.54        16.90         6.02        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       11.34        11.64         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        9.27        47.18        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-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       19.92        26.17        32.78        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       29.82        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 
        7.10         5.13        35.41        29.95        48.39       129.21 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       76.24        19.20        17.95       107.51        87.55        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-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-6942 TCGA-CV-6943 TCGA-CV-6945 
       20.52         4.73        21.90       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       42.38        15.09        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 
       10.98         7.13        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-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-7250 TCGA-CV-7252 TCGA-CV-7253 
       77.16         4.73        47.47        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-7418 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       25.94       100.57        14.89        56.48       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 
        3.52        16.27        84.49        19.76         7.17        16.64 
TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45U 
        6.38        27.98        21.01       169.38       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 
        1.05        45.96         6.51        88.87        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        0.76        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
       23.47        19.92        22.52        10.42        10.42        10.55 
TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
       18.84        34.36        51.12         9.60         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       28.77         7.63        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        58.45        37.25        30.94        33.86        18.02 
TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       46.45        37.58        40.24        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V 
       37.18        32.71        21.63        20.25         3.02        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 
        0.46        17.85        11.80        20.25        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 
       13.61        21.11        20.94         0.07        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       27.48        27.48        14.66        22.03        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-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 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A66S 
       33.57         5.29        13.68        13.84        19.04        13.35 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI 
       19.27        10.75         7.96        12.62        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
       16.08        17.98        29.92        15.78        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       10.85        36.82        47.01        19.00        75.55        18.97 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       29.00        12.99        16.01        13.15        21.07        21.21 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC 
        7.30        21.47         9.34        12.72        18.64        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP 
        6.51         5.62        17.82        15.32         8.32        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HJ 
        6.87        15.91         7.10        32.45        13.71        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA 
       20.35        64.80        54.67        49.51        48.03        74.47 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36        32.65         2.96        17.03        20.55        14.56 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.07               0.07 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            180.16             210.97 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             20.55              21.04 
[1] "0.1 - 180.2 (20.6)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1"  
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  12Q GAIN MUTATED         6       10        17        44         1         0
  12Q GAIN WILD-TYPE      21       66        65       209        11         1
D24V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  6                 21
  STAGE II                10                 66
  STAGE III               17                 65
  STAGE IVA               44                209
  STAGE IVB                1                 11
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12Q GAIN MUTATED      10  23  19  28
  12Q GAIN WILD-TYPE    40 114  81 145
D24V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1               10                 40
  T2                  23                114
  T3                  19                 81
  T4                  28                145
[1] 4 2
[1] 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
  12Q GAIN MUTATED    37  11  28   0
  12Q GAIN WILD-TYPE 142  57 140   8
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               37                142
  N1               11                 57
  N2               28                140
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    30   0
  12Q GAIN WILD-TYPE 159   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     30    0
  12Q GAIN WILD-TYPE  159    1
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               30                159
  1                0                  1
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    23  66
  12Q GAIN WILD-TYPE 117 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     23   66
  12Q GAIN WILD-TYPE  117  316
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               23                117
  MALE                 66                316
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    25  53
  12Q GAIN WILD-TYPE 126 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     25   53
  12Q GAIN WILD-TYPE  126  230
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                25                126
  YES               53                230
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  12Q GAIN MUTATED                                      88
  12Q GAIN WILD-TYPE                                   423
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  12Q GAIN MUTATED                                                             0
  12Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  12Q GAIN MUTATED                                                     1
  12Q GAIN WILD-TYPE                                                   9
D24V9, multiclass
                                                             clus
vv                                                            12Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     88
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            12Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      423
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, continuous
D24V11, continuous
D24V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     1
  12Q GAIN WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                           8    78
  12Q GAIN WILD-TYPE                        40   368
D24V13, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       8                 40
  WHITE                                          78                368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V14, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     5  78
  12Q GAIN WILD-TYPE  21 381
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      5   78
  12Q GAIN WILD-TYPE   21  381
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 21
  NOT HISPANIC OR LATINO               78                381
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    29  28
  13Q GAIN WILD-TYPE 274 190
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                57                464 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                28                190 
$`13Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BB-4225 TCGA-CN-4726 TCGA-CN-4728 
        9.30        14.83        29.42         4.60         4.67        56.68 
TCGA-CN-4729 TCGA-CN-4737 TCGA-CN-4742 TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6989 
       12.89        20.55        13.05         8.52        23.90        32.22 
TCGA-CN-6996 TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-7072 TCGA-CQ-A4CH 
       17.42        22.32        12.39        16.57        77.56        12.46 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7367 
       31.23        11.77        11.64        12.46        39.16        47.34 
TCGA-CR-7370 TCGA-CR-7380 TCGA-CR-7390 TCGA-CV-5440 TCGA-CV-6003 TCGA-CV-6933 
        3.45        19.92        29.82       107.51        54.74        90.12 
TCGA-CV-6939 TCGA-CV-6956 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7178 
       21.90         7.13       126.15        18.81        12.66        71.21 
TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7437 TCGA-CV-A45X 
       31.36        18.97        25.08       100.57        16.64         6.51 
TCGA-CV-A463 TCGA-D6-6823 TCGA-D6-8569 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-F7-A50J 
        0.76        23.05        25.32        30.94        18.02        31.13 
TCGA-IQ-A61G TCGA-MT-A51W TCGA-MT-A51X TCGA-P3-A6T5 TCGA-QK-A6IH TCGA-T2-A6WZ 
       11.84        14.37         7.96        29.00        21.47        15.91 
TCGA-UF-A719 TCGA-UF-A7JH TCGA-WA-A7GZ 
       54.67        29.46        20.55 

$`13Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 
       65.59        68.48        15.52        21.17         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
        4.01        41.85        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-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        9.14         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       50.20        44.98        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-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4727 
        6.28        12.69        48.76        55.86        38.04        51.29 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
       26.86        32.81        52.14        57.11        12.99        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       45.83        27.58        73.61        42.02        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       12.39        71.31         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
       11.57        12.49        52.08        56.94        50.07        30.67 
TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       48.00        47.44        28.04        19.07        34.13         6.74 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
        9.07         9.24        52.08        11.08        10.45        35.05 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       38.89         3.68        32.48        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       23.57        17.29        29.72        21.21         7.40        31.69 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
        4.24        41.19        32.38        32.88        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       13.25         4.24        14.99        38.76        70.13        64.87 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
       53.52        16.73        43.04        41.88        43.10        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       11.61        23.24        29.36        33.60        29.49        14.14 
TCGA-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-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 
       11.90        10.22        11.34         7.69        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 
        9.27        47.18        40.93        35.84         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
       29.23         0.99        31.96         9.17        34.06        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 
       17.13        32.78        47.01        27.06        12.89        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58         7.10         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        5.95        35.41        29.95        48.39       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 
      129.21       108.95        76.24        19.20        17.95        87.55 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 
       86.83        48.59        60.49         7.07        43.23        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
       62.43         9.60         2.14         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        4.73        26.43        11.24       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       42.38        15.09        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
       10.98         8.42        28.34         2.50         4.14        64.83 
TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 
      111.16         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-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       47.47        36.00        26.20        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-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7425 
       22.85        25.94         0.07        34.09        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
      156.49        54.94         3.52        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
        7.17       153.86         6.38        22.19        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
      169.38       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 
       88.87        48.20        60.43        67.86        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ 
       10.42        10.42        10.55        18.84        34.36        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       13.25        25.41         9.60         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       18.67        24.95        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       58.45        37.25        33.86        14.04        46.32        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45        37.58        40.24        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S 
       37.18        32.71        21.63        20.25         3.02        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       24.95         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
        4.27         3.65         6.90        34.75        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       14.50        37.71        37.41         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T 
       13.68        13.84        19.04        15.48        13.35        18.15 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       19.27        10.75        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       75.55        18.97         2.04        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
       21.07        21.21        23.15         7.30         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       18.64        21.07        19.73         6.51         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
        6.87         7.10        32.45        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D 
       13.25        20.35        64.80         2.83        49.51        48.03 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.45        44.65        74.47        17.95        24.30        55.43 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       18.05        13.94        20.75        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7H4 
       17.03        14.56 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.76               0.07 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            126.15             210.97 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             20.55              21.04 
[1] "0.8 - 126.2 (20.6)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1.2"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  13Q GAIN MUTATED         1       12        10        23         2         0
  13Q GAIN WILD-TYPE      26       64        72       230        10         1
D25V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  1                 26
  STAGE II                12                 64
  STAGE III               10                 72
  STAGE IVA               23                230
  STAGE IVB                2                 10
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  13Q GAIN MUTATED       2  19  11  18
  13Q GAIN WILD-TYPE    48 118  89 155
D25V4, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1                2                 48
  T2                  19                118
  T3                  11                 89
  T4                  18                155
[1] 4 2
[1] 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
  13Q GAIN MUTATED    19   8  17   0
  13Q GAIN WILD-TYPE 160  60 151   8
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               19                160
  N1                8                 60
  N2               17                151
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    19   0
  13Q GAIN WILD-TYPE 170   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     19    0
  13Q GAIN WILD-TYPE  170    1
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               19                170
  1                0                  1
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    16  41
  13Q GAIN WILD-TYPE 124 341
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     16   41
  13Q GAIN WILD-TYPE  124  341
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               16                124
  MALE                 41                341
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    14  30
  13Q GAIN WILD-TYPE 137 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     14   30
  13Q GAIN WILD-TYPE  137  253
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                14                137
  YES               30                253
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  13Q GAIN MUTATED                                      56
  13Q GAIN WILD-TYPE                                   455
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  13Q GAIN MUTATED                                                             0
  13Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  13Q GAIN MUTATED                                                     1
  13Q GAIN WILD-TYPE                                                   9
D25V9, multiclass
                                                             clus
vv                                                            13Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     56
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            13Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      455
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, continuous
D25V11, continuous
D25V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     2
  13Q GAIN WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           4    48
  13Q GAIN WILD-TYPE                        44   398
D25V13, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       4                 44
  WHITE                                          48                398
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V14, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4  49
  13Q GAIN WILD-TYPE  22 410
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4   49
  13Q GAIN WILD-TYPE   22  410
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 22
  NOT HISPANIC OR LATINO               49                410
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    76  75
  14Q GAIN WILD-TYPE 227 143
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               151                370 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                75                143 
$`14Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5555 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
        9.30        17.10        12.62         4.01        41.85        29.42 
TCGA-BA-A6DA TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-8601 TCGA-BB-A5HU 
       11.54         2.27        11.05        20.48        20.52        25.71 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 
       10.55        27.19         8.81         6.28        12.69        55.86 
TCGA-CN-4730 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5363 TCGA-CN-5366 
       26.86        14.33        27.58        46.32         8.32        11.84 
TCGA-CN-5367 TCGA-CN-6021 TCGA-CN-6994 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A63T 
       11.57         9.07        38.89        23.57        17.29         7.40 
TCGA-CN-A63W TCGA-CN-A640 TCGA-CQ-5323 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 
       12.39         4.41        48.20         2.93        70.45        62.37 
TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6229 
        4.24        32.38        56.58        13.25         4.24        38.76 
TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CE TCGA-CQ-A4CG 
       16.73        41.88        77.56        44.48        29.49        14.14 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7367 TCGA-CR-7370 
       18.54        16.90        12.46        22.78        47.34         3.45 
TCGA-CR-7372 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7388 
       24.95         9.17        34.06        19.92        17.13        27.06 
TCGA-CR-7390 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5444 
       29.82       129.21       108.95        17.95       107.51        80.12 
TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6934 TCGA-CV-6940 
       13.35        86.83        60.49        54.74         2.14        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6954 TCGA-CV-7090 
       11.24       140.78        12.03        15.09        65.82       126.15 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7238 
      111.16        18.81         5.26        71.21        10.75        47.47 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7409 
       31.36        26.20        17.13        47.97         2.10        17.85 
TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7429 TCGA-CV-7434 
        9.67        22.85        25.08        25.94         3.52         7.17 
TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45Q TCGA-CV-A45U TCGA-CV-A6JE TCGA-CV-A6JM 
       16.64        22.19       169.38        35.47        35.34         6.38 
TCGA-CV-A6K0 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6825 
       19.92        18.84        34.36        25.41        23.05        16.14 
TCGA-D6-A4Z9 TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-7588 
       17.72        13.94        11.11        37.25        30.94        14.04 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A624 
       46.32        37.58        40.24         3.02        31.13        12.43 
TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61J 
       28.47        21.93        27.48         3.65        37.71        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X 
        5.29        13.68        15.48        18.15        14.37         7.96 
TCGA-P3-A5Q6 TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T7 TCGA-QK-A6IG 
       15.78        47.01        18.97         2.04        16.01         7.30 
TCGA-QK-A6VB TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WZ 
       21.07        14.76        12.20         8.32        12.72        15.91 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-UF-A71A TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JK 
        3.12        13.55         2.83        24.30        29.46        13.94 
TCGA-UF-A7JO 
       20.75 

$`14Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       23.74        42.35        57.93        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A4IG 
       68.48        15.52        21.17        14.83         3.55        28.11 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       20.45        30.18        27.95         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
        7.82        13.38        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       50.20        44.98        66.28        24.66        38.40        71.05 
TCGA-BB-A6UM TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
       12.92        48.76        38.04         4.67        51.29        56.68 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       12.89        32.81        52.14        57.11        12.99        20.55 
TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 
       45.83        73.61        13.05        42.02         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       71.31        16.21        11.54        12.49         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       56.94        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 
       28.04        19.07        34.13         6.74         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6996 
       11.08        10.45        32.22        35.05         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A49C 
       32.48        11.74        35.01        25.41        29.72        21.21 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       31.69        22.32        16.57        12.07         2.70        23.44 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
       19.82        24.39        20.88        19.53        52.37        21.50 
TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6221 
       54.58        45.99        10.42        11.21        41.19        32.88 
TCGA-CQ-6223 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
       46.95        14.99        70.13        64.87        53.52        43.04 
TCGA-CQ-7071 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH 
       43.10        11.61        23.24        29.36        33.60        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-6478 
       58.42        50.01        39.52        34.52        36.99         6.02 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6492 
       11.90        10.22        11.34        11.64         7.69        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
        9.27        47.18        39.16        40.93        35.84         3.09 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
       29.23         0.99        31.96        26.17        32.78        47.01 
TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       12.89        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         5.13         5.95        35.41        29.95        48.39 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 
      139.43        17.16        76.24        19.20        87.55        76.50 
TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
       91.53        17.92        23.05        48.59         7.07        43.23 
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-6943 TCGA-CV-6948 TCGA-CV-6951 
       20.52         4.73        21.90        19.79        42.38        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
        6.08        53.95        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        2.50         4.14        64.83        12.66         7.99         9.01 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7183 TCGA-CV-7235 
        1.84        52.31        12.92        21.80       130.88        77.16 
TCGA-CV-7236 TCGA-CV-7242 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
        4.73        36.00        18.97        95.34         4.96        11.87 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 
       36.13        18.41        57.47        35.54       210.97        89.33 
TCGA-CV-7414 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
        0.46         0.07        34.09       100.57        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 
      156.49        54.94        16.27        84.49        19.76       153.86 
TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V 
        6.38        27.98        21.01       180.16       159.65         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-A6JN 
        0.76        56.61         7.07        15.25         5.98        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K1 
        6.48        28.01         3.62        21.24        23.47        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 
       10.42        10.42        10.55        51.12        13.25         9.60 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB 
        2.53        11.44        18.67        24.95        25.32        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES 
       28.77         7.63        22.59        24.95        12.10        12.79 
TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 
       58.45        33.86        18.02        46.45        20.45        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       39.12        41.59        37.18        32.71        21.63        20.25 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        24.95         0.46        17.85        11.80        20.25 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
        0.07        25.74        27.48        14.66        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       22.85         0.36        13.84         4.27         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       15.95        38.53        14.50        11.84        37.41         0.07 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A 
       13.84        19.04        13.35        19.27        10.75        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
        1.84        12.62         6.25        15.42         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       17.98        29.92        71.74        51.25        10.85        36.82 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A64Z 
       19.00        75.55        29.00        12.99        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.21        23.15        21.47         9.34        12.72        18.64 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TP 
       19.73         6.51         5.62        17.82        15.32        16.96 
TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HJ TCGA-TN-A7HL 
        6.87         7.10        32.45        13.71        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       64.80        54.67        49.51        48.03        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS TCGA-UF-A7JT 
       74.47        17.95        55.43        18.05        22.36        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        17.03        20.55        14.56 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              2.04               0.07 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            169.38             210.97 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            18.810             21.225 
[1] "2.0 - 169.4 (18.8)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.4"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  14Q GAIN MUTATED        10       22        23        72         4         0
  14Q GAIN WILD-TYPE      17       54        59       181         8         1
D26V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                 10                 17
  STAGE II                22                 54
  STAGE III               23                 59
  STAGE IVA               72                181
  STAGE IVB                4                  8
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  14Q GAIN MUTATED      12  40  29  53
  14Q GAIN WILD-TYPE    38  97  71 120
D26V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1               12                 38
  T2                  40                 97
  T3                  29                 71
  T4                  53                120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  14Q GAIN MUTATED    50  18  53   2
  14Q GAIN WILD-TYPE 129  50 115   6
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               50                129
  N1               18                 50
  N2               53                115
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    51   0
  14Q GAIN WILD-TYPE 138   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     51    0
  14Q GAIN WILD-TYPE  138    1
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               51                138
  1                0                  1
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    45 106
  14Q GAIN WILD-TYPE  95 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     45  106
  14Q GAIN WILD-TYPE   95  276
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               45                 95
  MALE                106                276
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    50  75
  14Q GAIN WILD-TYPE 101 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     50   75
  14Q GAIN WILD-TYPE  101  208
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                50                101
  YES               75                208
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  14Q GAIN MUTATED                                     151
  14Q GAIN WILD-TYPE                                   360
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  14Q GAIN MUTATED                                                             0
  14Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  14Q GAIN MUTATED                                                     0
  14Q GAIN WILD-TYPE                                                  10
D26V9, multiclass
                                                             clus
vv                                                            14Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    151
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            14Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      360
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, continuous
D26V11, continuous
D26V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  1     3
  14Q GAIN WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                          21   121
  14Q GAIN WILD-TYPE                        27   325
D26V13, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                      21                 27
  WHITE                                         121                325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V14, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     6 134
  14Q GAIN WILD-TYPE  20 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      6  134
  14Q GAIN WILD-TYPE   20  325
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 20
  NOT HISPANIC OR LATINO              134                325
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    40  32
  15Q GAIN WILD-TYPE 263 186
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                72                449 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                32                186 
$`15Q GAIN MUTATED`
TCGA-BA-6871 TCGA-BA-6873 TCGA-BB-7861 TCGA-BB-8596 TCGA-C9-A47Z TCGA-CN-4729 
        3.55         4.01        22.42        71.05         6.28        12.89 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5365 TCGA-CN-5366 
       20.55        45.83        27.58        46.32        11.54        11.84 
TCGA-CN-6010 TCGA-CN-6995 TCGA-CN-A63U TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7069 
       50.07         3.68        31.69        13.25        14.99        41.88 
TCGA-CQ-A4C9 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-7364 
       23.24        18.54        16.90        11.64        22.78        47.18 
TCGA-CR-7365 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7390 TCGA-CV-6003 TCGA-CV-6934 
       39.16        34.06        19.92        29.82        54.74         2.14 
TCGA-CV-6959 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7178 TCGA-CV-7235 
        8.42       126.15       111.16         5.26        71.21        77.16 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 
       47.97         2.10        36.13         9.67        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7427 TCGA-CV-7433 TCGA-CV-7437 TCGA-CV-A6JD 
       25.94         0.07       156.49        19.76        16.64         5.98 
TCGA-CV-A6K2 TCGA-D6-6516 TCGA-D6-8569 TCGA-D6-A6EM TCGA-DQ-5629 TCGA-DQ-7588 
       10.42        25.41        25.32         7.63        30.94        14.04 
TCGA-DQ-7589 TCGA-F7-7848 TCGA-H7-8501 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A633 
       46.32        37.18        15.16        28.47        27.48        13.84 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7632 TCGA-IQ-A6SH TCGA-MT-A67A TCGA-MT-A67G 
        3.65         6.90        14.50        15.48        30.05         6.25 
TCGA-QK-A6IH TCGA-QK-A8Z7 TCGA-TN-A7HJ TCGA-UF-A71E TCGA-UF-A7JH TCGA-UF-A7JK 
       21.47         6.51        13.25        49.45        29.46        13.94 

$`15Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       20.48        65.59        68.48        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
       12.62        41.85        29.42        28.11        20.45        30.18 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       27.95        11.54         7.10         5.69        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
        2.27        11.05        13.38        20.48        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 
      105.90         9.14         4.60         4.41        18.38        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       33.70        50.20        44.98        66.28        24.66        38.40 
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-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
       12.69        48.76        55.86        38.04         4.67        51.29 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       56.68        26.86        32.81        52.14        57.11        12.99 
TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 
       14.33        73.61        13.05        42.02         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       71.31         8.32        16.21        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       52.08        56.94        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       28.04        19.07        34.13         6.74         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
       52.08        11.08        10.45        32.22        35.05        38.89 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        32.48        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W 
       17.29        29.72        21.21         7.40        22.32        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       24.39        20.88        19.53        48.20        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 
       11.21         4.24        41.19        32.38        32.88        46.95 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
       56.58         4.24        38.76        70.13        64.87        53.52 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       16.73        43.04        43.10        77.56        44.48        11.61 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 
       50.01        39.52        34.52        36.99         6.02        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 
       10.22        11.34         7.69        12.46        15.75         9.27 
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-7382 TCGA-CR-7383 
       29.23         0.99        31.96         9.17        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
       32.78        47.01        27.06        12.89        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58         7.10         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      108.95        76.24        19.20        17.95       107.51        87.55 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 
       86.83        48.59        60.49         7.07        43.23        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
       62.43         9.60        90.12         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       65.82        10.98         7.13        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
       64.83        18.81        12.66         7.99         9.01         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 
       52.31        12.92        21.80        10.75       130.88         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-7263 TCGA-CV-7406 TCGA-CV-7407 
       95.34         4.96        11.87        18.41        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7422 TCGA-CV-7423 
       17.85       210.97        89.33         0.46        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       14.89        56.48        54.94         3.52        16.27        84.49 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
        7.17       153.86         6.38        22.19        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
      169.38       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
       56.61         7.07        15.25        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ 
       22.52        10.42        10.55        18.84        34.36        51.12 
TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       13.25         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN 
       18.67        24.95        17.72        12.36        28.77        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        13.94        12.10        12.79        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       37.25        33.86        18.02        46.45        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
       40.24        40.04        39.12        41.59        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8502 
       17.85        11.80        20.25        12.43        13.38        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 
       13.61        21.11        20.94         0.07        25.74        21.93 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
       27.48        14.66        22.03        12.66        22.85         0.36 
TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61G 
        4.27        34.75        15.95        38.53        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       37.41         0.07        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       19.04        13.35        18.15        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
        7.96         1.84        12.62        15.42         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       17.98        29.92        15.78        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       36.82        47.01        19.00        75.55        18.97         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       29.00        12.99        16.01        13.15        21.07        21.21 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
       23.15         7.30         9.34        12.72        18.64        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       19.73         5.62        14.76        12.20        17.82        15.32 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
        8.32        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 
       32.45        13.71         3.12        13.55        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        48.03        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS 
       17.95        24.30        55.43        18.05        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 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.07               0.07 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            156.49             210.97 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             21.01              20.94 
[1] "0.1 - 156.5 (21.0)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1.1"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  15Q GAIN MUTATED         4       10        12        37         3         0
  15Q GAIN WILD-TYPE      23       66        70       216         9         1
D27V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  4                 23
  STAGE II                10                 66
  STAGE III               12                 70
  STAGE IVA               37                216
  STAGE IVB                3                  9
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  15Q GAIN MUTATED       7  20   6  33
  15Q GAIN WILD-TYPE    43 117  94 140
D27V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1                7                 43
  T2                  20                117
  T3                   6                 94
  T4                  33                140
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  15Q GAIN MUTATED    27  11  20   1
  15Q GAIN WILD-TYPE 152  57 148   7
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               27                152
  N1               11                 57
  N2               20                148
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    26   0
  15Q GAIN WILD-TYPE 163   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     26    0
  15Q GAIN WILD-TYPE  163    1
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               26                163
  1                0                  1
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    22  50
  15Q GAIN WILD-TYPE 118 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     22   50
  15Q GAIN WILD-TYPE  118  332
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               22                118
  MALE                 50                332
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    20  37
  15Q GAIN WILD-TYPE 131 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     20   37
  15Q GAIN WILD-TYPE  131  246
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                20                131
  YES               37                246
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  15Q GAIN MUTATED                                      70
  15Q GAIN WILD-TYPE                                   441
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  15Q GAIN MUTATED                                                             0
  15Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  15Q GAIN MUTATED                                                     2
  15Q GAIN WILD-TYPE                                                   8
D27V9, multiclass
                                                             clus
vv                                                            15Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     70
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            15Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      441
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, continuous
D27V11, continuous
D27V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     2
  15Q GAIN WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           6    61
  15Q GAIN WILD-TYPE                        42   385
D27V13, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       6                 42
  WHITE                                          61                385
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1  64
  15Q GAIN WILD-TYPE  25 395
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   64
  15Q GAIN WILD-TYPE   25  395
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               64                395
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    53  53
  16P GAIN WILD-TYPE 250 165
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               106                415 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                53                165 
$`16P GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
        9.30        17.10        68.48        15.52        21.17        14.83 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A6DI TCGA-BA-A6DL 
        3.55         4.01        29.42        28.11        11.05        20.48 
TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-5356 
        6.28        56.68        26.86        20.55        45.83        46.32 
TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A49A 
       23.90         6.74         9.24        38.89        17.42        17.29 
TCGA-CN-A63U TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-7067 
       31.69         2.93        70.45        32.38        46.95        16.73 
TCGA-CQ-7072 TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-7365 
       77.56        11.77        16.90         6.02        10.22        39.16 
TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7388 
       47.34         3.45        24.95        34.06        19.92        27.06 
TCGA-CR-7390 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 
       29.82        17.16        17.95        60.49         7.07        54.74 
TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6954 
       90.12        20.52        21.90        11.24        12.03        65.82 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
      111.16        18.81        10.75        36.00        31.36        26.20 
TCGA-CV-7248 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7423 
       17.13         2.10        18.41        17.85        22.85       100.57 
TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A461 
       19.76       153.86       180.16        35.47        45.96        67.86 
TCGA-CV-A465 TCGA-CV-A6JM TCGA-CV-A6JY TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 
        7.07         6.38        21.24        18.84        25.41        23.05 
TCGA-D6-8569 TCGA-D6-A6EP TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-F7-A50J 
       25.32        13.94        37.25        18.02        14.04        31.13 
TCGA-F7-A623 TCGA-HD-7831 TCGA-HD-8634 TCGA-IQ-7631 TCGA-IQ-A61L TCGA-IQ-A6SH 
       20.25        21.93        12.66        38.53        13.68        15.48 
TCGA-MT-A51W TCGA-MT-A7BN TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-QK-A6II 
       14.37        15.42        18.97         2.04        29.00         9.34 
TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-RS-A6TO TCGA-UF-A71E TCGA-UF-A7J9 
       12.72        21.07         6.51        12.72        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       74.47        24.30        55.43        29.46 

$`16P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       23.74        42.35        57.93        23.84        20.48        65.59 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
       12.62        41.85        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-A6DJ 
        7.10         5.69        14.47         7.82         2.27        13.38 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.60         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
       18.38        22.42        36.72        33.70        50.20        44.98 
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-A480 TCGA-CN-4722 
       10.55        27.19        12.92         8.81        12.69        48.76 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4731 
       55.86        38.04         4.67        51.29        12.89        32.81 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 
       52.14        57.11        12.99        14.33        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
       13.05        42.02         8.58        12.39        71.31         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       16.21        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 
       52.08        56.94        50.07        30.67        48.00        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 
       28.04        19.07        34.13         9.07        52.08        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-6998 
       10.45        32.22        35.05         3.68        32.48        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       35.01        25.41        23.57        29.72        21.21         7.40 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       23.44        19.82        24.39        20.88        19.53        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
       52.37        21.50        54.58        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6225 
       11.21         4.24        41.19        32.88        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        4.24        14.99        38.76        70.13        64.87        53.52 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       43.04        41.88        43.10        44.48        11.61        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       84.23        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6482 
       39.52        34.52        36.99        18.54        11.90        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 
       47.18        40.93        35.84         3.09        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       31.96         9.17        26.17        17.13        32.78        47.01 
TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       12.89        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         5.13         5.95        35.41        29.95        48.39 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 
      139.43       129.21       108.95        76.24        19.20       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       87.55        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
       23.05        86.83        48.59        43.23        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6940 
        9.60         2.14         9.70         5.46         4.73        26.43 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
      140.78        19.79        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       53.95        10.98         7.13         8.42        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        4.14        64.83       126.15        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-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7247 TCGA-CV-7250 
      130.88        77.16         4.73        47.47        18.97        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 
        4.96        11.87        47.97        36.13        57.47        35.54 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 
      210.97        89.33         9.67         0.46        25.08        25.94 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
        0.07        34.09        14.89        56.48       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 
        3.52        16.27        84.49         7.17        16.64         6.38 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V 
       22.19        27.98        21.01       169.38       159.65         1.05 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 
        6.51        88.87        48.20        60.43         0.76        56.61 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
       15.25         5.98        35.34        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
        3.62        23.47        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6824 
       10.55        34.36        51.12        13.25         9.60         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       16.14        11.44        18.67        24.95        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES 
       28.77         7.63        22.59        24.95        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 
       11.11        58.45        30.94        33.86        46.32        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45        37.58        40.24        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S 
       37.18        32.71        21.63        20.25         3.02        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 
       24.95         0.46        17.85        11.80        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       15.16        15.06        13.61        21.11        20.94         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        27.48        27.48        14.66        22.03 
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-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       34.75        15.95        14.50        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A66S 
        0.07        33.57         5.29        13.84        19.04        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       18.15        19.27        10.75         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
       12.62         6.25         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       15.78        71.74        51.25        10.85        36.82        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       19.00        75.55        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A6VC 
       21.21        23.15         7.30        21.47        18.64        19.73 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         8.32 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       16.96         6.87        15.91         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        3.12        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JC TCGA-UF-A7JJ TCGA-UF-A7JK 
        2.83        49.51        48.03        17.95        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              2.04               0.07 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            180.16             210.97 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             20.81              20.94 
[1] "2.0 - 180.2 (20.8)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1.2"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  16P GAIN MUTATED         6       15        17        46         4         0
  16P GAIN WILD-TYPE      21       61        65       207         8         1
D28V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  6                 21
  STAGE II                15                 61
  STAGE III               17                 65
  STAGE IVA               46                207
  STAGE IVB                4                  8
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16P GAIN MUTATED       9  24  19  37
  16P GAIN WILD-TYPE    41 113  81 136
D28V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1                9                 41
  T2                  24                113
  T3                  19                 81
  T4                  37                136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16P GAIN MUTATED    40  14  27   2
  16P GAIN WILD-TYPE 139  54 141   6
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               40                139
  N1               14                 54
  N2               27                141
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    36   0
  16P GAIN WILD-TYPE 153   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     36    0
  16P GAIN WILD-TYPE  153    1
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               36                153
  1                0                  1
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    26  81
  16P GAIN WILD-TYPE 114 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     26   81
  16P GAIN WILD-TYPE  114  301
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               26                114
  MALE                 81                301
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    35  54
  16P GAIN WILD-TYPE 116 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     35   54
  16P GAIN WILD-TYPE  116  229
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                35                116
  YES               54                229
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  16P GAIN MUTATED                                     105
  16P GAIN WILD-TYPE                                   406
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  16P GAIN MUTATED                                                             0
  16P GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  16P GAIN MUTATED                                                     2
  16P GAIN WILD-TYPE                                                   8
D28V9, multiclass
                                                             clus
vv                                                            16P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    105
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            16P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      406
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, continuous
D28V11, continuous
D28V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  0     1
  16P GAIN WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                          16    87
  16P GAIN WILD-TYPE                        32   359
D28V13, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                      16                 32
  WHITE                                          87                359
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     7  88
  16P GAIN WILD-TYPE  19 371
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      7   88
  16P GAIN WILD-TYPE   19  371
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                 19
  NOT HISPANIC OR LATINO               88                371
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    52  54
  16Q GAIN WILD-TYPE 251 164
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               106                415 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                54                164 
$`16Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF 
        9.30        15.52        14.83         3.55         4.01        29.42 
TCGA-BA-A4IG TCGA-BA-A6DA TCGA-BA-A6DI TCGA-BA-A6DL TCGA-C9-A47Z TCGA-CN-4728 
       28.11        11.54        11.05        20.48         6.28        56.68 
TCGA-CN-4730 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6022 
       26.86        20.55        45.83        23.90         6.74         9.24 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A49A TCGA-CQ-5329 TCGA-CQ-5330 
       32.22        38.89        17.42        17.29        70.45        62.37 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CR-5247 
       32.38        46.95        13.25        16.73        77.56        11.77 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7379 
       16.90         6.02        39.16        24.95         0.99        34.06 
TCGA-CR-7380 TCGA-CR-7388 TCGA-CR-7390 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5977 
       19.92        27.06        29.82        17.16        17.95        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6939 
        7.07        43.23        54.74        90.12        20.52        21.90 
TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 
       11.24        12.03        65.82       111.16        18.81         7.99 
TCGA-CV-7102 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 
        1.84        21.80        71.21        10.75        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7415 
       26.20        17.13        18.41        57.47        17.85        22.85 
TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45U 
       25.08       100.57        19.76       153.86       180.16        35.47 
TCGA-CV-A465 TCGA-CV-A6JM TCGA-CV-A6JY TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-8568 
        7.07         6.38        21.24        25.41        23.05        24.95 
TCGA-D6-8569 TCGA-D6-A6EP TCGA-DQ-5631 TCGA-DQ-7588 TCGA-F7-A50J TCGA-F7-A623 
       25.32        13.94        18.02        14.04        31.13        20.25 
TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-8314 TCGA-HD-8634 TCGA-IQ-7631 TCGA-IQ-A61K 
       28.47        21.93        22.03        12.66        38.53         5.29 
TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A7BN TCGA-P3-A5Q6 
       13.68        15.48        14.37         7.96        15.42        15.78 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A8Z7 
       18.97         2.04        29.00        12.72        21.07         6.51 
TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       74.47        24.30        55.43        29.46 

$`16Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19        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-6872 TCGA-BA-7269 TCGA-BA-A4IH 
       65.59        68.48        21.17        12.62        41.85        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-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
        2.27        13.38        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       50.20        44.98        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-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
       12.69        48.76        55.86        38.04         4.67        51.29 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
       12.89        32.81        52.14        57.11        12.99        14.33 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        73.61        13.05        42.02        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       12.39        71.31         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.57        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       30.67        48.00        47.44        28.04        19.07        34.13 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6995 
        9.07        52.08        11.08        10.45        35.05         3.68 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B 
       32.48        11.74        35.01        25.41        23.57        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       54.58        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       32.88        56.58         4.24        14.99        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
       64.87        53.52        43.04        41.88        43.10        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       11.61        23.24        29.36        33.60        29.49        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       12.46        31.23        84.23        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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
       22.78        15.75         9.27        47.18        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 
       35.84         3.45         3.09        29.23        31.96         9.17 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 
       26.17        17.13        32.78        47.01        12.89        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58         7.10         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 
        5.95        35.41        29.95        48.39       139.43       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
      108.95        76.24        19.20       107.51        87.55        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
       48.59        21.07        62.43         9.60         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 
        5.46         4.73        26.43       140.78        19.79        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 
       15.09        30.08         6.08        53.95        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-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7183 
       12.66         9.01         5.26        52.31        12.92       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 
       77.16         4.73        47.47        18.97        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7410 
       11.87        47.97         2.10        36.13        35.54       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
       89.33         9.67         0.46        25.94         0.07        34.09 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
       14.89        56.48       156.49        54.94         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
       84.49         7.17        16.64         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
       21.01       169.38       159.65         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-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
       15.25         5.98        35.34        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
        3.62        23.47        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 
       10.55        18.84        34.36        51.12        13.25         9.60 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
        2.53        16.14        11.44        18.67        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES 
       28.77         7.63        22.59        24.95        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7589 
       11.11        58.45        37.25        30.94        33.86        46.32 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       46.45        20.45        37.58        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 
       18.94        24.95         0.46        17.85        11.80        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8635 
        0.07        25.74        27.48        27.48        14.66        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-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       15.95        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
       33.57        13.84        19.04        13.35        18.15        19.27 
TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI 
       10.75        30.05         1.84        12.62         6.25         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       16.08        17.98        29.92        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-P3-A6T7 
       36.82        47.01        19.00        75.55        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
        9.34        18.64        19.73         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       17.82        15.32         8.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
       15.91         7.10        32.45        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.25        20.35        64.80        54.67         2.83        49.51 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JJ TCGA-UF-A7JK 
       48.03        49.45        44.65        17.95        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.99               0.07 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            180.16             210.97 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             20.81              20.94 
[1] "1.0 - 180.2 (20.8)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1.3"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  16Q GAIN MUTATED         7       18        16        47         4         0
  16Q GAIN WILD-TYPE      20       58        66       206         8         1
D29V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  7                 20
  STAGE II                18                 58
  STAGE III               16                 66
  STAGE IVA               47                206
  STAGE IVB                4                  8
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16Q GAIN MUTATED      12  28  19  34
  16Q GAIN WILD-TYPE    38 109  81 139
D29V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1               12                 38
  T2                  28                109
  T3                  19                 81
  T4                  34                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"
                    vv
clus                  N0  N1  N2  N3
  16Q GAIN MUTATED    38  13  31   2
  16Q GAIN WILD-TYPE 141  55 137   6
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               38                141
  N1               13                 55
  N2               31                137
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    34   0
  16Q GAIN WILD-TYPE 155   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     34    0
  16Q GAIN WILD-TYPE  155    1
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               34                155
  1                0                  1
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    31  76
  16Q GAIN WILD-TYPE 109 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     31   76
  16Q GAIN WILD-TYPE  109  306
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               31                109
  MALE                 76                306
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    33  53
  16Q GAIN WILD-TYPE 118 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     33   53
  16Q GAIN WILD-TYPE  118  230
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                33                118
  YES               53                230
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  16Q GAIN MUTATED                                     105
  16Q GAIN WILD-TYPE                                   406
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  16Q GAIN MUTATED                                                             0
  16Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  16Q GAIN MUTATED                                                     2
  16Q GAIN WILD-TYPE                                                   8
D29V9, multiclass
                                                             clus
vv                                                            16Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    105
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            16Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      406
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, continuous
D29V11, continuous
D29V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  0     1
  16Q GAIN WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                          15    88
  16Q GAIN WILD-TYPE                        33   358
D29V13, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                      15                 33
  WHITE                                          88                358
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V14, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     7  89
  16Q GAIN WILD-TYPE  19 370
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      7   89
  16Q GAIN WILD-TYPE   19  370
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                 19
  NOT HISPANIC OR LATINO               89                370
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    38  29
  17P GAIN WILD-TYPE 265 189
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                67                454 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                29                189 
$`17P GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DI TCGA-BB-4225 
        9.30        12.62        41.85        29.42        11.05         4.60 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-5356 TCGA-CN-5366 
       20.52        10.55         6.28        56.68        46.32        11.84 
TCGA-CN-5370 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-A63U TCGA-CQ-5329 
        8.52        52.08        32.22        38.89        31.69        70.45 
TCGA-CQ-6229 TCGA-CQ-7072 TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6478 
       38.76        77.56        29.49        11.77        58.42         6.02 
TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7383 TCGA-CR-7404 TCGA-CV-5430 
       12.46        39.16         3.45        17.13        48.39       139.43 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6933 
      129.21       108.95       107.51        60.49        54.74        90.12 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6962 
       26.43        11.24        12.03        15.09        30.08         4.14 
TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7414 
       18.81         5.26        17.13        47.97        36.13         0.46 
TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A6JZ TCGA-D6-A6EP TCGA-F7-8298 TCGA-F7-A50I 
      180.16        45.96        23.47        13.94        32.71         3.02 
TCGA-HD-7917 TCGA-HD-A6HZ TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-MZ-A7D7 
       27.48         3.65        13.68        13.84        19.04        17.98 
TCGA-P3-A6T3 TCGA-QK-A6IG TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-UF-A719 TCGA-UF-A71E 
       18.97         7.30        21.07         6.51        54.67        49.45 
TCGA-UF-A7JH 
       29.46 

$`17P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6873 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01        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-A6DJ 
        7.10         5.69        14.47         7.82         2.27        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 
       20.48        16.41         6.15       105.90         9.14         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
       18.38        22.42        36.72        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A5HZ 
       66.28        24.66        38.40        71.05        25.71        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
       12.92         8.81        12.69        48.76        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        4.67        51.29        12.89        26.86        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       57.11        12.99        20.55        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       73.61        13.05        42.02         8.58        12.39        71.31 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 
        8.32        16.21        11.54        11.57        12.49        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       56.94        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       28.04        19.07        34.13         6.74         9.07         9.24 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       11.08        10.45        35.05         3.68        17.42        32.48 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
       21.21         7.40        22.32        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        23.44        19.82        24.39        20.88 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       19.53        48.20        52.37        21.50         2.93        54.58 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.38        32.88        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       14.99        70.13        64.87        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        44.48        11.61        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
       33.60        14.14        12.46        31.23        84.23        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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 
        7.69        22.78        15.75         9.27        47.18        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       40.93        35.84         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 
       31.96         9.17        34.06        19.92        26.17        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        29.82        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58         7.10         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       35.41        29.95        17.16        76.24        19.20        17.95 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       87.55        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 
       23.05        86.83        48.59         7.07        43.23        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
       62.43         9.60         2.14         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6952 
        4.73        21.90       140.78        19.79        42.38         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 
        2.50        64.83       126.15       111.16        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        9.01         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-7250 TCGA-CV-7252 TCGA-CV-7253 
       31.36        26.20        18.97        95.34         4.96        11.87 
TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
        2.10        18.41        57.47        35.54        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
       89.33         9.67        22.85        25.08        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       34.09       100.57        14.89        56.48       156.49        54.94 
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-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       16.64         6.38        22.19        27.98        21.01       169.38 
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-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
        3.62        21.24        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.55        18.84        34.36        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       22.59        24.95        12.10        12.79        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       37.25        30.94        33.86        18.02        14.04        46.32 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       46.45        20.45        37.58        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S 
       41.59        37.18        21.63        20.25        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       24.95         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
        0.07        28.47        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       22.03        12.66        22.85         0.36        13.84         4.27 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A6SH 
       11.84        37.41         0.07        33.57         5.29        15.48 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        19.27        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       30.05         1.84        12.62         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       16.08        29.92        15.78        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T5 
       36.82        47.01        19.00        75.55         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z8 
       21.47         9.34        12.72        18.64        19.73         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       16.96         6.87        15.91         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A 
        3.12        13.55        13.25        20.35        64.80         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        48.03        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       55.43        18.05        13.94        20.75        22.36        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        17.03        20.55        14.56 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.46               0.07 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            180.16             210.97 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            23.470             20.815 
[1] "0.5 - 180.2 (23.5)" "0.1 - 211.0 (20.8)"
[1] "hr=" "1.1"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  17P GAIN MUTATED         2       13        17        27         0         0
  17P GAIN WILD-TYPE      25       63        65       226        12         1
D30V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  2                 25
  STAGE II                13                 63
  STAGE III               17                 65
  STAGE IVA               27                226
  STAGE IVB                0                 12
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17P GAIN MUTATED       2  22  18  17
  17P GAIN WILD-TYPE    48 115  82 156
D30V4, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1                2                 48
  T2                  22                115
  T3                  18                 82
  T4                  17                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
  17P GAIN MUTATED    25  11  19   0
  17P GAIN WILD-TYPE 154  57 149   8
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               25                154
  N1               11                 57
  N2               19                149
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    26   0
  17P GAIN WILD-TYPE 163   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     26    0
  17P GAIN WILD-TYPE  163    1
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               26                163
  1                0                  1
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    14  53
  17P GAIN WILD-TYPE 126 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     14   53
  17P GAIN WILD-TYPE  126  329
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               14                126
  MALE                 53                329
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    20  37
  17P GAIN WILD-TYPE 131 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     20   37
  17P GAIN WILD-TYPE  131  246
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                20                131
  YES               37                246
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  17P GAIN MUTATED                                      64
  17P GAIN WILD-TYPE                                   447
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  17P GAIN MUTATED                                                             1
  17P GAIN WILD-TYPE                                                           0
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  17P GAIN MUTATED                                                     2
  17P GAIN WILD-TYPE                                                   8
D30V9, multiclass
                                                             clus
vv                                                            17P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     64
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            17P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      447
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, continuous
D30V11, continuous
D30V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  0     1
  17P GAIN WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                           8    55
  17P GAIN WILD-TYPE                        40   391
D30V13, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       8                 40
  WHITE                                          55                391
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     7  55
  17P GAIN WILD-TYPE  19 404
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      7   55
  17P GAIN WILD-TYPE   19  404
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                 19
  NOT HISPANIC OR LATINO               55                404
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    46  41
  17Q GAIN WILD-TYPE 257 177
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                87                434 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                41                177 
$`17Q GAIN MUTATED`
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DI TCGA-BB-4225 TCGA-BB-8601 
       12.62        41.85        29.42        11.05         4.60        20.52 
TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-4737 TCGA-CN-5356 TCGA-CN-5359 
       10.55         6.28        56.68        20.55        46.32        12.39 
TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 
       11.84         8.52         9.24        52.08        10.45        32.22 
TCGA-CN-6994 TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-6225 TCGA-CQ-7069 
       38.89        31.69        12.39        12.07        13.25        41.88 
TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6473 
       77.56        23.24        29.49        11.77        58.42        36.99 
TCGA-CR-6478 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7399 
        6.02        39.16         3.45        17.13        29.82         5.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5440 TCGA-CV-5970 TCGA-CV-5977 
       48.39       139.43       129.21       107.51        13.35        60.49 
TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 
       54.74        90.12        26.43        11.24        12.03        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6962 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 
       30.08         6.08         4.14        18.81         5.26         1.84 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7415 TCGA-CV-7421 
       17.13        95.34        47.97        36.13        22.85         0.07 
TCGA-CV-7424 TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A465 TCGA-CV-A6JZ TCGA-CX-A4AQ 
       14.89       180.16        45.96         7.07        23.47        51.12 
TCGA-D6-8569 TCGA-D6-A6EP TCGA-DQ-7588 TCGA-H7-8502 TCGA-HD-7753 TCGA-HD-7917 
       25.32        13.94        14.04        15.06        28.47        27.48 
TCGA-HD-A6HZ TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-MT-A67D TCGA-P3-A6T7 
        3.65        13.68        13.84        19.04         1.84        16.01 
TCGA-QK-A6IG TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-AA3K 
        7.30        21.07        19.73         6.51         5.62         8.32 
TCGA-RS-A6TO TCGA-UF-A71E TCGA-UF-A7JH 
       12.72        49.45        29.46 

$`17Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       20.48        65.59        68.48        15.52        21.17        14.83 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
        3.55         4.01        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-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.41        18.38        22.42        36.72        33.70        50.20 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A5HU 
       44.98        66.28        24.66        38.40        71.05        25.71 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
       27.19        12.92         8.81        12.69        48.76        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        51.29        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       52.14        57.11        12.99        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
       73.61        13.05        42.02         8.58        71.31         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-5374 
       16.21        11.54        11.57        12.49        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6992 
       19.07        34.13         6.74         9.07        11.08        35.05 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        3.68        17.42        32.48        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V 
       23.57        17.29        29.72        21.21         7.40        22.32 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
       16.57         4.41         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
        4.24        41.19        32.38        32.88        46.95        56.58 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        4.24        14.99        38.76        70.13        64.87        53.52 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB 
       16.73        43.04        43.10        44.48        11.61        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
       33.60        14.14        12.46        31.23        84.23        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6474 
       37.87        26.27        50.01        39.52        34.52        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       16.90        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 
       12.46        22.78        15.75         9.27        47.18        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       40.93        35.84         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 
       31.96         9.17        34.06        19.92        26.17        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       47.01        27.06        12.89        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 
       44.25        30.58         7.10         5.13        35.41        29.95 
TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 
       17.16       108.95        76.24        19.20        17.95        87.55 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 
       76.50        91.53        80.12        17.92        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
       48.59         7.07        43.23        21.07        62.43         9.60 
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-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
      140.78        19.79        42.38        53.95        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-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7103 TCGA-CV-7104 
      111.16        12.66         7.99         9.01        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-7252 
       47.47        36.00        31.36        26.20        18.97         4.96 
TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 
       11.87         2.10        18.41        57.47        35.54        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 
      210.97        89.33         9.67         0.46        25.08        25.94 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 
       34.09       100.57        56.48       156.49        54.94         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-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T 
        6.38        22.19        27.98        21.01       169.38       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-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
       67.86         0.76        56.61        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-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-A4Z9 TCGA-D6-A4ZB 
       16.14        11.44        18.67        24.95        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES 
       28.77         7.63        22.59        24.95        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
       11.11        58.45        37.25        30.94        33.86        18.02 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       46.32        46.45        20.45        37.58        40.24        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       39.12        41.59        37.18        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 
       11.80        20.25        12.43        13.38        15.16        13.61 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       21.11        20.94         0.07        25.74        21.93        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         6.90        34.75        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       15.48        13.35        18.15        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
        7.96        30.05        12.62         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
       16.08        17.98        29.92        15.78        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       10.85        36.82        47.01        19.00        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        2.04        29.00        12.99        13.15        21.07        21.21 
TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z9 
       23.15        21.47         9.34        12.72        18.64        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       12.20        17.82        15.32        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ 
        7.10        32.45        13.71         3.12        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D 
       20.35        64.80        54.67         2.83        49.51        48.03 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ 
       44.65        74.47        17.95        24.30        55.43        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-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 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.07               0.07 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            180.16             210.97 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             18.81              21.14 
[1] "0.1 - 180.2 (18.8)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.2"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  17Q GAIN MUTATED         2       12        19        43         0         1
  17Q GAIN WILD-TYPE      25       64        63       210        12         0
D31V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  2                 25
  STAGE II                12                 64
  STAGE III               19                 63
  STAGE IVA               43                210
  STAGE IVB                0                 12
  STAGE IVC                1                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17Q GAIN MUTATED       2  24  24  27
  17Q GAIN WILD-TYPE    48 113  76 146
D31V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1                2                 48
  T2                  24                113
  T3                  24                 76
  T4                  27                146
[1] 4 2
[1] 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
  17Q GAIN MUTATED    27  15  31   0
  17Q GAIN WILD-TYPE 152  53 137   8
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               27                152
  N1               15                 53
  N2               31                137
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    35   1
  17Q GAIN WILD-TYPE 154   0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     35    1
  17Q GAIN WILD-TYPE  154    0
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               35                154
  1                1                  0
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    20  67
  17Q GAIN WILD-TYPE 120 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     20   67
  17Q GAIN WILD-TYPE  120  315
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               20                120
  MALE                 67                315
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    23  49
  17Q GAIN WILD-TYPE 128 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     23   49
  17Q GAIN WILD-TYPE  128  234
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                23                128
  YES               49                234
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  17Q GAIN MUTATED                                      84
  17Q GAIN WILD-TYPE                                   427
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  17Q GAIN MUTATED                                                             1
  17Q GAIN WILD-TYPE                                                           0
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  17Q GAIN MUTATED                                                     2
  17Q GAIN WILD-TYPE                                                   8
D31V9, multiclass
                                                             clus
vv                                                            17Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     84
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            17Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      427
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, continuous
D31V11, continuous
D31V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0     2
  17Q GAIN WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                          10    72
  17Q GAIN WILD-TYPE                        38   374
D31V13, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                      10                 38
  WHITE                                          72                374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V14, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     9  74
  17Q GAIN WILD-TYPE  17 385
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      9   74
  17Q GAIN WILD-TYPE   17  385
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    9                 17
  NOT HISPANIC OR LATINO               74                385
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    68  55
  18P GAIN WILD-TYPE 235 163
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               123                398 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                55                163 
$`18P GAIN MUTATED`
TCGA-BA-4076 TCGA-BA-5151 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 
       13.64        23.74        17.10        65.59        68.48        21.17 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IG TCGA-BA-A6DL TCGA-BB-4223 
        3.55        12.62         4.01        28.11        20.48       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-A5HU 
        9.14         4.60        22.42        36.72        66.28        25.71 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-4730 
       10.55        27.19         8.81         6.28        56.68        26.86 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-6012 TCGA-CN-6020 
       12.99        20.55         8.32        11.84        48.00         6.74 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-A497 TCGA-CN-A63T TCGA-CN-A63U 
        9.24        11.08        10.45        35.01         7.40        31.69 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6UY TCGA-CQ-5332 TCGA-CQ-6227 TCGA-CQ-7067 
       12.39        12.07        23.44        10.42         4.24        16.73 
TCGA-CQ-A4C9 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6482 TCGA-CR-6493 TCGA-CR-7364 
       23.24        11.77        58.42        11.34         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7390 TCGA-CR-7399 TCGA-CR-7401 
       39.16         3.45        24.95        29.82         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 
       29.95        48.39       129.21       108.95       107.51        87.55 
TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6935 
       86.83        60.49        43.23        21.07         9.60         9.70 
TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6962 TCGA-CV-7101 
       11.24        12.03        15.09        30.08         4.14         5.26 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7253 TCGA-CV-7255 
        1.84        10.75        31.36        18.97        11.87         2.10 
TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7434 TCGA-CV-7435 
       57.47        17.85        22.85         0.07         7.17       153.86 
TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45W TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A6JM 
       16.64        22.19        45.96        48.20        67.86         6.38 
TCGA-CX-A4AQ TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EO TCGA-D6-A6EP TCGA-DQ-5631 
       51.12        24.95        25.32        24.95        13.94        18.02 
TCGA-DQ-7590 TCGA-DQ-7595 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7831 
       46.45        39.12        15.06        21.11        20.94        21.93 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61K TCGA-IQ-A6SH TCGA-KU-A66T 
        4.27         3.65        11.84         5.29        15.48        18.15 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6T3 TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA 
       17.98        15.78        18.97         6.51         5.62        12.20 
TCGA-QK-A8ZB TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-UF-A719 TCGA-UF-A71A 
       17.82        12.72        15.91        32.45        54.67         2.83 
TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JD 
       49.45        74.47        24.30 

$`18P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19         9.30        37.28         9.07        26.50 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-6868 TCGA-BA-6870 
       42.35        57.93        23.84        20.48        15.52        14.83 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
       41.85        29.42        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-A8YP TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 
       13.38        16.41         6.15         4.41        18.38        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       50.20        44.98        24.66        38.40        71.05        20.52 
TCGA-BB-A6UM TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
       12.92        12.69        48.76        55.86        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 
       51.29        12.89        32.81        52.14        57.11        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       45.83        27.58        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 
        8.58        12.39        71.31        16.21        11.54        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
       12.49         8.52        52.08        56.94        50.07        30.67 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 
       23.90        47.44        28.04        19.07        34.13         9.07 
TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       52.08        32.22        35.05        38.89         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       32.48        11.74        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6V1 
       21.21        22.32        16.57         4.41         2.70        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       24.39        20.88        19.53        48.20        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
        2.93        54.58        70.45        62.37        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
        4.24        41.19        32.38        32.88        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25        14.99        38.76        70.13        64.87        53.52 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       43.04        41.88        43.10        77.56        44.48        11.61 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 
       84.23        54.67        37.87        26.27        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-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       10.22        11.64         7.69        12.46        22.78        15.75 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 
       47.34        40.93        35.84         3.09        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-7391 TCGA-CR-7392 
       32.78        47.01        27.06        12.89        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CV-5430 
       32.65        44.25        30.58         7.10         5.13       139.43 
TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5443 
       17.16        76.24        19.20        17.95        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 
       80.12        17.92        13.35        23.05        48.59         7.07 
TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 
       54.74        62.43        90.12         2.14         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 
        4.73        21.90        26.43       140.78        19.79        42.38 
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-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
       28.34         2.50        64.83       126.15       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
       12.66         7.99         9.01        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       71.21       130.88        77.16         4.73        47.47        36.00 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7261 
       26.20        17.13        95.34         4.96        47.97        36.13 
TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       18.41        35.54       210.97        89.33         9.67         0.46 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
       25.08        25.94        34.09       100.57        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
      156.49        54.94         3.52        16.27        84.49        19.76 
TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
        6.38        27.98        21.01       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A463 
       35.47         1.05         6.51        88.87        60.43         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
       56.61         7.07        15.25         5.98        35.34        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
       22.52        10.42        10.42        10.55        18.84        34.36 
TCGA-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-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       11.44        18.67        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       22.59        12.10        12.79        11.11        58.45        37.25 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 
       30.94        33.86        14.04        46.32        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       40.24        40.04        41.59        37.18        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       17.85        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 
       13.61         0.07        28.47        25.74        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        38.53        14.50        37.71 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
       37.41         0.07        33.57        13.68        13.84        19.04 
TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       13.35        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
        1.84        12.62         6.25        15.42         7.13        16.08 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       29.92        71.74        51.25        10.85        36.82        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       19.00        75.55         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z9 
        9.34        12.72        18.64        21.07        19.73        14.76 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T3-A92M 
       15.32         8.32        16.96         6.87         7.10        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71B 
        3.12        13.55        13.25        20.35        64.80        49.51 
TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       48.03        44.65        17.95        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       13.94        20.75        22.36        32.65         2.96        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.07               0.07 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            153.86             210.97 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            18.150             21.225 
[1] "0.1 - 153.9 (18.1)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.2"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  18P GAIN MUTATED         3       12        19        64         2         1
  18P GAIN WILD-TYPE      24       64        63       189        10         0
D32V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  3                 24
  STAGE II                12                 64
  STAGE III               19                 63
  STAGE IVA               64                189
  STAGE IVB                2                 10
  STAGE IVC                1                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  18P GAIN MUTATED       9  25  32  40
  18P GAIN WILD-TYPE    41 112  68 133
D32V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1                9                 41
  T2                  25                112
  T3                  32                 68
  T4                  40                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
  18P GAIN MUTATED    32  16  50   2
  18P GAIN WILD-TYPE 147  52 118   6
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               32                147
  N1               16                 52
  N2               50                118
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    37   1
  18P GAIN WILD-TYPE 152   0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     37    1
  18P GAIN WILD-TYPE  152    0
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               37                152
  1                1                  0
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    17 106
  18P GAIN WILD-TYPE 123 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     17  106
  18P GAIN WILD-TYPE  123  276
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               17                123
  MALE                106                276
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    32  67
  18P GAIN WILD-TYPE 119 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     32   67
  18P GAIN WILD-TYPE  119  216
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                32                119
  YES               67                216
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  18P GAIN MUTATED                                     121
  18P GAIN WILD-TYPE                                   390
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  18P GAIN MUTATED                                                             0
  18P GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  18P GAIN MUTATED                                                     2
  18P GAIN WILD-TYPE                                                   8
D32V9, multiclass
                                                             clus
vv                                                            18P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    121
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            18P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      390
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, continuous
D32V11, continuous
D32V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     1
  18P GAIN WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                          14   103
  18P GAIN WILD-TYPE                        34   343
D32V13, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                      14                 34
  WHITE                                         103                343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V14, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     4 111
  18P GAIN WILD-TYPE  22 348
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4  111
  18P GAIN WILD-TYPE   22  348
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 22
  NOT HISPANIC OR LATINO              111                348
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    30  23
  18Q GAIN WILD-TYPE 273 195
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                53                468 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                23                195 
$`18Q GAIN MUTATED`
TCGA-BA-5151 TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6871 TCGA-BB-4223 TCGA-BB-4225 
       23.74        17.10        68.48         3.55       105.90         4.60 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7870 TCGA-CN-4730 TCGA-CN-4736 TCGA-CN-6012 
       18.38        22.42        66.28        26.86        12.99        48.00 
TCGA-CN-6020 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-A497 TCGA-CN-A6UY TCGA-CR-6467 
        6.74        11.08        10.45        35.01        23.44        58.42 
TCGA-CR-6482 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7401 TCGA-CR-7404 
       11.34        47.34         3.45        24.95        35.41        48.39 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6950 TCGA-CV-6951 
      129.21       108.95        21.07         9.60        15.09        30.08 
TCGA-CV-6962 TCGA-CV-7103 TCGA-CV-7406 TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-A45W 
        4.14        52.31        57.47        22.85         0.07        45.96 
TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A6JM TCGA-CX-A4AQ TCGA-D6-A6EO TCGA-DQ-7590 
       48.20        67.86         6.38        51.12        24.95        46.45 
TCGA-H7-A76A TCGA-HD-A634 TCGA-P3-A5Q6 TCGA-QK-A6IG TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       20.94         4.27        15.78         7.30         6.51         5.62 
TCGA-T2-A6X2 TCGA-TN-A7HL TCGA-UF-A719 TCGA-UF-A71E TCGA-UF-A7JA 
       32.45        20.35        54.67        49.45        74.47 

$`18Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       26.50        42.35        57.93        23.84        20.48        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       15.52        21.17        14.83        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-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-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 
       13.38        20.48        16.41         6.15         9.14         4.41 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 
       36.72        33.70        50.20        44.98        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-4722 TCGA-CN-4723 TCGA-CN-4725 
        8.81         6.28        12.69        48.76        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 
        4.67        51.29        56.68        12.89        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       57.11        20.55        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        42.02        46.32         8.58        12.39        71.31 
TCGA-CN-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-6013 
        8.52        52.08        56.94        50.07        30.67        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 
       47.44        28.04        19.07        34.13         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       52.08        32.22        35.05        38.89         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       32.48        11.74        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
        4.41        12.07         2.70        19.82        24.39        20.88 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       19.53        48.20        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       70.45        62.37        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       41.19        32.38        32.88        46.95        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        4.24        14.99        38.76        70.13        64.87        53.52 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       16.73        43.04        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       11.61        23.24        29.36        33.60        29.49        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       12.46        31.23        84.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
       26.27        50.01        39.52        34.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 
       16.90         6.02        11.90        10.22        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       12.46        22.78        15.75         9.27        47.18        39.16 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
       40.93        35.84         3.09        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        29.82        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58         7.10         5.13         5.95 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       29.95       139.43        17.16        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        87.55        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       43.23        54.74        62.43        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6952 TCGA-CV-6953 
      140.78        19.79        12.03        42.38         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       65.82        10.98         7.13         8.42        28.34         2.50 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       126.15       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        9.01         5.26         1.84        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-7416 
       17.85       210.97        89.33         9.67         0.46        25.08 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
       25.94        34.09       100.57        14.89        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
       54.94         3.52        16.27        84.49        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
      153.86        16.64         6.38        22.19        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X 
      169.38       180.16       159.65        35.47         1.05         6.51 
TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       88.87        60.43         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        5.98        35.34        29.79         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-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-A6EN 
       25.32        17.72        12.36        28.77         7.63        22.59 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        11.11        58.45        37.25 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 
       30.94        33.86        18.02        14.04        46.32        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       37.58        40.24        40.04        39.12        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       24.95         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 
       13.38        15.16        15.06        13.61        21.11         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       28.47        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ 
       22.03        12.66        22.85         0.36        13.84         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        37.41         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
       13.84        19.04        15.48        13.35        18.15        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        6.25        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
       13.15        21.07        21.21        23.15        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       12.72        18.64        21.07        19.73        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       17.82        15.32         8.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ 
       15.91         7.10        13.71         3.12        13.55        13.25 
TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JC 
       64.80         2.83        49.51        48.03        44.65        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36        32.65         2.96        17.03        20.55        14.56 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.07               0.07 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            129.21             210.97 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             23.74              20.52 
[1] "0.1 - 129.2 (23.7)" "0.1 - 211.0 (20.5)"
[1] "hr=" "1"  
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  18Q GAIN MUTATED         2        5         9        25         0         1
  18Q GAIN WILD-TYPE      25       71        73       228        12         0
D33V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  2                 25
  STAGE II                 5                 71
  STAGE III                9                 73
  STAGE IVA               25                228
  STAGE IVB                0                 12
  STAGE IVC                1                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  18Q GAIN MUTATED       6  10  11  16
  18Q GAIN WILD-TYPE    44 127  89 157
D33V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1                6                 44
  T2                  10                127
  T3                  11                 89
  T4                  16                157
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18Q GAIN MUTATED    15   9  17   0
  18Q GAIN WILD-TYPE 164  59 151   8
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               15                164
  N1                9                 59
  N2               17                151
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    16   1
  18Q GAIN WILD-TYPE 173   0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     16    1
  18Q GAIN WILD-TYPE  173    0
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               16                173
  1                1                  0
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     4  49
  18Q GAIN WILD-TYPE 136 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4   49
  18Q GAIN WILD-TYPE  136  333
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                4                136
  MALE                 49                333
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    16  28
  18Q GAIN WILD-TYPE 135 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     16   28
  18Q GAIN WILD-TYPE  135  255
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                16                135
  YES               28                255
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  18Q GAIN MUTATED                                      51
  18Q GAIN WILD-TYPE                                   460
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  18Q GAIN MUTATED                                                             0
  18Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  18Q GAIN MUTATED                                                     2
  18Q GAIN WILD-TYPE                                                   8
D33V9, multiclass
                                                             clus
vv                                                            18Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     51
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            18Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      460
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, continuous
D33V11, continuous
D33V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     0
  18Q GAIN WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           6    45
  18Q GAIN WILD-TYPE                        42   401
D33V13, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       6                 42
  WHITE                                          45                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"
D33V14, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2  47
  18Q GAIN WILD-TYPE  24 412
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   47
  18Q GAIN WILD-TYPE   24  412
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 24
  NOT HISPANIC OR LATINO               47                412
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    37  19
  19P GAIN WILD-TYPE 266 199
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                56                465 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                19                199 
$`19P GAIN MUTATED`
TCGA-BA-5559 TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7871 
       68.48        16.41       105.90         4.60        22.42        24.66 
TCGA-BB-8601 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-A63T 
       20.52         9.07        52.08        11.08        32.22         7.40 
TCGA-CN-A63V TCGA-CN-A641 TCGA-CN-A6V6 TCGA-CQ-5323 TCGA-CR-6467 TCGA-CR-6487 
       22.32        12.07        20.88        48.20        58.42         7.69 
TCGA-CR-6488 TCGA-CR-7370 TCGA-CR-7389 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5440 
       12.46         3.45        12.89        48.39        17.16       107.51 
TCGA-CV-5442 TCGA-CV-5977 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7247 
       76.50        60.49         5.26        77.16        26.20        18.97 
TCGA-CV-7261 TCGA-CV-7415 TCGA-CV-A45Z TCGA-CV-A6JM TCGA-CV-A6K2 TCGA-CX-7219 
       36.13        22.85        48.20         6.38        10.42        34.36 
TCGA-F7-8298 TCGA-F7-A50J TCGA-F7-A623 TCGA-H7-A76A TCGA-HD-A6HZ TCGA-IQ-A61K 
       32.71        31.13        20.25        20.94         3.65         5.29 
TCGA-MT-A67G TCGA-MZ-A5BI TCGA-P3-A5Q6 TCGA-P3-A6T4 TCGA-QK-A6V9 TCGA-QK-A6VB 
        6.25         7.13        15.78         2.04        18.64        21.07 
TCGA-QK-A8Z7 TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A71A 
        6.51         8.32        15.91        13.55        20.35         2.83 
TCGA-UF-A71E TCGA-UF-A7JO 
       49.45        20.75 

$`19P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       20.48        65.59        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        27.95        11.54         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        9.14         4.41        18.38        36.72        33.70        50.20 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A5HY 
       44.98        66.28        38.40        71.05        25.71        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
       27.19        12.92         8.81         6.28        12.69        48.76 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       55.86        38.04         4.67        51.29        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       26.86        32.81        52.14        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 
       46.32         8.58        12.39        71.31         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       56.94        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6988 
       28.04        19.07        34.13         6.74         9.24        10.45 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       35.05        38.89         3.68        17.42        32.48        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY 
       31.69        12.39        16.57         4.41         2.70        23.44 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       19.82        24.39        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
        4.24        41.19        32.38        32.88        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       13.25         4.24        14.99        38.76        70.13        64.87 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       53.52        16.73        43.04        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       14.14        12.46        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-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-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       11.64        22.78        15.75         9.27        47.18        39.16 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       47.34        40.93        35.84         3.09        24.95        29.23 
TCGA-CR-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-7390 TCGA-CR-7391 
       17.13        32.78        47.01        27.06        29.82        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58         7.10         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
        5.95        35.41        29.95       139.43       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 
       76.24        19.20        17.95        87.55        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 
       17.92        13.35        23.05        86.83        48.59         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       140.78        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       15.09        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
        7.13         8.42        28.34         2.50         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      126.15       111.16        18.81        12.66         7.99         9.01 
TCGA-CV-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-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 
      130.88         4.73        47.47        36.00        31.36        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 
       95.34         4.96        11.87        47.97         2.10        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-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
        0.46        25.08        25.94         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
       14.89        56.48       156.49        54.94         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-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
       22.19        27.98        21.01       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 
       35.47         1.05        45.96         6.51        88.87        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-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
       35.34        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
       23.47        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       16.14        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       12.36        28.77         7.63        22.59        24.95        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
       12.10        12.79        11.11        58.45        37.25        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
       33.86        18.02        14.04        46.32        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       37.58        40.24        40.04        39.12        41.59        37.18 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       21.63        20.25         3.02        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       17.85        11.80        12.43        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       13.61        21.11         0.07        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       27.48        27.48        14.66        22.03        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-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 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S 
       33.57        13.68        13.84        19.04        15.48        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        1.84        12.62        15.42        16.08        17.98        29.92 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       75.55        18.97        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       12.72        19.73         5.62        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
       15.32        12.72        16.96         6.87         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B 
       13.71         3.12        13.25        64.80        54.67        49.51 
TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       48.03        44.65        74.47        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       29.46        18.05        13.94        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              2.04               0.07 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            107.51             210.97 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             20.30              21.17 
[1] "2.0 - 107.5 (20.3)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.1"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  19P GAIN MUTATED         3        5         6        31         1         0
  19P GAIN WILD-TYPE      24       71        76       222        11         1
D34V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  3                 24
  STAGE II                 5                 71
  STAGE III                6                 76
  STAGE IVA               31                222
  STAGE IVB                1                 11
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19P GAIN MUTATED       7   9  12  19
  19P GAIN WILD-TYPE    43 128  88 154
D34V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1                7                 43
  T2                   9                128
  T3                  12                 88
  T4                  19                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
  19P GAIN MUTATED    15   5  25   1
  19P GAIN WILD-TYPE 164  63 143   7
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               15                164
  N1                5                 63
  N2               25                143
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    20   0
  19P GAIN WILD-TYPE 169   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     20    0
  19P GAIN WILD-TYPE  169    1
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               20                169
  1                0                  1
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    10  46
  19P GAIN WILD-TYPE 130 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     10   46
  19P GAIN WILD-TYPE  130  336
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               10                130
  MALE                 46                336
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    12  35
  19P GAIN WILD-TYPE 139 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     12   35
  19P GAIN WILD-TYPE  139  248
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                12                139
  YES               35                248
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  19P GAIN MUTATED                                      54
  19P GAIN WILD-TYPE                                   457
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  19P GAIN MUTATED                                                             0
  19P GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  19P GAIN MUTATED                                                     2
  19P GAIN WILD-TYPE                                                   8
D34V9, multiclass
                                                             clus
vv                                                            19P GAIN 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                        2
                                                             clus
vv                                                            19P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      457
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, continuous
D34V11, continuous
D34V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     0
  19P GAIN WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           6    50
  19P GAIN WILD-TYPE                        42   396
D34V13, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       6                 42
  WHITE                                          50                396
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V14, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     3  50
  19P GAIN WILD-TYPE  23 409
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3   50
  19P GAIN WILD-TYPE   23  409
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               50                409
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    51  27
  19Q GAIN WILD-TYPE 252 191
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                78                443 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                27                191 
$`19Q GAIN MUTATED`
TCGA-4P-AA8J TCGA-BA-5153 TCGA-BA-5559 TCGA-BA-7269 TCGA-BA-A6DL TCGA-BA-A8YP 
        3.35        57.93        68.48        41.85        20.48        16.41 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-7861 TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6021 
      105.90         4.60        22.42        48.00         6.74         9.07 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A641 TCGA-CN-A6UY 
       52.08        11.08         7.40        22.32        12.07        23.44 
TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CR-6467 
       20.88        52.37        62.37        46.95        13.25        58.42 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7389 TCGA-CR-7404 
        7.69        12.46        47.34         3.45        12.89        48.39 
TCGA-CV-5431 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5977 TCGA-CV-6937 TCGA-CV-7101 
       17.16       107.51        76.50        60.49        20.52         5.26 
TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7253 TCGA-CV-7406 TCGA-CV-7407 
       77.16        31.36        18.97        11.87        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45Z TCGA-CV-A6JM 
       17.85        22.85       153.86        16.64        48.20         6.38 
TCGA-CV-A6K2 TCGA-CX-7219 TCGA-D6-6825 TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-A50I 
       10.42        34.36        16.14        37.58        32.71         3.02 
TCGA-F7-A50J TCGA-F7-A623 TCGA-H7-A76A TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7631 
       31.13        20.25        20.94         3.65        34.75        38.53 
TCGA-IQ-A61G TCGA-IQ-A61K TCGA-KU-A66T TCGA-MT-A67G TCGA-MZ-A5BI TCGA-P3-A5Q5 
       11.84         5.29        18.15         6.25         7.13        29.92 
TCGA-P3-A6T4 TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-AA3K TCGA-T2-A6WZ 
        2.04        18.64        21.07         6.51         8.32        15.91 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7JJ TCGA-UF-A7JO 
       13.55        13.25         2.83        49.45        18.05        20.75 

$`19Q GAIN WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       23.74        42.35        17.10        23.84        20.48        65.59 
TCGA-BA-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-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-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 
       13.38         6.15         9.14         4.41        18.38        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       33.70        50.20        44.98        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-4722 TCGA-CN-4723 TCGA-CN-4725 
        8.81         6.28        12.69        48.76        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
        4.67        51.29        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       52.14        57.11        12.99        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        73.61        13.05        42.02        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       12.39        71.31         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.57        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       30.67        23.90        47.44        28.04        19.07        34.13 
TCGA-CN-6022 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
        9.24        10.45        32.22        35.05        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        32.48        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y 
       17.29        29.72        21.21        31.69        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 
        4.41         2.70        19.82        24.39        19.53        48.20 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 
       21.50         2.93        54.58        70.45        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6224 
       11.21         4.24        41.19        32.38        32.88        56.58 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        4.24        14.99        38.76        70.13        64.87        53.52 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       16.73        43.04        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       11.61        23.24        29.36        33.60        29.49        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       12.46        31.23        84.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
       26.27        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-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 
       22.78        15.75         9.27        47.18        39.16        40.93 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
       35.84         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-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-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       47.01        27.06        29.82        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58         7.10         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
       29.95       139.43       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       17.95        87.55        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       23.05        86.83        48.59         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-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
        5.46         4.73        21.90        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        2.50         4.14        64.83       126.15       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
       12.66         7.99         9.01         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 
       21.80        71.21        10.75       130.88         4.73        47.47 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7254 
       36.00        26.20        17.13        95.34         4.96        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
        2.10        36.13        18.41       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
        0.46        25.08        25.94         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
       14.89        56.48       156.49        54.94         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
       84.49        19.76         7.17         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       21.01       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
       45.96         6.51        88.87        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
       56.61         7.07        15.25         5.98        35.34        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 
       25.41         9.60        23.05         2.53        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       58.45        37.25        30.94        33.86        18.02        14.04 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       46.32        46.45        20.45        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61S TCGA-F7-A61V 
       41.59        37.18        21.63        20.25        18.94        24.95 
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-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.06        13.61        21.11         0.07        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
       21.93        27.48        27.48        14.66        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7630 
       22.85         0.36        13.84         4.27         6.90        15.95 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61L 
       14.50        37.71        37.41         0.07        33.57        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.84        19.04        15.48        13.35        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN 
       14.37         7.96        30.05         1.84        12.62        15.42 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       16.08        17.98        15.78        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 
       36.82        47.01        19.00        75.55        18.97        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VC TCGA-QK-A8Z8 
        7.30        21.47         9.34        12.72        19.73         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP 
       14.76        12.20        17.82        15.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HL 
        6.87         7.10        32.45        13.71         3.12        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA 
       64.80        54.67        49.51        48.03        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JS 
       17.95        24.30        55.43        29.46        13.94        22.36 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       32.65         2.96        17.03        20.55        14.56 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              2.04               0.07 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            153.86             210.97 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            20.365             21.170 
[1] "2.0 - 153.9 (20.4)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.2"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  19Q GAIN MUTATED         3       11        10        38         2         0
  19Q GAIN WILD-TYPE      24       65        72       215        10         1
D35V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  3                 24
  STAGE II                11                 65
  STAGE III               10                 72
  STAGE IVA               38                215
  STAGE IVB                2                 10
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19Q GAIN MUTATED       8  21  15  23
  19Q GAIN WILD-TYPE    42 116  85 150
D35V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1                8                 42
  T2                  21                116
  T3                  15                 85
  T4                  23                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
  19Q GAIN MUTATED    24   8  29   2
  19Q GAIN WILD-TYPE 155  60 139   6
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               24                155
  N1                8                 60
  N2               29                139
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    24   0
  19Q GAIN WILD-TYPE 165   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     24    0
  19Q GAIN WILD-TYPE  165    1
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               24                165
  1                0                  1
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    14  64
  19Q GAIN WILD-TYPE 126 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     14   64
  19Q GAIN WILD-TYPE  126  318
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               14                126
  MALE                 64                318
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    21  43
  19Q GAIN WILD-TYPE 130 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     21   43
  19Q GAIN WILD-TYPE  130  240
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                21                130
  YES               43                240
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  19Q GAIN MUTATED                                      75
  19Q GAIN WILD-TYPE                                   436
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  19Q GAIN MUTATED                                                             0
  19Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  19Q GAIN MUTATED                                                     3
  19Q GAIN WILD-TYPE                                                   7
D35V9, multiclass
                                                             clus
vv                                                            19Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     75
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        3
                                                             clus
vv                                                            19Q GAIN 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                          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"
D35V10, continuous
D35V11, continuous
D35V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  1     0
  19Q GAIN WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           9    66
  19Q GAIN WILD-TYPE                        39   380
D35V13, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       9                 39
  WHITE                                          66                380
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V14, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     3  69
  19Q GAIN WILD-TYPE  23 390
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3   69
  19Q GAIN WILD-TYPE   23  390
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               69                390
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   112  78
  20P GAIN WILD-TYPE 191 140
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               190                331 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                78                140 
$`20P GAIN MUTATED`
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6868 
        9.07        26.50        23.74        23.84        68.48        15.52 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BB-4224 
       12.62        41.85         7.10         2.27        11.05         9.14 
TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7872 TCGA-BB-A5HU TCGA-BB-A5HY 
        4.60        22.42        36.72        38.40        25.71        10.55 
TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
        6.28        56.68        26.86        32.81        52.14        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        45.83        27.58        73.61        13.05 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5374 
       46.32        12.39        71.31         8.32        11.84        56.94 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       48.00        23.90         6.74         9.24        52.08        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-A63T TCGA-CN-A63U TCGA-CQ-5329 TCGA-CQ-5330 
       10.45        32.22         7.40        31.69        70.45        62.37 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7064 
       32.38        46.95        56.58        13.25        38.76        64.87 
TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CE 
       16.73        41.88        44.48        11.61        23.24        29.49 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6484 TCGA-CR-6488 
       31.23        84.23        11.77        58.42        11.64        12.46 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7377 
       39.16        47.34         3.45        24.95        29.23         9.17 
TCGA-CR-7380 TCGA-CR-7389 TCGA-CR-7392 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5430 
       19.92        12.89        46.85         5.95        35.41       139.43 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5970 
      108.95        76.24        19.20        76.50        80.12        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6933 
       23.05        86.83        60.49         7.07        54.74        90.12 
TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6954 
       20.52        21.90        26.43        12.03        42.38        65.82 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7177 
        7.13         8.42         4.14       126.15        18.81        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
       71.21        10.75        36.00        31.36        26.20        17.13 
TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7429 
        2.10        18.41        25.08         0.07       100.57         3.52 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45X 
       16.64         6.38       180.16       159.65        35.47         6.51 
TCGA-CV-A45Z TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JU 
       48.20        56.61         7.07        35.34        29.79         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6516 
       21.24        23.47        19.92        10.42        18.84        25.41 
TCGA-D6-6517 TCGA-D6-6825 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-D6-A6EQ 
        9.60        16.14        25.32        12.36        13.94        12.10 
TCGA-DQ-5624 TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-A50J TCGA-F7-A61S 
       58.45        14.04        20.45        37.58        31.13        18.94 
TCGA-H7-8501 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6HZ 
       15.16        28.47        21.93        22.03         4.27         3.65 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L 
       14.50        37.71        11.84         0.07         5.29        13.68 
TCGA-IQ-A6SH TCGA-KU-A66T TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN 
       15.48        18.15        30.05         1.84         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T3 
        7.13        17.98        15.78        71.74        19.00        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-QK-A6VB 
        2.04        29.00        21.21         7.30        12.72        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-T2-A6WZ TCGA-T3-A92M TCGA-TN-A7HI 
       19.73         6.51        14.76        15.91        13.71        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       13.25        20.35         2.83        49.45        44.65        74.47 
TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JV 
       55.43        18.05        13.94         2.96 

$`20P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5152 
        3.35        15.19         9.30        13.64        37.28        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 
       57.93        17.10        20.48        65.59        21.17        14.83 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        3.55         4.01        29.42        28.11        20.45        30.18 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DJ 
       27.95        11.54         5.69        14.47         7.82        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4227 TCGA-BB-4228 
       20.48        16.41         6.15       105.90         4.41        18.38 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 
       33.70        50.20        44.98        66.28        24.66        71.05 
TCGA-BB-8601 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 
       20.52        27.19        12.92         8.81        12.69        48.76 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4735 
       55.86        38.04         4.67        51.29        12.89        57.11 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5369 
       42.02         8.58        16.21        11.54        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6017 
        8.52        52.08        50.07        30.67        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       19.07        34.13         9.07        35.05        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        32.48        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       17.29        29.72        21.21        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       54.58        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 
       32.88         4.24        14.99        70.13        53.52        43.04 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH 
       43.10        77.56        29.36        33.60        14.14        12.46 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
       54.67        37.87        26.27        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-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
       11.34         7.69        22.78        15.75         9.27        47.18 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7379 
       40.93        35.84         3.09         0.99        31.96        34.06 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 
       26.17        17.13        32.78        47.01        27.06        29.82 
TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       30.02        32.65        44.25        30.58         7.10         5.13 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5440 
       29.95        48.39        17.16       129.21        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6433 
       87.55        91.53        17.92        48.59        43.23        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 
       62.43         9.60         2.14         9.70         5.46         4.73 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       11.24       140.78        19.79        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7091 
       53.95        10.98        28.34         2.50        64.83       111.16 
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-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7247 
       12.92       130.88        77.16         4.73        47.47        18.97 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
       95.34         4.96        11.87        47.97        36.13        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-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
       22.85        25.94        34.09        14.89        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
       54.94        16.27        84.49        19.76         7.17       153.86 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45V TCGA-CV-A45W 
       22.19        27.98        21.01       169.38         1.05        45.96 
TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A468 TCGA-CV-A6JD 
       88.87        60.43        67.86         0.76        15.25         5.98 
TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
        6.38         6.48        28.01        22.52        10.42        10.55 
TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6826 
       34.36        51.12        13.25        23.05         2.53        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN 
       18.67        24.95        17.72        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
       24.95        12.79        11.11        37.25        30.94        33.86 
TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       18.02        46.32        46.45        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       24.95         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       13.38        15.06        13.61        21.11        20.94         0.07 
TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 
       25.74        27.48        27.48        14.66        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
        0.36        13.84         6.90        34.75        15.95        38.53 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A66S TCGA-KU-A6H7 
       37.41        33.57        13.84        19.04        13.35        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       10.75        14.37         7.96        12.62        16.08        29.92 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T6 
       51.25        10.85        36.82        47.01        75.55        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
       16.01        13.15        21.07        23.15        21.47         9.34 
TCGA-QK-A6V9 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
       18.64         5.62        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92N 
       12.72        16.96         6.87         7.10        32.45         3.12 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JC TCGA-UF-A7JD 
       64.80        54.67        49.51        48.03        17.95        24.30 
TCGA-UF-A7JH TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       29.46        20.75        22.36        32.65        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.07               0.07 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            180.16             210.97 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            20.485             21.070 
[1] "0.1 - 180.2 (20.5)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1"  
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  20P GAIN MUTATED        12       23        36        94         5         0
  20P GAIN WILD-TYPE      15       53        46       159         7         1
D36V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                 12                 15
  STAGE II                23                 53
  STAGE III               36                 46
  STAGE IVA               94                159
  STAGE IVB                5                  7
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  20P GAIN MUTATED      21  43  38  69
  20P GAIN WILD-TYPE    29  94  62 104
D36V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1               21                 29
  T2                  43                 94
  T3                  38                 62
  T4                  69                104
[1] 4 2
[1] 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
  20P GAIN MUTATED    59  34  62   3
  20P GAIN WILD-TYPE 120  34 106   5
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               59                120
  N1               34                 34
  N2               62                106
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    76   0
  20P GAIN WILD-TYPE 113   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     76    0
  20P GAIN WILD-TYPE  113    1
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               76                113
  1                0                  1
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    50 140
  20P GAIN WILD-TYPE  90 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     50  140
  20P GAIN WILD-TYPE   90  242
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               50                 90
  MALE                140                242
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    54 105
  20P GAIN WILD-TYPE  97 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     54  105
  20P GAIN WILD-TYPE   97  178
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                54                 97
  YES              105                178
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  20P GAIN MUTATED                                     186
  20P GAIN WILD-TYPE                                   325
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  20P GAIN MUTATED                                                             0
  20P GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  20P GAIN MUTATED                                                     4
  20P GAIN WILD-TYPE                                                   6
D36V9, multiclass
                                                             clus
vv                                                            20P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    186
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        4
                                                             clus
vv                                                            20P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      325
  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"
D36V10, continuous
D36V11, continuous
D36V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  1     4
  20P GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          20   157
  20P GAIN WILD-TYPE                        28   289
D36V13, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           4                  7
  BLACK OR AFRICAN AMERICAN                      20                 28
  WHITE                                         157                289
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V14, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    12 161
  20P GAIN WILD-TYPE  14 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     12  161
  20P GAIN WILD-TYPE   14  298
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                   12                 14
  NOT HISPANIC OR LATINO              161                298
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   116  85
  20Q GAIN WILD-TYPE 187 133
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               201                320 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                85                133 
$`20Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-6868 
        9.30         9.07        26.50        23.74        23.84        15.52 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DI 
       12.62        41.85        29.42         7.10         2.27        11.05 
TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7872 TCGA-BB-A5HU 
        4.60        22.42        36.72        50.20        38.40        25.71 
TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 
       10.55         6.28        38.04        56.68        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       52.14        12.99        20.55        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 
       73.61        13.05        46.32        12.39         8.32        11.84 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6018 TCGA-CN-6022 
       56.94        30.67        48.00        23.90        19.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A49A 
       52.08        11.08        10.45        38.89         3.68        17.29 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A6UY TCGA-CN-A6V3 TCGA-CQ-5329 TCGA-CQ-5330 
        7.40        31.69        23.44        24.39        70.45        62.37 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7064 
       32.38        46.95        56.58        13.25        38.76        64.87 
TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       16.73        41.88        77.56        44.48        11.61        23.24 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6474 TCGA-CR-6477 
       29.49        14.14        11.77        58.42        18.54        16.90 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7372 
       11.64        12.46         9.27        39.16        47.34        24.95 
TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7389 
       29.23         9.17        34.06        19.92        17.13        12.89 
TCGA-CR-7392 TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       46.85        35.41       139.43       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 
       19.20        76.50        80.12        60.49         7.07        54.74 
TCGA-CV-6933 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6945 TCGA-CV-6948 
       90.12         5.46        20.52        26.43        12.03        42.38 
TCGA-CV-6951 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 
       30.08        65.82         7.13         8.42        28.34         4.14 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
      126.15        18.81        12.66        21.80        71.21        10.75 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7255 TCGA-CV-7263 
       36.00        31.36        26.20        17.13         2.10        18.41 
TCGA-CV-7409 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7429 TCGA-CV-7437 
       17.85        25.08         0.07       100.57         3.52        16.64 
TCGA-CV-7438 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A464 
        6.38       180.16        35.47         6.51        48.20        56.61 
TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
        7.07        35.34        29.79         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8569 
       19.92        18.84        25.41        23.05        16.14        25.32 
TCGA-D6-A6EP TCGA-DQ-5624 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 
       13.94        58.45        18.02        14.04        46.32        37.58 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A623 TCGA-H7-8501 TCGA-HD-7753 TCGA-HD-7831 
       31.13        18.94        20.25        15.16        28.47        21.93 
TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
       22.03         4.27         3.65        14.50        37.71        11.84 
TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-KU-A66T TCGA-MT-A51W 
        0.07         5.29        13.68        15.48        18.15        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
        7.96        30.05         1.84         6.25        15.42         7.13 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 
       17.98        15.78        71.74        19.00        18.97         2.04 
TCGA-P3-A6T5 TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
       29.00        21.21         7.30        12.72        18.64        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-T2-A6WZ TCGA-T3-A92M TCGA-TN-A7HI 
       19.73         6.51        14.76        15.91        13.71        13.55 
TCGA-TN-A7HJ TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF 
       13.25        48.03        49.45        44.65        74.47        55.43 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JV 
       18.05        13.94         2.96 

$`20Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5152 TCGA-BA-5153 
        3.35        15.19        13.64        37.28        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 
       17.10        20.48        65.59        68.48        21.17        14.83 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
        3.55         4.01        28.11        20.45        30.18        27.95 
TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DJ TCGA-BA-A6DL 
       11.54         5.69        14.47         7.82        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 
       16.41         6.15       105.90         9.14         4.41        18.38 
TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 
       33.70        44.98        66.28        24.66        71.05        20.52 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
       27.19        12.92         8.81        12.69        48.76        55.86 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-5355 TCGA-CN-5358 
        4.67        51.29        12.89        57.11        42.02         8.58 
TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       71.31        16.21        11.54        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 
       52.08        50.07        47.44        28.04        34.13         6.74 
TCGA-CN-6021 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
        9.07        32.22        35.05        17.42        32.48        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V 
       35.01        25.41        23.57        29.72        21.21        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6V1 
       12.39        16.57         4.41        12.07         2.70        19.82 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       54.58        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 
       32.88         4.24        14.99        70.13        53.52        43.04 
TCGA-CQ-7071 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       43.10        29.36        33.60        12.46        31.23        84.23 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
       54.67        37.87        26.27        50.01        39.52        34.52 
TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
       36.99         6.02        11.90        10.22        11.34         7.69 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       22.78        15.75        47.18        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
        3.09         0.99        31.96        26.17        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       27.06        29.82        30.02        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
        7.10         5.13         5.95        29.95        48.39        17.16 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 
       17.95       107.51        87.55        91.53        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
       23.05        86.83        48.59        43.23        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 
        9.60         2.14         9.70         4.73        21.90        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 
      140.78        19.79        15.09         6.08        53.95        10.98 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        2.50        64.83       111.16         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
        1.84        52.31        12.92       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       47.47        18.97        95.34         4.96        11.87        47.97 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       36.13        57.47        35.54       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7425 
        0.46        22.85        25.94        34.09        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
      156.49        54.94        16.27        84.49        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T 
      153.86        22.19        27.98        21.01       169.38       159.65 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        1.05        45.96        88.87        60.43        67.86         0.76 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6K1 
       15.25         5.98         6.38         6.48        28.01        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 
       10.42        10.42        10.55        34.36        51.12        13.25 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 
        9.60         2.53        11.44        18.67        24.95        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ 
       12.36        28.77         7.63        22.59        24.95        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7590 
       12.79        11.11        37.25        30.94        33.86        46.45 
TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       20.45        40.24        40.04        39.12        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W 
       32.71        21.63        20.25         3.02        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8502 TCGA-H7-A6C4 
       17.85        11.80        12.43        13.38        15.06        13.61 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 
       21.11        20.94         0.07        25.74        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 
       14.66        12.66        22.85         0.36        13.84         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O 
       34.75        15.95        38.53        37.41        33.57        13.84 
TCGA-IQ-A6SG TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67F TCGA-MZ-A6I9 
       19.04        13.35        19.27        10.75        12.62        16.08 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
       29.92        51.25        10.85        36.82        47.01        75.55 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IH 
       12.99        16.01        13.15        21.07        23.15        21.47 
TCGA-QK-A6II TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        9.34         5.62        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92N 
       12.72        16.96         6.87         7.10        32.45         3.12 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7JC 
       20.35        64.80        54.67         2.83        49.51        17.95 
TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       24.30        29.46        20.75        22.36        32.65        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.07               0.07 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            180.16             210.97 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             20.52              21.04 
[1] "0.1 - 180.2 (20.5)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1"  
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  20Q GAIN MUTATED        14       27        35        98         7         0
  20Q GAIN WILD-TYPE      13       49        47       155         5         1
D37V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                 14                 13
  STAGE II                27                 49
  STAGE III               35                 47
  STAGE IVA               98                155
  STAGE IVB                7                  5
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  20Q GAIN MUTATED      24  46  39  73
  20Q GAIN WILD-TYPE    26  91  61 100
D37V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1               24                 26
  T2                  46                 91
  T3                  39                 61
  T4                  73                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20Q GAIN MUTATED    69  30  64   4
  20Q GAIN WILD-TYPE 110  38 104   4
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               69                110
  N1               30                 38
  N2               64                104
  N3                4                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    80   0
  20Q GAIN WILD-TYPE 109   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     80    0
  20Q GAIN WILD-TYPE  109    1
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               80                109
  1                0                  1
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    53 148
  20Q GAIN WILD-TYPE  87 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     53  148
  20Q GAIN WILD-TYPE   87  234
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               53                 87
  MALE                148                234
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    60 108
  20Q GAIN WILD-TYPE  91 175
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     60  108
  20Q GAIN WILD-TYPE   91  175
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                60                 91
  YES              108                175
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  20Q GAIN MUTATED                                     198
  20Q GAIN WILD-TYPE                                   313
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  20Q GAIN MUTATED                                                             0
  20Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  20Q GAIN MUTATED                                                     3
  20Q GAIN WILD-TYPE                                                   7
D37V9, multiclass
                                                             clus
vv                                                            20Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    198
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        3
                                                             clus
vv                                                            20Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      313
  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"
D37V10, continuous
D37V11, continuous
D37V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  1     4
  20Q GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                          23   165
  20Q GAIN WILD-TYPE                        25   281
D37V13, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           4                  7
  BLACK OR AFRICAN AMERICAN                      23                 25
  WHITE                                         165                281
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V14, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    11 173
  20Q GAIN WILD-TYPE  15 286
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     11  173
  20Q GAIN WILD-TYPE   15  286
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   11                 15
  NOT HISPANIC OR LATINO              173                286
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    21  14
  21Q GAIN WILD-TYPE 282 204
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                35                486 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                14                204 
$`21Q GAIN MUTATED`
TCGA-BA-6873 TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4225 TCGA-CN-4727 TCGA-CN-4729 
        4.01        11.05        20.48         4.60        51.29        12.89 
TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-A63U 
       27.58        46.32        11.08        35.05         3.68        31.69 
TCGA-CR-6467 TCGA-CR-6478 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5441 
       58.42         6.02        29.95       139.43       129.21        87.55 
TCGA-CV-6940 TCGA-CV-6945 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7433 TCGA-CV-A461 
       26.43        12.03         0.46        22.85        19.76        67.86 
TCGA-D6-A6EP TCGA-DQ-7591 TCGA-HD-8224 TCGA-HD-8314 TCGA-IQ-A61O TCGA-MT-A7BN 
       13.94        20.45        14.66        22.03        13.84        15.42 
TCGA-MZ-A5BI TCGA-P3-A6SW TCGA-QK-A6VB TCGA-TN-A7HI TCGA-UF-A7JA 
        7.13        36.82        21.07        13.55        74.47 

$`21Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       20.48        65.59        68.48        15.52        21.17        14.83 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
        3.55        12.62        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       30.18        27.95        11.54         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
        7.82         2.27        13.38        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        9.14         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       50.20        44.98        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-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        6.28        12.69        48.76        55.86        38.04         4.67 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       56.68        26.86        32.81        52.14        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       20.55        14.33        45.83        73.61        13.05        42.02 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
        8.58        12.39        71.31         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.84        11.57        12.49         8.52        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        34.13         6.74         9.07         9.24        52.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       10.45        32.22        38.89        17.42        32.48        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
        7.40        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
        2.70        23.44        19.82        24.39        20.88        19.53 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.38        32.88        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
       14.99        38.76        70.13        64.87        53.52        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       43.04        41.88        43.10        77.56        44.48        11.61 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       22.78        15.75         9.27        47.18        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       40.93        35.84         3.45         3.09        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
        0.99        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       17.13        32.78        47.01        27.06        12.89        29.82 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58         7.10 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 
        5.13         5.95        35.41        48.39        17.16       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 
       76.24        19.20        17.95       107.51        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       60.49         7.07        43.23        54.74        21.07        62.43 
TCGA-CV-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-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 
        4.73        21.90        11.24       140.78        19.79        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-7416 
       35.54        17.85       210.97        89.33         9.67        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-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 
      156.49        54.94         3.52        16.27        84.49         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
      153.86        16.64         6.38        22.19        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
      169.38       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 
        6.51        88.87        48.20        60.43         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
        7.07        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
       22.52        10.42        10.42        10.55        18.84        34.36 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       16.14        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ 
       12.36        28.77         7.63        22.59        24.95        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
       12.79        11.11        58.45        37.25        30.94        33.86 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7593 
       18.02        14.04        46.32        46.45        37.58        40.24 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       40.04        39.12        41.59        37.18        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       17.85        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       15.06        13.61        21.11        20.94         0.07        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8634 TCGA-HD-8635 
       25.74        21.93        27.48        27.48        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
        0.36        13.84         4.27         3.65         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-IQ-A6SH 
        0.07        33.57         5.29        13.68        19.04        15.48 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        19.27        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       30.05         1.84        12.62         6.25        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SX 
       29.92        15.78        71.74        51.25        10.85        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       19.00        75.55        18.97         2.04        29.00        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       16.01        13.15        21.07        21.21        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 
       21.47         9.34        12.72        18.64        19.73         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.72        16.96         6.87        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       13.71         3.12        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC 
        2.83        49.51        48.03        49.45        44.65        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36        32.65         2.96        17.03        20.55        14.56 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.46               0.07 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            139.43             210.97 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            20.480             20.975 
[1] "0.5 - 139.4 (20.5)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1.1"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  21Q GAIN MUTATED         0        0         7        19         1         0
  21Q GAIN WILD-TYPE      27       76        75       234        11         1
D38V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  0                 27
  STAGE II                 0                 76
  STAGE III                7                 75
  STAGE IVA               19                234
  STAGE IVB                1                 11
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  21Q GAIN MUTATED       2   5   7  13
  21Q GAIN WILD-TYPE    48 132  93 160
D38V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1                2                 48
  T2                   5                132
  T3                   7                 93
  T4                  13                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
  21Q GAIN MUTATED     8   5  13   1
  21Q GAIN WILD-TYPE 171  63 155   7
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                8                171
  N1                5                 63
  N2               13                155
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    10   0
  21Q GAIN WILD-TYPE 179   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     10    0
  21Q GAIN WILD-TYPE  179    1
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               10                179
  1                0                  1
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     4  31
  21Q GAIN WILD-TYPE 136 351
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4   31
  21Q GAIN WILD-TYPE  136  351
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                4                136
  MALE                 31                351
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    10  20
  21Q GAIN WILD-TYPE 141 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     10   20
  21Q GAIN WILD-TYPE  141  263
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                10                141
  YES               20                263
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  21Q GAIN MUTATED                                      32
  21Q GAIN WILD-TYPE                                   479
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  21Q GAIN MUTATED                                                             1
  21Q GAIN WILD-TYPE                                                           0
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  21Q GAIN MUTATED                                                     2
  21Q GAIN WILD-TYPE                                                   8
D38V9, multiclass
                                                             clus
vv                                                            21Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     32
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            21Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      479
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, continuous
D38V11, continuous
D38V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  0     0
  21Q GAIN WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           1    34
  21Q GAIN WILD-TYPE                        47   412
D38V13, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       1                 47
  WHITE                                          34                412
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V14, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     4  28
  21Q GAIN WILD-TYPE  22 431
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4   28
  21Q GAIN WILD-TYPE   22  431
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 22
  NOT HISPANIC OR LATINO               28                431
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    53  59
  22Q GAIN WILD-TYPE 250 159
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               112                409 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                59                159 
$`22Q GAIN MUTATED`
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-7269 TCGA-BA-A6DA 
       15.19         9.07        17.10        20.48        41.85        11.54 
TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU 
       11.05        20.48        66.28        71.05        20.52        25.71 
TCGA-C9-A480 TCGA-CN-4728 TCGA-CN-4737 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5367 
       12.69        56.68        20.55        13.05        46.32        11.57 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6994 
       50.07        48.00        47.44        11.08        32.22        38.89 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-6220 TCGA-CQ-6221 
       25.41        17.29         2.93        10.42        32.38        32.88 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 
       56.58        13.25        38.76        16.73        41.88        77.56 
TCGA-CR-6471 TCGA-CR-6474 TCGA-CR-6482 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7371 
       39.52        18.54        11.34        39.16         3.45         3.09 
TCGA-CR-7383 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5430 
       17.13        12.89        29.82         7.10        35.41       139.43 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5970 TCGA-CV-5978 TCGA-CV-6933 TCGA-CV-6940 
      129.21       108.95        13.35         7.07        90.12        26.43 
TCGA-CV-6941 TCGA-CV-6950 TCGA-CV-7090 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7178 
       11.24        15.09       126.15         5.26         1.84        71.21 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7407 
       26.20        17.13        95.34        47.97        36.13        35.54 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 
       34.09        14.89         3.52        19.76         7.17        16.64 
TCGA-CV-7440 TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A6JE TCGA-CV-A6JM 
       22.19        45.96        88.87        48.20        35.34         6.38 
TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-DQ-5625 TCGA-DQ-5629 
       34.36        51.12        12.36        13.94        37.25        30.94 
TCGA-DQ-7589 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-8634 TCGA-IQ-A61H 
       46.32        28.47        21.93        27.48        12.66        37.41 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-KU-A66T TCGA-MT-A51X TCGA-MZ-A5BI 
       13.68        13.84        15.48        18.15         7.96         7.13 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 
       17.98        15.78        10.85        47.01        18.97         2.04 
TCGA-P3-A6T5 TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-T2-A6WZ TCGA-UF-A719 TCGA-UF-A71A 
       29.00         6.51        12.20        15.91        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JD 
       49.51        49.45        44.65        24.30 

$`22Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
        3.35         9.30        13.64        37.28        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
       42.35        57.93        23.84        65.59        68.48        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF 
       21.17        14.83         3.55        12.62         4.01        29.42 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD 
       28.11        20.45        30.18        27.95         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 
       14.47         7.82         2.27        13.38        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 
       36.72        33.70        50.20        44.98        24.66        38.40 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4722 
       10.55        27.19        12.92         8.81         6.28        48.76 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 
       55.86        38.04         4.67        51.29        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 
       32.81        52.14        57.11        12.99        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       27.58        73.61        42.02         8.58        12.39        71.31 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 
        8.32        16.21        11.54        11.84        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6018 
       52.08        56.94        30.67        23.90        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 
       34.13         6.74         9.07         9.24        52.08        10.45 
TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 
       35.05         3.68        17.42        32.48        11.74        35.01 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       23.57        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       19.82        24.39        20.88        19.53        48.20        52.37 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
       21.50        54.58        70.45        62.37        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 
        4.24        41.19        46.95         4.24        14.99        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       64.87        53.52        43.04        43.10        44.48        11.61 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 
       58.42        50.01        34.52        36.99        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        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       15.75         9.27        47.18        47.34        40.93        35.84 
TCGA-CR-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-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7391 
       19.92        26.17        32.78        47.01        27.06        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 
       46.85        32.65        44.25        30.58         5.13         5.95 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       29.95        48.39        17.16        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        87.55        76.50        91.53        80.12        17.92 
TCGA-CV-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-6934 TCGA-CV-6935 TCGA-CV-6936 
       21.07        62.43         9.60         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       20.52         4.73        21.90       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       42.38        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
        7.13         8.42        28.34         2.50         4.14        64.83 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7103 
      111.16        18.81        12.66         7.99         9.01        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-7247 TCGA-CV-7252 TCGA-CV-7253 
       47.47        36.00        31.36        18.97         4.96        11.87 
TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
        2.10        18.41        57.47        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-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
      100.57        56.48       156.49        54.94        16.27        84.49 
TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
      153.86         6.38        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A460 TCGA-CV-A461 
      159.65        35.47         1.05         6.51        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN 
        0.76        56.61         7.07        15.25         5.98        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 
       22.52        10.42        10.42        10.55        18.84        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM 
       18.67        24.95        25.32        17.72        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       22.59        24.95        12.10        12.79        11.11        58.45 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       33.86        18.02        14.04        46.45        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       40.24        40.04        39.12        41.59        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       21.63        20.25         3.02        31.13        18.94        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
        0.46        17.85        11.80        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       15.16        15.06        13.61        21.11        20.94         0.07 
TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 
       25.74        27.48        14.66        22.03        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-A61I TCGA-IQ-A61J 
       38.53        14.50        37.71        11.84         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A6SG TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
        5.29        19.04        13.35        19.27        10.75        14.37 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 
       30.05         1.84        12.62         6.25        15.42        16.08 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
       29.92        71.74        51.25        36.82        19.00        75.55 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        21.47         9.34        12.72        18.64        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
       19.73         5.62        14.76        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       12.72        16.96         6.87         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71D 
        3.12        13.55        13.25        20.35        64.80        48.03 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       74.47        17.95        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1.84               0.07 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            139.43             210.97 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             21.24              20.94 
[1] "1.8 - 139.4 (21.2)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1.3"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  22Q GAIN MUTATED         5       15        18        57         2         0
  22Q GAIN WILD-TYPE      22       61        64       196        10         1
D39V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  5                 22
  STAGE II                15                 61
  STAGE III               18                 64
  STAGE IVA               57                196
  STAGE IVB                2                 10
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  22Q GAIN MUTATED       9  27  24  41
  22Q GAIN WILD-TYPE    41 110  76 132
D39V4, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1                9                 41
  T2                  27                110
  T3                  24                 76
  T4                  41                132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  22Q GAIN MUTATED    39  13  40   1
  22Q GAIN WILD-TYPE 140  55 128   7
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               39                140
  N1               13                 55
  N2               40                128
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    35   0
  22Q GAIN WILD-TYPE 154   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     35    0
  22Q GAIN WILD-TYPE  154    1
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               35                154
  1                0                  1
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    24  88
  22Q GAIN WILD-TYPE 116 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     24   88
  22Q GAIN WILD-TYPE  116  294
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               24                116
  MALE                 88                294
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    32  57
  22Q GAIN WILD-TYPE 119 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     32   57
  22Q GAIN WILD-TYPE  119  226
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                32                119
  YES               57                226
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  22Q GAIN MUTATED                                     109
  22Q GAIN WILD-TYPE                                   402
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  22Q GAIN MUTATED                                                             1
  22Q GAIN WILD-TYPE                                                           0
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  22Q GAIN MUTATED                                                     2
  22Q GAIN WILD-TYPE                                                   8
D39V9, multiclass
                                                             clus
vv                                                            22Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    109
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            22Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      402
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, continuous
D39V11, continuous
D39V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  1     2
  22Q GAIN WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                          13    92
  22Q GAIN WILD-TYPE                        35   354
D39V13, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                      13                 35
  WHITE                                          92                354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V14, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     9  96
  22Q GAIN WILD-TYPE  17 363
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      9   96
  22Q GAIN WILD-TYPE   17  363
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    9                 17
  NOT HISPANIC OR LATINO               96                363
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    30  23
  XP GAIN WILD-TYPE 273 195
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               53               468 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               23               195 
$`XP GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-7269 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 
        9.30        37.28        41.85       105.90         4.60         4.41 
TCGA-BB-7864 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-6023 TCGA-CN-A6V6 TCGA-CQ-5327 
       50.20        27.58        13.05        52.08        20.88        54.58 
TCGA-CQ-5329 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-A4CG TCGA-CR-6467 TCGA-CR-6488 
       70.45        64.87        16.73        14.14        58.42        12.46 
TCGA-CR-7370 TCGA-CR-7389 TCGA-CV-5434 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5970 
        3.45        12.89       108.95        76.50        80.12        13.35 
TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6951 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7407 
       86.83        60.49        30.08        95.34        47.97        35.54 
TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7435 TCGA-CV-A45X 
       17.85        22.85        25.08         0.07       153.86         6.51 
TCGA-CV-A6JM TCGA-D6-6823 TCGA-D6-A6EP TCGA-HD-7832 TCGA-HD-A6I0 TCGA-IQ-A61G 
        6.38        23.05        13.94        27.48         6.90        11.84 
TCGA-IQ-A61J TCGA-IQ-A6SH TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6T5 TCGA-P3-A6T6 
       33.57        15.48        15.78        71.74        29.00        12.99 
TCGA-QK-A8ZA TCGA-RS-A6TO TCGA-TN-A7HI TCGA-UF-A71B TCGA-UF-A7JA 
       12.20        12.72        13.55        49.51        74.47 

$`XP GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
        3.35        15.19        13.64         9.07        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       42.35        57.93        17.10        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       68.48        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
        4.01        29.42        28.11        20.45        30.18        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 
       11.05        13.38        20.48        16.41         6.15         9.14 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7870 
       18.38        22.42        36.72        33.70        44.98        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-4722 
       27.19        12.92         8.81         6.28        12.69        48.76 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       55.86        38.04         4.67        51.29        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       26.86        32.81        52.14        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       14.33        45.83        73.61        42.02        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       12.39        71.31         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.57        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        48.00        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 
       34.13         6.74         9.07         9.24        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       32.22        35.05        38.89         3.68        17.42        32.48 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5330 
       19.53        48.20        52.37        21.50         2.93        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       45.99        10.42        11.21         4.24        41.19        32.38 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       32.88        46.95        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
       38.76        70.13        53.52        43.04        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       77.56        44.48        11.61        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       29.49        12.46        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-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-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
       11.64         7.69        22.78        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 
       39.16        47.34        40.93        35.84         3.09        24.95 
TCGA-CR-7373 TCGA-CR-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-7390 
       26.17        17.13        32.78        47.01        27.06        29.82 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58         7.10 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
       17.16       129.21        76.24        19.20        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 
       87.55        91.53        17.92        23.05        48.59         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       140.78        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       15.09         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-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-7410 TCGA-CV-7411 TCGA-CV-7413 
       36.13        18.41        57.47       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
        0.46        25.94        34.09       100.57        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
      156.49        54.94         3.52        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
        7.17        16.64         6.38        22.19        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
      169.38       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-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-A6JN TCGA-CV-A6JO 
        7.07        15.25         5.98        35.34        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ 
       10.42        10.42        10.55        18.84        34.36        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       13.25        25.41         9.60         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        22.59        24.95        12.10        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       58.45        37.25        30.94        33.86        18.02        14.04 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       46.32        46.45        20.45        37.58        40.24        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       39.12        41.59        37.18        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.61        21.11        20.94         0.07        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       21.93        27.48        14.66        22.03        12.66        22.85 
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-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61K 
       38.53        14.50        37.71        37.41         0.07         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
       13.68        13.84        19.04        13.35        18.15        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        6.25        15.42         7.13        16.08        17.98        29.92 
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-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       18.97         2.04        16.01        13.15        21.07        21.21 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       23.15         7.30        21.47         9.34        12.72        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB 
       21.07        19.73         6.51         5.62        14.76        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       15.32         8.32        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       32.45        13.71         3.12        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC 
       54.67         2.83        48.03        49.45        44.65        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36        32.65         2.96        17.03        20.55        14.56 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.07              0.07 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           153.86            210.97 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            25.08             20.55 
[1] "0.1 - 153.9 (25.1)" "0.1 - 211.0 (20.6)"
[1] "hr=" "1.2"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  XP GAIN MUTATED         2        5         8        32         1         0
  XP GAIN WILD-TYPE      25       71        74       221        11         1
D40V3, multiclass
           clus
vv          XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 2                25
  STAGE II                5                71
  STAGE III               8                74
  STAGE IVA              32               221
  STAGE IVB               1                11
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  XP GAIN MUTATED       2  15   9  23
  XP GAIN WILD-TYPE    48 122  91 150
D40V4, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  T0+T1               2                48
  T2                 15               122
  T3                  9                91
  T4                 23               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
  XP GAIN MUTATED    14   8  21   1
  XP GAIN WILD-TYPE 165  60 147   7
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              14               165
  N1               8                60
  N2              21               147
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    17   0
  XP GAIN WILD-TYPE 172   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     17    0
  XP GAIN WILD-TYPE  172    1
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              17               172
  1               0                 1
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    18  35
  XP GAIN WILD-TYPE 122 347
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     18   35
  XP GAIN WILD-TYPE  122  347
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              18               122
  MALE                35               347
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    14  31
  XP GAIN WILD-TYPE 137 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     14   31
  XP GAIN WILD-TYPE  137  252
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               14               137
  YES              31               252
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  XP GAIN MUTATED                                      53
  XP GAIN WILD-TYPE                                   458
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  XP GAIN MUTATED                                                             0
  XP GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  XP GAIN MUTATED                                                     0
  XP GAIN WILD-TYPE                                                  10
D40V9, multiclass
                                                             clus
vv                                                            XP GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    53
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            XP GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     458
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V10, continuous
D40V11, continuous
D40V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP GAIN MUTATED                                  0     1
  XP GAIN WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED                           7    44
  XP GAIN WILD-TYPE                        41   402
D40V13, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      7                41
  WHITE                                         44               402
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V14, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     2  47
  XP GAIN WILD-TYPE  24 412
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      2   47
  XP GAIN WILD-TYPE   24  412
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                24
  NOT HISPANIC OR LATINO              47               412
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    47  48
  XQ GAIN WILD-TYPE 256 170
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               95               426 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               48               170 
$`XQ GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-6872 TCGA-BA-7269 TCGA-BB-4223 
        9.30        37.28        26.50        12.62        41.85       105.90 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-A5HU TCGA-BB-A6UO TCGA-CN-4728 TCGA-CN-4737 
        4.60         4.41        25.71         8.81        56.68        20.55 
TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5359 TCGA-CN-5367 TCGA-CN-6012 TCGA-CN-6023 
       27.58        13.05        12.39        11.57        48.00        52.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-A49B TCGA-CN-A6V6 TCGA-CQ-5327 TCGA-CQ-5329 
       10.45        32.22        29.72        20.88        54.58        70.45 
TCGA-CQ-6220 TCGA-CQ-6229 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4CG TCGA-CR-5247 
       32.38        38.76        77.56        11.61        14.14        11.77 
TCGA-CR-6467 TCGA-CR-6477 TCGA-CR-6493 TCGA-CR-7370 TCGA-CR-7380 TCGA-CV-5434 
       58.42        16.90         9.27         3.45        19.92       108.95 
TCGA-CV-5435 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-6933 
       76.24        76.50        80.12        13.35        60.49        90.12 
TCGA-CV-6936 TCGA-CV-6951 TCGA-CV-6959 TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7235 
        5.46        30.08         8.42         1.84        71.21        77.16 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7407 
       31.36        26.20        95.34        47.97         2.10        35.54 
TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7432 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45Q 
       17.85        22.85        84.49        16.64         6.38       169.38 
TCGA-CV-A45X TCGA-CV-A465 TCGA-CV-A6JM TCGA-CV-A6JY TCGA-CX-7086 TCGA-D6-6516 
        6.51         7.07         6.38        21.24        18.84        25.41 
TCGA-D6-6823 TCGA-D6-8568 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7592 
       23.05        24.95        37.25        30.94        18.02        37.58 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-A6I0 TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A6SG 
       27.48        27.48         6.90        11.84        33.57        19.04 
TCGA-IQ-A6SH TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A7BN TCGA-P3-A5Q6 TCGA-P3-A6T5 
       15.48        18.15         7.96        15.42        15.78        29.00 
TCGA-P3-A6T6 TCGA-QK-A8ZA TCGA-RS-A6TO TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
       12.99        12.20        12.72        13.71         3.12        13.55 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JH TCGA-WA-A7H4 
       54.67        49.51        49.45        29.46        14.56 

$`XQ GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
        3.35        15.19        13.64         9.07        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       57.93        17.10        23.84        20.48        65.59        68.48 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF 
       15.52        21.17        14.83         3.55         4.01        29.42 
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-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7861 
       20.48        16.41         6.15         9.14        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
       36.72        33.70        50.20        44.98        66.28        24.66 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       38.40        71.05        20.52        10.55        27.19        12.92 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        6.28        12.69        48.76        55.86        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       51.29        12.89        26.86        32.81        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 
       12.99        14.33        45.83        73.61        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
        8.58        71.31         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        52.08        56.94        50.07        30.67 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       23.90        47.44        28.04        19.07        34.13         6.74 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
        9.07         9.24        11.08        35.05        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        32.48        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       17.29        21.21         7.40        31.69        22.32        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       24.39        19.53        48.20        52.37        21.50         2.93 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       32.88        46.95        56.58        13.25         4.24        14.99 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
       70.13        64.87        53.52        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       43.10        44.48        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       12.46        31.23        84.23        54.67        37.87        26.27 
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-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       22.78        15.75        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
       35.84         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
        9.17        34.06        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        29.82        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58         7.10         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5436 
       29.95        48.39       139.43        17.16       129.21        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5971 
       17.95       107.51        87.55        91.53        17.92        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       86.83        48.59         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6938 
       62.43         9.60         2.14         9.70        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       21.90        26.43        11.24       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-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-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        7.13        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-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 
       52.31        12.92        21.80        10.75       130.88         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 
       47.47        36.00        18.97        17.13         4.96        11.87 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       36.13        18.41        57.47       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
        0.46        25.08        25.94         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
       14.89        56.48       156.49        54.94         3.52        16.27 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
       19.76         7.17       153.86        22.19        27.98        21.01 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Y 
      180.16       159.65        35.47         1.05        45.96        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 
       48.20        60.43        67.86         0.76        56.61        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        5.98        35.34        29.79         6.48        28.01         3.62 
TCGA-CV-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-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
       34.36        51.12        13.25         9.60         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       11.44        18.67        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        7.63        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       11.11        58.45        33.86        14.04        46.32        46.45 
TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       20.45        40.24        40.04        39.12        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       24.95         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-8224 TCGA-HD-8314 
        0.07        28.47        25.74        21.93        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-A61H 
       34.75        15.95        38.53        14.50        37.71        37.41 
TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 
        0.07         5.29        13.68        13.84        13.35        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       10.75        14.37        30.05         1.84        12.62         6.25 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
        7.13        16.08        17.98        29.92        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       10.85        36.82        47.01        19.00        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
        2.04        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        21.47         9.34        12.72        18.64        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J 
       19.73         6.51         5.62        14.76        17.82        15.32 
TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
        8.32        16.96         6.87        15.91         7.10        32.45 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A7J9 
       13.25        20.35        64.80         2.83        48.03        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK 
       74.47        17.95        24.30        55.43        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             1.84              0.07 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           169.38            210.97 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            22.85             20.65 
[1] "1.8 - 169.4 (22.9)" "0.1 - 211.0 (20.6)"
[1] "hr=" "1.2"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  XQ GAIN MUTATED         2       13        14        52         2         0
  XQ GAIN WILD-TYPE      25       63        68       201        10         1
D41V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 2                25
  STAGE II               13                63
  STAGE III              14                68
  STAGE IVA              52               201
  STAGE IVB               2                10
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  XQ GAIN MUTATED       3  25  19  36
  XQ GAIN WILD-TYPE    47 112  81 137
D41V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1               3                47
  T2                 25               112
  T3                 19                81
  T4                 36               137
[1] 4 2
[1] 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
  XQ GAIN MUTATED    30  10  37   1
  XQ GAIN WILD-TYPE 149  58 131   7
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              30               149
  N1              10                58
  N2              37               131
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    27   0
  XQ GAIN WILD-TYPE 162   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     27    0
  XQ GAIN WILD-TYPE  162    1
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              27               162
  1               0                 1
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    22  73
  XQ GAIN WILD-TYPE 118 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     22   73
  XQ GAIN WILD-TYPE  118  309
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              22               118
  MALE                73               309
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    24  55
  XQ GAIN WILD-TYPE 127 228
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     24   55
  XQ GAIN WILD-TYPE  127  228
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               24               127
  YES              55               228
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  XQ GAIN MUTATED                                      94
  XQ GAIN WILD-TYPE                                   417
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  XQ GAIN MUTATED                                                             0
  XQ GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  XQ GAIN MUTATED                                                     1
  XQ GAIN WILD-TYPE                                                   9
D41V9, multiclass
                                                             clus
vv                                                            XQ GAIN 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                       1
                                                             clus
vv                                                            XQ GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     417
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, continuous
D41V11, continuous
D41V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  1     1
  XQ GAIN WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                          12    79
  XQ GAIN WILD-TYPE                        36   367
D41V13, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                     12                36
  WHITE                                         79               367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V14, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     5  83
  XQ GAIN WILD-TYPE  21 376
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      5   83
  XQ GAIN WILD-TYPE   21  376
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                21
  NOT HISPANIC OR LATINO              83               376
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    28  29
  1P LOSS WILD-TYPE 275 189
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               57               464 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               29               189 
$`1P LOSS MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5152 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A6D8 
        3.35         9.30        42.35         3.55        41.85        27.95 
TCGA-CN-4736 TCGA-CN-5355 TCGA-CN-5360 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6021 
       12.99        42.02        71.31        48.00        19.07         9.07 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-A63T 
       11.08        35.05        38.89         3.68        32.48         7.40 
TCGA-CN-A63W TCGA-CQ-5332 TCGA-CQ-6225 TCGA-CQ-7072 TCGA-CQ-A4CI TCGA-CR-7365 
       12.39        10.42        13.25        77.56        31.23        39.16 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 
        3.45         3.09        24.95       129.21       108.95        17.95 
TCGA-CV-5440 TCGA-CV-6003 TCGA-CV-6935 TCGA-CV-6940 TCGA-CV-6950 TCGA-CV-6962 
      107.51        54.74         9.70        26.43        15.09         4.14 
TCGA-CV-7101 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7424 TCGA-D6-6516 TCGA-D6-A6EM 
        5.26        47.97        36.13        14.89        25.41         7.63 
TCGA-DQ-7589 TCGA-F7-8489 TCGA-F7-A61W TCGA-HD-8634 TCGA-HD-A6HZ TCGA-IQ-A61L 
       46.32        21.63         0.46        12.66         3.65        13.68 
TCGA-MZ-A6I9 TCGA-P3-A6T5 TCGA-P3-A6T8 TCGA-T3-A92N TCGA-UF-A71A TCGA-UF-A7J9 
       16.08        29.00        13.15         3.12         2.83        44.65 
TCGA-UF-A7JD TCGA-UF-A7JO TCGA-WA-A7GZ 
       24.30        20.75        20.55 

$`1P LOSS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
       15.19        13.64        37.28         9.07        26.50        23.74 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       57.93        17.10        23.84        20.48        65.59        68.48 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF 
       15.52        21.17        14.83        12.62         4.01        29.42 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       28.11        20.45        30.18        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.60         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
       18.38        22.42        36.72        33.70        50.20        44.98 
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-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
       48.76        55.86        38.04         4.67        51.29        56.68 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 
       12.89        26.86        32.81        52.14        57.11        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 
       14.33        45.83        27.58        73.61        13.05        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
        8.58        12.39         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.57        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 
       30.67        23.90        47.44        28.04        34.13         6.74 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-6998 
        9.24        52.08        10.45        32.22        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       31.69        22.32        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       23.44        19.82        24.39        20.88        19.53        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 
       45.99        11.21         4.24        41.19        32.38        32.88 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       46.95        56.58         4.24        14.99        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
       64.87        53.52        16.73        43.04        41.88        43.10 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       14.14        12.46        84.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
       26.27        58.42        50.01        39.52        34.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       18.54        16.90         6.02        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7373 TCGA-CR-7374 
       47.18        47.34        40.93        35.84        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        29.82        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58         7.10         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        5.95        35.41        29.95        48.39       139.43        17.16 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       76.24        19.20        87.55        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-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-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 
        2.14         5.46        20.52         4.73        21.90        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 
      140.78        19.79        12.03        42.38        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        2.50        64.83       126.15       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        7.99         9.01         1.84        52.31        12.92        21.80 
TCGA-CV-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-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
        4.96        11.87         2.10        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-7425 
       25.08        25.94         0.07        34.09       100.57        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
      156.49        54.94         3.52        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
        7.17       153.86        16.64         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       21.01       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
       45.96         6.51        88.87        48.20        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        0.76        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
       23.47        19.92        22.52        10.42        10.42        10.55 
TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 
       18.84        34.36        51.12        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-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       17.72        12.36        28.77        22.59        24.95        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
       12.10        12.79        11.11        58.45        37.25        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       33.86        18.02        14.04        46.45        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       40.24        40.04        39.12        41.59        37.18        32.71 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 
       20.25         3.02        31.13        18.94        24.95        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.61        21.11        20.94         0.07        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 
       21.93        27.48        27.48        14.66        22.03        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 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S 
       33.57         5.29        13.84        19.04        15.48        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A7D7 
        1.84        12.62         6.25        15.42         7.13        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        71.74        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 
       47.01        19.00        75.55        18.97         2.04        12.99 
TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       16.01        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        18.64        21.07        19.73         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.72        16.96         6.87        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       13.71        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF 
       49.51        48.03        49.45        74.47        17.95        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       29.46        18.05        13.94        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7H4 
       17.03        14.56 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.46              0.07 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           129.21            210.97 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            19.07             21.07 
[1] "0.5 - 129.2 (19.1)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.4"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  1P LOSS MUTATED         3        6        11        31         0         0
  1P LOSS WILD-TYPE      24       70        71       222        12         1
D42V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 3                24
  STAGE II                6                70
  STAGE III              11                71
  STAGE IVA              31               222
  STAGE IVB               0                12
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1P LOSS MUTATED       4  16  13  20
  1P LOSS WILD-TYPE    46 121  87 153
D42V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1               4                46
  T2                 16               121
  T3                 13                87
  T4                 20               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
  1P LOSS MUTATED    22   7  20   0
  1P LOSS WILD-TYPE 157  61 148   8
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              22               157
  N1               7                61
  N2              20               148
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    19   0
  1P LOSS WILD-TYPE 170   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     19    0
  1P LOSS WILD-TYPE  170    1
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              19               170
  1               0                 1
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    14  44
  1P LOSS WILD-TYPE 126 338
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     14   44
  1P LOSS WILD-TYPE  126  338
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              14               126
  MALE                44               338
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    22  25
  1P LOSS WILD-TYPE 129 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     22   25
  1P LOSS WILD-TYPE  129  258
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               22               129
  YES              25               258
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  1P LOSS MUTATED                                      57
  1P LOSS WILD-TYPE                                   454
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  1P LOSS MUTATED                                                             0
  1P LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  1P LOSS MUTATED                                                     1
  1P LOSS WILD-TYPE                                                   9
D42V9, multiclass
                                                             clus
vv                                                            1P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    57
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            1P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     454
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V10, continuous
D42V11, continuous
D42V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     2
  1P LOSS WILD-TYPE                                2     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           6    48
  1P LOSS WILD-TYPE                        42   398
D42V13, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      6                42
  WHITE                                         48               398
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V14, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     2  49
  1P LOSS WILD-TYPE  24 410
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2   49
  1P LOSS WILD-TYPE   24  410
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                24
  NOT HISPANIC OR LATINO              49               410
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    17  21
  1Q LOSS WILD-TYPE 286 197
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               38               483 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               21               197 
$`1Q LOSS MUTATED`
TCGA-4P-AA8J TCGA-BA-5149 TCGA-BA-5152 TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-CN-4736 
        3.35        26.50        42.35        27.19         6.28        12.99 
TCGA-CN-5355 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A63T 
       42.02        48.00        19.07        38.89         3.68         7.40 
TCGA-CN-A63W TCGA-CQ-6220 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-A4C7 TCGA-CR-7365 
       12.39        32.38        13.25         4.24        11.61        39.16 
TCGA-CR-7372 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-6003 TCGA-CV-6950 
       24.95       129.21        17.95        87.55        54.74        15.09 
TCGA-CV-7416 TCGA-CV-7424 TCGA-DQ-7588 TCGA-F7-8489 TCGA-F7-A61W TCGA-HD-8634 
       25.08        14.89        14.04        21.63         0.46        12.66 
TCGA-HD-A6HZ TCGA-IQ-A61L TCGA-MZ-A6I9 TCGA-P3-A6T8 TCGA-T3-A92N TCGA-UF-A71A 
        3.65        13.68        16.08        13.15         3.12         2.83 
TCGA-UF-A7JC TCGA-WA-A7GZ 
       17.95        20.55 

$`1Q LOSS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 
       15.19         9.30        13.64        37.28         9.07        23.74 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       57.93        17.10        23.84        20.48        65.59        68.48 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
       15.52        21.17        14.83         3.55        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
       41.85        29.42        28.11        20.45        30.18        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       33.70        50.20        44.98        66.28        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-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
       12.69        48.76        55.86        38.04         4.67        51.29 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       56.68        12.89        26.86        32.81        52.14        57.11 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        45.83        27.58        73.61        13.05 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 
       46.32         8.58        12.39        71.31         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       56.94        50.07        30.67        23.90        47.44        28.04 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       34.13         6.74         9.07         9.24        52.08        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       10.45        32.22        35.05        17.42        32.48        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       31.69        22.32        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       23.44        19.82        24.39        20.88        19.53        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
       45.99        10.42        11.21         4.24        41.19        32.88 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       46.95        56.58        14.99        38.76        70.13        64.87 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       53.52        16.73        43.04        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       44.48        23.24        29.36        33.60        29.49        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       12.46        31.23        84.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
       26.27        58.42        50.01        39.52        34.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       18.54        16.90         6.02        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-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-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       29.23         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       26.17        17.13        32.78        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       29.82        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         5.13         5.95        35.41        29.95        48.39 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 
      139.43        17.16       108.95        76.24        19.20       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-6433 
       86.83        48.59        60.49         7.07        43.23        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       19.79        12.03        42.38        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-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-7418 TCGA-CV-7421 TCGA-CV-7422 
        9.67         0.46        22.85        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
      100.57        56.48       156.49        54.94         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-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
       22.19        27.98        21.01       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
       35.47         1.05        45.96         6.51        88.87        48.20 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       60.43        67.86         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 
       10.42        10.55        18.84        34.36        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        7.63        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
       11.11        58.45        37.25        30.94        33.86        18.02 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       46.32        46.45        20.45        37.58        40.24        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I 
       39.12        41.59        37.18        32.71        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       31.13        18.94        24.95        17.85        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
       12.43        13.38        15.16        15.06        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       20.94         0.07        28.47        25.74        21.93        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       27.48        14.66        22.03        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         6.90        34.75        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
       13.84        19.04        15.48        13.35        18.15        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
        6.25        15.42         7.13        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        18.64        21.07        19.73         6.51         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       16.96         6.87        15.91         7.10        32.45        13.71 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B 
       13.55        13.25        20.35        64.80        54.67        49.51 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF 
       48.03        49.45        44.65        74.47        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       29.46        18.05        13.94        20.75        22.36        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
        2.96        17.03        14.56 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.46              0.07 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           129.21            210.97 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           15.585            21.110 
[1] "0.5 - 129.2 (15.6)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.7"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  1Q LOSS MUTATED         2        3         7        23         0         0
  1Q LOSS WILD-TYPE      25       73        75       230        12         1
D43V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 2                25
  STAGE II                3                73
  STAGE III               7                75
  STAGE IVA              23               230
  STAGE IVB               0                12
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1Q LOSS MUTATED       3  10  12  12
  1Q LOSS WILD-TYPE    47 127  88 161
D43V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1               3                47
  T2                 10               127
  T3                 12                88
  T4                 12               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
  1Q LOSS MUTATED    14   5  16   0
  1Q LOSS WILD-TYPE 165  63 152   8
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              14               165
  N1               5                63
  N2              16               152
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    12   0
  1Q LOSS WILD-TYPE 177   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     12    0
  1Q LOSS WILD-TYPE  177    1
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              12               177
  1               0                 1
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     9  30
  1Q LOSS WILD-TYPE 131 352
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      9   30
  1Q LOSS WILD-TYPE  131  352
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               9               131
  MALE                30               352
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    21  12
  1Q LOSS WILD-TYPE 130 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     21   12
  1Q LOSS WILD-TYPE  130  271
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               21               130
  YES              12               271
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  1Q LOSS MUTATED                                      39
  1Q LOSS WILD-TYPE                                   472
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  1Q LOSS MUTATED                                                             0
  1Q LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  1Q LOSS MUTATED                                                     0
  1Q LOSS WILD-TYPE                                                  10
D43V9, multiclass
                                                             clus
vv                                                            1Q LOSS 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                                                            1Q LOSS 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                        10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, continuous
D43V11, continuous
D43V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     3
  1Q LOSS WILD-TYPE                                2     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           3    32
  1Q LOSS WILD-TYPE                        45   414
D43V13, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      3                45
  WHITE                                         32               414
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V14, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1  35
  1Q LOSS WILD-TYPE  25 424
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   35
  1Q LOSS WILD-TYPE   25  424
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO              35               424
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    17  16
  2P LOSS WILD-TYPE 286 202
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               33               488 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               16               202 
$`2P LOSS MUTATED`
TCGA-BA-4076 TCGA-BA-5559 TCGA-BA-6873 TCGA-BB-7861 TCGA-BB-7862 TCGA-C9-A47Z 
       13.64        68.48         4.01        22.42        36.72         6.28 
TCGA-CN-6011 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63W TCGA-CQ-6218 TCGA-CQ-7064 
       30.67        23.57        29.72        12.39        41.19        64.87 
TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-6003 TCGA-CV-6961 TCGA-CV-7252 TCGA-CV-7255 
       17.92        86.83        54.74         2.50         4.96         2.10 
TCGA-CV-7432 TCGA-CV-A45R TCGA-CV-A465 TCGA-CV-A6JY TCGA-D6-6826 TCGA-DQ-7588 
       84.49       180.16         7.07        21.24        11.44        14.04 
TCGA-F7-A50J TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-P3-A5Q6 
       31.13        13.68        18.15        15.42        16.08        15.78 
TCGA-P3-A6T5 TCGA-QK-AA3K TCGA-UF-A7JS 
       29.00         8.32        22.36 

$`2P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19         9.30        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       65.59        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
       41.85        29.42        28.11        20.45        30.18        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 
        9.14         4.60         4.41        18.38        33.70        50.20 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       44.98        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-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
       48.76        55.86        38.04         4.67        51.29        56.68 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       12.89        26.86        32.81        52.14        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        45.83        27.58        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
       42.02        46.32         8.58        12.39        71.31         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 
       52.08        56.94        50.07        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       28.04        19.07        34.13         6.74         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
       52.08        11.08        10.45        32.22        35.05        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        3.68        17.42        32.48        11.74        35.01        25.41 
TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
       17.29        21.21         7.40        31.69        22.32        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
        4.24        32.38        32.88        46.95        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 
        4.24        14.99        38.76        70.13        53.52        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       43.04        41.88        43.10        77.56        44.48        11.61 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
       58.42        50.01        39.52        34.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       16.90         6.02        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        22.78        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       39.16        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        29.82        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58         7.10         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        87.55        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       80.12        13.35        23.05        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       43.23        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        9.70         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       140.78        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
        8.42        28.34         4.14        64.83       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-7261 
       18.97        17.13        95.34        11.87        47.97        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-7428 
       34.09       100.57        14.89        56.48       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 
        3.52        16.27        19.76         7.17       153.86        16.64 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T 
        6.38        22.19        27.98        21.01       169.38       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-A468 TCGA-CV-A6JD 
       60.43        67.86         0.76        56.61        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       35.34         6.38        29.79         6.48        28.01         3.62 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
       23.47        19.92        22.52        10.42        10.42        10.55 
TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       18.84        34.36        51.12        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
       23.05         2.53        16.14        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        11.11        58.45        37.25 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
       30.94        33.86        18.02        46.32        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       37.58        40.24        40.04        39.12        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V 
       32.71        21.63        20.25         3.02        18.94        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
        0.46        17.85        11.80        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       15.16        15.06        13.61        21.11        20.94         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       28.47        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       22.03        12.66        22.85         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        3.65         6.90        34.75        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.84        19.04        15.48        13.35        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         6.25 
TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
        7.13        17.98        29.92        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       36.82        47.01        19.00        75.55        18.97         2.04 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        21.47         9.34        12.72        18.64        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       19.73         6.51         5.62        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       15.32        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       32.45        13.71         3.12        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       64.80        54.67         2.83        49.51        48.03        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       18.05        13.94        20.75        32.65         2.96        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.10              0.07 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           180.16            210.97 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           18.150            20.975 
[1] "2.1 - 180.2 (18.1)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1.1"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  2P LOSS MUTATED         0        4         9        16         0         0
  2P LOSS WILD-TYPE      27       72        73       237        12         1
D44V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 0                27
  STAGE II                4                72
  STAGE III               9                73
  STAGE IVA              16               237
  STAGE IVB               0                12
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2P LOSS MUTATED       1   7   8  12
  2P LOSS WILD-TYPE    49 130  92 161
D44V4, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1               1                49
  T2                  7               130
  T3                  8                92
  T4                 12               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
  2P LOSS MUTATED    12   8   8   0
  2P LOSS WILD-TYPE 167  60 160   8
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              12               167
  N1               8                60
  N2               8               160
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     8   0
  2P LOSS WILD-TYPE 181   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      8    0
  2P LOSS WILD-TYPE  181    1
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               8               181
  1               0                 1
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    15  18
  2P LOSS WILD-TYPE 125 364
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     15   18
  2P LOSS WILD-TYPE  125  364
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              15               125
  MALE                18               364
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    12  20
  2P LOSS WILD-TYPE 139 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     12   20
  2P LOSS WILD-TYPE  139  263
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               12               139
  YES              20               263
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  2P LOSS MUTATED                                      33
  2P LOSS WILD-TYPE                                   478
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  2P LOSS MUTATED                                                             0
  2P LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  2P LOSS MUTATED                                                     0
  2P LOSS WILD-TYPE                                                  10
D44V9, multiclass
                                                             clus
vv                                                            2P LOSS 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                                                            2P LOSS 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                        10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V10, continuous
D44V11, continuous
D44V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     1
  2P LOSS WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           2    30
  2P LOSS WILD-TYPE                        46   416
D44V13, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      2                46
  WHITE                                         30               416
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V14, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     4  27
  2P LOSS WILD-TYPE  22 432
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      4   27
  2P LOSS WILD-TYPE   22  432
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              27               432
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    26  20
  2Q LOSS WILD-TYPE 277 198
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               46               475 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               20               198 
$`2Q LOSS MUTATED`
TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-6873 TCGA-BB-7861 
       13.64        42.35        68.48         3.55         4.01        22.42 
TCGA-BB-7862 TCGA-C9-A47Z TCGA-CN-4736 TCGA-CN-6018 TCGA-CN-6995 TCGA-CN-A499 
       36.72         6.28        12.99        19.07         3.68        23.57 
TCGA-CN-A49B TCGA-CN-A63W TCGA-CQ-5327 TCGA-CQ-7064 TCGA-CR-6472 TCGA-CR-6484 
       29.72        12.39        54.58        64.87        34.52        11.64 
TCGA-CR-7371 TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5973 TCGA-CV-6003 TCGA-CV-6933 
        3.09         5.95        29.95        86.83        54.74        90.12 
TCGA-CV-6961 TCGA-CV-7252 TCGA-CV-7255 TCGA-CV-7432 TCGA-CV-A45R TCGA-CV-A465 
        2.50         4.96         2.10        84.49       180.16         7.07 
TCGA-CV-A6JY TCGA-D6-6826 TCGA-D6-A6EM TCGA-DQ-7593 TCGA-F7-A50J TCGA-F7-A620 
       21.24        11.44         7.63        40.24        31.13        17.85 
TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MZ-A6I9 TCGA-P3-A5Q6 
       13.68        15.48        18.15        19.27        16.08        15.78 
TCGA-QK-A8Z7 TCGA-QK-AA3K TCGA-T3-A92N TCGA-UF-A71E 
        6.51         8.32         3.12        49.45 

$`2Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19         9.30        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       23.74        57.93        17.10        23.84        20.48        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
       15.52        21.17        14.83        12.62        41.85        29.42 
TCGA-BA-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-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       20.48        16.41         6.15       105.90         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
        4.41        18.38        33.70        50.20        44.98        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-A480 TCGA-CN-4722 TCGA-CN-4723 
       27.19        12.92         8.81        12.69        48.76        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       38.04         4.67        51.29        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       32.81        52.14        57.11        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        73.61        13.05        42.02        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       12.39        71.31         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.57        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
       30.67        48.00        23.90        47.44        28.04        34.13 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       32.22        35.05        38.89        17.42        32.48        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       35.01        25.41        17.29        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       22.32        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       19.82        24.39        20.88        19.53        48.20        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
       21.50         2.93        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 
       11.21         4.24        41.19        32.38        32.88        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       56.58        13.25         4.24        14.99        38.76        70.13 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       53.52        16.73        43.04        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       14.14        12.46        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       37.87        26.27        58.42        50.01        39.52        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-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        22.78        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 
       39.16        47.34        40.93        35.84         3.45        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       29.23         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       26.17        17.13        32.78        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       29.82        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        7.10         5.13        35.41        48.39       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
      129.21       108.95        76.24        19.20        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       87.55        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 
       23.05        48.59        60.49         7.07        43.23        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
       62.43         9.60         2.14         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 
       65.82        10.98         7.13         8.42        28.34         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       126.15       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        9.01         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        47.47 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 
       36.00        31.36        26.20        18.97        17.13        95.34 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       11.87        47.97        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-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 
       56.48       156.49        54.94         3.52        16.27        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
        7.17       153.86        16.64         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
       21.01       169.38       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-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
       56.61        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
        6.48        28.01         3.62        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ 
       10.42        10.42        10.55        18.84        34.36        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       58.45        37.25        30.94        33.86        18.02        14.04 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 
       46.32        46.45        20.45        37.58        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       18.94        24.95         0.46        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
        4.27         3.65         6.90        34.75        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        37.71        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A51W 
        5.29        13.84        19.04        13.35        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
        7.13        17.98        29.92        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       36.82        47.01        19.00        75.55        18.97         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       29.00        12.99        16.01        13.15        21.07        21.21 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       23.15         7.30        21.47         9.34        12.72        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       21.07        19.73         5.62        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       15.32        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       32.45        13.71        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        48.03        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             2.10              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           180.16            210.97 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           16.965            21.070 
[1] "2.1 - 180.2 (17.0)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  2Q LOSS MUTATED         0        4        14        20         0         0
  2Q LOSS WILD-TYPE      27       72        68       233        12         1
D45V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 0                27
  STAGE II                4                72
  STAGE III              14                68
  STAGE IVA              20               233
  STAGE IVB               0                12
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2Q LOSS MUTATED       2  11  12  14
  2Q LOSS WILD-TYPE    48 126  88 159
D45V4, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1               2                48
  T2                 11               126
  T3                 12                88
  T4                 14               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
  2Q LOSS MUTATED    13  12  13   0
  2Q LOSS WILD-TYPE 166  56 155   8
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              13               166
  N1              12                56
  N2              13               155
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    17   0
  2Q LOSS WILD-TYPE 172   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     17    0
  2Q LOSS WILD-TYPE  172    1
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              17               172
  1               0                 1
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    20  26
  2Q LOSS WILD-TYPE 120 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     20   26
  2Q LOSS WILD-TYPE  120  356
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              20               120
  MALE                26               356
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    16  28
  2Q LOSS WILD-TYPE 135 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     16   28
  2Q LOSS WILD-TYPE  135  255
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               16               135
  YES              28               255
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  2Q LOSS MUTATED                                      44
  2Q LOSS WILD-TYPE                                   467
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  2Q LOSS MUTATED                                                             0
  2Q LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  2Q LOSS MUTATED                                                     2
  2Q LOSS WILD-TYPE                                                   8
D45V9, multiclass
                                                             clus
vv                                                            2Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    44
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            2Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     467
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, continuous
D45V11, continuous
D45V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     3
  2Q LOSS WILD-TYPE                                2     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           5    38
  2Q LOSS WILD-TYPE                        43   408
D45V13, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      5                43
  WHITE                                         38               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"
D45V14, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     4  39
  2Q LOSS WILD-TYPE  22 420
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      4   39
  2Q LOSS WILD-TYPE   22  420
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              39               420
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   162 134
  3P LOSS WILD-TYPE 141  84
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              296               225 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              134                84 
$`3P LOSS MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5555 
        3.35        15.19         9.30        13.64        26.50        17.10 
TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 
       65.59        21.17        14.83         3.55        12.62        41.85 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DI 
       30.18        27.95        11.54         7.10        14.47        11.05 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7864 
       20.48        16.41         9.14         4.41        36.72        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-A6UO TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
       27.19         8.81         6.28        38.04         4.67        56.68 
TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       12.89        57.11        12.99        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       27.58        13.05        42.02        46.32         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       71.31         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6018 
       52.08        50.07        30.67        48.00        47.44        19.07 
TCGA-CN-6019 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6996 
       34.13        11.08        32.22        35.05         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B 
       32.48        11.74        35.01        25.41        17.29        29.72 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A6V3 
        7.40        31.69        12.39         4.41        12.07        24.39 
TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 
        2.93        62.37        10.42        41.19        32.38        32.88 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       56.58         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       16.73        41.88        77.56        44.48        11.61        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.36        33.60        29.49        31.23        84.23        11.77 
TCGA-CR-5250 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6482 
       26.27        36.99        16.90         6.02        11.90        11.34 
TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 
       22.78         9.27        47.18        47.34        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
        3.09        24.95        29.23         9.17        34.06        19.92 
TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7401 
       17.13        47.01        27.06        29.82         5.13        35.41 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
       29.95       139.43       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       17.95       107.51        87.55        80.12        17.92        13.35 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 
       86.83        48.59         7.07        43.23        54.74         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6941 
       90.12         2.14         9.70         5.46        20.52        11.24 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6954 
       12.03        42.38        15.09        30.08         6.08        65.82 
TCGA-CV-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-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
      111.16        18.81         7.99         9.01         5.26         1.84 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7247 
       12.92        21.80        10.75        36.00        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 
       17.13         4.96        11.87        47.97         2.10        18.41 
TCGA-CV-7410 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7422 
      210.97         9.67         0.46        25.08        25.94        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
      100.57        14.89        54.94         3.52        16.27        84.49 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X 
        7.17       153.86       180.16        35.47        45.96         6.51 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JT 
       48.20        60.43        67.86         7.07        35.34        28.01 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 
        3.62        23.47        22.52        10.42        18.84        34.36 
TCGA-CX-A4AQ TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 
       51.12        25.41         9.60        23.05        16.14        11.44 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       24.95        25.32        12.36        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       12.79        11.11        30.94        33.86        18.02        14.04 
TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G 
       46.32        20.45        37.58        37.18        32.71        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
        3.02        31.13        18.94         0.46        17.85        11.80 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7831 
       15.06        13.61        21.11         0.07        28.47        21.93 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 
       27.48        14.66        22.85        13.84         3.65        15.95 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O 
       11.84        37.41         0.07        33.57        13.68        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D 
       19.04        15.48        18.15        14.37         7.96         1.84 
TCGA-P3-A5QA TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 
       71.74        18.97         2.04        16.01        21.07        21.21 
TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.47        18.64        21.07         6.51        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-T3-A92M TCGA-T3-A92N 
       17.82        15.32         8.32        15.91        13.71         3.12 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
       64.80        54.67         2.83        49.51        49.45        44.65 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO 
       17.95        24.30        55.43        29.46        13.94        20.75 
TCGA-UF-A7JS TCGA-WA-A7GZ 
       22.36        20.55 

$`3P LOSS WILD-TYPE`
TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 
       37.28         9.07        23.74        42.35        57.93        23.84 
TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG 
       20.48        68.48        15.52         4.01        29.42        28.11 
TCGA-BA-A4IH TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 
       20.45         5.69         7.82         2.27        13.38         6.15 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 
      105.90         4.60        18.38        22.42        33.70        44.98 
TCGA-BB-A5HY TCGA-BB-A6UM TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4727 
       10.55        12.92        12.69        48.76        55.86        51.29 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4741 TCGA-CN-5369 TCGA-CN-5370 
       26.86        32.81        52.14        73.61        12.49         8.52 
TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       56.94        23.90        28.04         6.74         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63V 
       52.08        10.45        38.89        23.57        21.21        22.32 
TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 
       16.57         2.70        23.44        19.82        20.88        19.53 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 
       48.20        52.37        21.50        54.58        70.45        45.99 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-7063 TCGA-CQ-7068 
       11.21         4.24        46.95        13.25        70.13        43.04 
TCGA-CQ-7071 TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-6467 
       43.10        14.14        12.46        54.67        37.87        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6481 TCGA-CR-6484 
       50.01        39.52        34.52        18.54        10.22        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7374 
        7.69        12.46        15.75        39.16        40.93         0.99 
TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
       31.96        26.17        32.78        12.89        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7404 
       32.65        44.25        30.58         7.10         5.95        48.39 
TCGA-CV-5431 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5977 TCGA-CV-6433 
       17.16        76.50        91.53        23.05        60.49        21.07 
TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 
       62.43         4.73        21.90        26.43       140.78        19.79 
TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7103 TCGA-CV-7178 
       53.95        10.98       126.15        12.66        52.31        71.21 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7250 
      130.88        77.16         4.73        47.47        31.36        95.34 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7411 TCGA-CV-7415 
       36.13        57.47        35.54        17.85        89.33        22.85 
TCGA-CV-7421 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7433 TCGA-CV-7437 TCGA-CV-7438 
        0.07        56.48       156.49        19.76        16.64         6.38 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V 
       22.19        27.98        21.01       169.38       159.65         1.05 
TCGA-CV-A45Y TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM 
       88.87         0.76        56.61        15.25         5.98         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 
       29.79         6.48        21.24        19.92        10.42        10.55 
TCGA-D6-6515 TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM 
       13.25         2.53        18.67        17.72        28.77         7.63 
TCGA-D6-A6EN TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 
       22.59        58.45        37.25        46.45        40.24        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A61V TCGA-F7-A623 TCGA-F7-A624 
       39.12        41.59        21.63        24.95        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 
       13.38        15.16        20.94        25.74        27.48        22.03 
TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
       12.66         0.36         4.27         6.90        34.75        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61K TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 
       14.50        37.71         5.29        13.35        19.27        10.75 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
       30.05        12.62         6.25        15.42         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       17.98        29.92        15.78        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T8 
       47.01        19.00        75.55        29.00        12.99        13.15 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VC TCGA-QK-A8Z8 
       23.15         7.30         9.34        12.72        19.73         5.62 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI 
       12.72        16.96         6.87         7.10        32.45        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JJ TCGA-UF-A7JT 
       13.25        20.35        48.03        74.47        18.05        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
        2.96        17.03        14.56 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.07              0.07 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           210.97            169.38 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           20.465            21.630 
[1] "0.1 - 211.0 (20.5)" "0.1 - 169.4 (21.6)"
[1] "hr=" "1.3"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  3P LOSS MUTATED        15       40        47       154         9         0
  3P LOSS WILD-TYPE      12       36        35        99         3         1
D46V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                15                12
  STAGE II               40                36
  STAGE III              47                35
  STAGE IVA             154                99
  STAGE IVB               9                 3
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  3P LOSS MUTATED      26  71  66 108
  3P LOSS WILD-TYPE    24  66  34  65
D46V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1              26                24
  T2                 71                66
  T3                 66                34
  T4                108                65
[1] 4 2
[1] 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
  3P LOSS MUTATED   102  37 109   5
  3P LOSS WILD-TYPE  77  31  59   3
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0             102                77
  N1              37                31
  N2             109                59
  N3               5                 3
[1] 4 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
  3P LOSS MUTATED   111   0
  3P LOSS WILD-TYPE  78   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    111    0
  3P LOSS WILD-TYPE   78    1
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0             111                78
  1               0                 1
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    66 231
  3P LOSS WILD-TYPE  74 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     66  231
  3P LOSS WILD-TYPE   74  151
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              66                74
  MALE               231               151
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    84 161
  3P LOSS WILD-TYPE  67 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     84  161
  3P LOSS WILD-TYPE   67  122
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               84                67
  YES             161               122
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  3P LOSS MUTATED                                     292
  3P LOSS WILD-TYPE                                   219
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  3P LOSS MUTATED                                                             1
  3P LOSS WILD-TYPE                                                           0
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  3P LOSS MUTATED                                                     4
  3P LOSS WILD-TYPE                                                   6
D46V9, multiclass
                                                             clus
vv                                                            3P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   292
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       4
                                                             clus
vv                                                            3P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     219
  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"
D46V10, continuous
D46V11, continuous
D46V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  1     6
  3P LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                          38   241
  3P LOSS WILD-TYPE                        10   205
D46V13, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          6                 5
  BLACK OR AFRICAN AMERICAN                     38                10
  WHITE                                        241               205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V14, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    16 254
  3P LOSS WILD-TYPE  10 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     16  254
  3P LOSS WILD-TYPE   10  205
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                  16                10
  NOT HISPANIC OR LATINO             254               205
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    29  32
  3Q LOSS WILD-TYPE 274 186
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               61               460 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               32               186 
$`3Q LOSS MUTATED`
TCGA-BA-4076 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6871 TCGA-BA-A6DB TCGA-BA-A6DL 
       13.64        17.10        65.59         3.55         7.10        20.48 
TCGA-BB-7870 TCGA-BB-A5HZ TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-6010 TCGA-CN-6018 
       66.28        27.19        57.11        14.33        50.07        19.07 
TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-5332 TCGA-CQ-6224 
        3.68        32.48        31.69        12.39        10.42        56.58 
TCGA-CQ-7065 TCGA-CQ-A4CD TCGA-CR-6473 TCGA-CR-6493 TCGA-CR-7373 TCGA-CR-7380 
       53.52        33.60        36.99         9.27        29.23        19.92 
TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7401 TCGA-CV-5434 TCGA-CV-5435 
       17.13        29.82         5.13        35.41       108.95        76.24 
TCGA-CV-5966 TCGA-CV-5976 TCGA-CV-6441 TCGA-CV-6937 TCGA-CV-6950 TCGA-CV-6952 
       17.92        48.59         9.60        20.52        15.09         6.08 
TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7100 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 
        8.42         2.50         9.01         4.96        11.87         2.10 
TCGA-CV-7418 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-A45X TCGA-CV-A6JE TCGA-D6-6826 
       25.94        54.94        16.27         6.51        35.34        11.44 
TCGA-DQ-7588 TCGA-F7-A620 TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-7832 TCGA-IQ-A61I 
       14.04        17.85        21.11        28.47        27.48         0.07 
TCGA-IQ-A61L TCGA-MT-A51W TCGA-MT-A51X TCGA-QK-A6IH TCGA-QK-A8ZB TCGA-QK-AA3K 
       13.68        14.37         7.96        21.47        17.82         8.32 
TCGA-WA-A7GZ 
       20.55 

$`3Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19         9.30        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 
       23.74        42.35        57.93        23.84        20.48        68.48 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       15.52        21.17        14.83        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-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-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-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.60         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
       18.38        22.42        36.72        33.70        50.20        44.98 
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-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
       12.92         8.81         6.28        12.69        48.76        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       38.04         4.67        51.29        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 
       32.81        52.14        12.99        20.55        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       73.61        13.05        42.02        46.32         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       71.31         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 
       12.49         8.52        52.08        56.94        30.67        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
       23.90        47.44        28.04        34.13         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        9.24        52.08        11.08        10.45        32.22        35.05 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       38.89        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y 
       17.29        29.72        21.21         7.40        22.32        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        70.45        62.37        45.99        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 
       41.19        32.38        32.88        46.95        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7068 
       14.99        38.76        70.13        64.87        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       29.36        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       39.52        34.52        18.54        16.90         6.02        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       15.75        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.45         3.09        24.95         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       34.06        26.17        32.78        47.01        27.06        12.89 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58         7.10 
TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        5.95        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        87.55        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 
       80.12        13.35        23.05        86.83        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 
       43.23        54.74        21.07        62.43        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        9.70         5.46         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6953 
      140.78        19.79        12.03        42.38        30.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 
       65.82        10.98         7.13        28.34         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7101 
      126.15       111.16        18.81        12.66         7.99         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-7254 TCGA-CV-7261 
       26.20        18.97        17.13        95.34        47.97        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-7421 TCGA-CV-7422 
        9.67         0.46        22.85        25.08         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7432 
      100.57        14.89        56.48       156.49         3.52        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-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        21.01       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
        1.05        45.96        88.87        48.20        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM 
        0.76        56.61         7.07        15.25         5.98         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
       19.92        22.52        10.42        10.42        10.55        18.84 
TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       34.36        51.12        13.25        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
        2.53        16.14        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       12.36        28.77         7.63        22.59        24.95        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
       12.10        12.79        11.11        58.45        37.25        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       33.86        18.02        46.32        46.45        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       40.24        40.04        39.12        41.59        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       21.63        20.25         3.02        31.13        18.94        24.95 
TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
        0.46        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 
       15.06        13.61        20.94         0.07        25.74        21.93 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
       27.48        14.66        22.03        12.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
       13.84         4.27         3.65         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
       38.53        14.50        37.71        11.84        37.41        33.57 
TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T 
        5.29        13.84        19.04        15.48        13.35        18.15 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       19.27        10.75        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
       13.15        21.07        21.21        23.15         7.30         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        18.64        21.07        19.73         6.51         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       14.76        12.20        15.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
       15.91         7.10        32.45        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.25        20.35        64.80        54.67         2.83        49.51 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       48.03        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
       32.65         2.96        17.03        14.56 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.07              0.07 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           108.95            210.97 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            17.85             21.21 
[1] "0.1 - 109.0 (17.9)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.6"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  3Q LOSS MUTATED         5        6         5        35         2         0
  3Q LOSS WILD-TYPE      22       70        77       218        10         1
D47V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 5                22
  STAGE II                6                70
  STAGE III               5                77
  STAGE IVA              35               218
  STAGE IVB               2                10
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  3Q LOSS MUTATED       8  10  12  25
  3Q LOSS WILD-TYPE    42 127  88 148
D47V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1               8                42
  T2                 10               127
  T3                 12                88
  T4                 25               148
[1] 4 2
[1] 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
  3Q LOSS MUTATED    28   5  22   0
  3Q LOSS WILD-TYPE 151  63 146   8
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              28               151
  N1               5                63
  N2              22               146
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    18   0
  3Q LOSS WILD-TYPE 171   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     18    0
  3Q LOSS WILD-TYPE  171    1
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              18               171
  1               0                 1
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    13  48
  3Q LOSS WILD-TYPE 127 334
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     13   48
  3Q LOSS WILD-TYPE  127  334
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              13               127
  MALE                48               334
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    20  30
  3Q LOSS WILD-TYPE 131 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     20   30
  3Q LOSS WILD-TYPE  131  253
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               20               131
  YES              30               253
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  3Q LOSS MUTATED                                      61
  3Q LOSS WILD-TYPE                                   450
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  3Q LOSS MUTATED                                                             0
  3Q LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  3Q LOSS MUTATED                                                     0
  3Q LOSS WILD-TYPE                                                  10
D47V9, multiclass
                                                             clus
vv                                                            3Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    61
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            3Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     450
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, continuous
D47V11, continuous
D47V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     1
  3Q LOSS WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                          10    50
  3Q LOSS WILD-TYPE                        38   396
D47V13, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                     10                38
  WHITE                                         50               396
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V14, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     2  57
  3Q LOSS WILD-TYPE  24 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2   57
  3Q LOSS WILD-TYPE   24  402
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                24
  NOT HISPANIC OR LATINO              57               402
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   111  83
  4P LOSS WILD-TYPE 192 135
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              194               327 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               83               135 
$`4P LOSS MUTATED`
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-5555 TCGA-BA-5557 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A4IG 
       17.10        20.48        14.83         3.55        29.42        28.11 
TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4224 
       27.95         7.10        20.48        16.41       105.90         9.14 
TCGA-BB-7861 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ 
       22.42        24.66        71.05        20.52        10.55        27.19 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
        6.28        12.69        55.86        38.04         4.67        56.68 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 
       12.89        26.86        57.11        45.83        13.05        42.02 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
       71.31         8.32        16.21        56.94        50.07        30.67 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6989 TCGA-CN-6992 
       48.00        19.07        34.13         9.07        32.22        35.05 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       38.89         3.68        32.48        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 
       23.57        29.72         7.40        31.69        12.39        12.07 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6228 
       24.39        48.20        32.38        46.95        13.25        14.99 
TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CI 
       64.87        16.73        77.56        23.24        33.60        31.23 
TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7365 
       54.67        34.52         7.69        12.46        22.78        39.16 
TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       47.34        35.84         3.45         3.09        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7404 
        0.99        17.13        27.06        29.82         5.13        48.39 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 
       17.16       129.21       108.95        76.24        19.20       107.51 
TCGA-CV-5444 TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       80.12         7.07         9.60        90.12         2.14         9.70 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
       26.43        11.24       140.78        42.38        15.09        30.08 
TCGA-CV-6956 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 
        7.13         2.50         4.14       111.16        12.66         5.26 
TCGA-CV-7103 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 
       52.31        77.16         4.73        47.47        36.00        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7413 TCGA-CV-7415 
       18.97        17.13        36.13        35.54         9.67        22.85 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7435 
       25.94        34.09       100.57        16.27        84.49       153.86 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45X TCGA-CV-A465 TCGA-CX-7082 TCGA-CX-7219 
        6.38        22.19         6.51         7.07        10.42        34.36 
TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP 
       25.41        23.05        17.72         7.63        24.95        13.94 
TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-F7-8298 TCGA-F7-A50G 
       11.11        30.94        14.04        46.32        32.71        20.25 
TCGA-F7-A61S TCGA-F7-A61V TCGA-H7-8502 TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-7831 
       18.94        24.95        15.06        21.11        28.47        21.93 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-A61E 
       27.48        14.66        22.03        13.84         3.65        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 
       11.84        37.41        33.57         6.25        15.42        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T8 
       17.98        15.78        71.74        36.82        47.01        13.15 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-AA3J 
       21.07        19.73         6.51         5.62        12.20        15.32 
TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T3-A92M TCGA-T3-A92N TCGA-UF-A71A 
        8.32        15.91         7.10        13.71         3.12         2.83 
TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       49.51        44.65        17.95        24.30        55.43        29.46 
TCGA-UF-A7JS TCGA-WA-A7GZ 
       22.36        20.55 

$`4P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 
        3.35        23.74        42.35        57.93        23.84        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       68.48        15.52        21.17        12.62         4.01        41.85 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       20.45        30.18        11.54         5.69        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4225 TCGA-BB-4227 
        2.27        11.05        13.38         6.15         4.60         4.41 
TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
       18.38        36.72        33.70        50.20        44.98        66.28 
TCGA-BB-7872 TCGA-BB-A5HU TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4722 TCGA-CN-4727 
       38.40        25.71        12.92         8.81        48.76        51.29 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 
       32.81        52.14        12.99        20.55        14.33        27.58 
TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 
       73.61        46.32         8.58        12.39        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6013 TCGA-CN-6016 
       11.57        12.49         8.52        52.08        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
       28.04         6.74         9.24        52.08        11.08        10.45 
TCGA-CN-6996 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       17.42        17.29        21.21        22.32        16.57         4.41 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
        2.70        23.44        19.82        20.88        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 
       10.42        11.21         4.24        41.19        32.88        56.58 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
        4.24        38.76        70.13        53.52        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG 
       43.10        44.48        11.61        29.36        29.49        14.14 
TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       12.46        84.23        11.77        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
       50.01        39.52        36.99        18.54        16.90         6.02 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6492 TCGA-CR-6493 
       11.90        10.22        11.34        11.64        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       47.18        40.93        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
       26.17        32.78        47.01        12.89        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 
       32.65        44.25        30.58         7.10         5.95        35.41 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       29.95       139.43        17.95        87.55        76.50        91.53 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6936 TCGA-CV-6937 
       43.23        54.74        21.07        62.43         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6953 
        4.73        21.90        19.79        12.03         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-7089 TCGA-CV-7090 
       65.82        10.98         8.42        28.34        64.83       126.15 
TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7177 
       18.81         7.99         9.01         1.84        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7252 
       71.21        10.75       130.88        31.36        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 
       11.87        47.97         2.10        18.41        57.47        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7424 
      210.97        89.33         0.46        25.08         0.07        14.89 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7433 TCGA-CV-7434 
       56.48       156.49        54.94         3.52        19.76         7.17 
TCGA-CV-7437 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
       16.64        27.98        21.01       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
       35.47         1.05        45.96        88.87        48.20        60.43 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
       67.86         0.76        56.61        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       23.47        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       51.12        13.25         9.60         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN 
       18.67        24.95        25.32        12.36        28.77        22.59 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.10        12.79        58.45        37.25        33.86        18.02 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       46.45        20.45        37.58        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61W 
       41.59        37.18        21.63         3.02        31.13         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-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8634 
       13.61        20.94         0.07        25.74        27.48        12.66 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
       22.85         0.36         4.27         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       38.53        14.50         0.07         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       19.04        15.48        13.35        18.15        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A5BI 
       14.37         7.96        30.05         1.84        12.62         7.13 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       29.92        51.25        10.85        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        21.21 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       23.15         7.30        21.47         9.34        12.72        18.64 
TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X2 
       14.76        17.82        12.72        16.96         6.87        32.45 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71D 
       13.55        13.25        20.35        64.80        54.67        48.03 
TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT 
       49.45        74.47        18.05        13.94        20.75        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
        2.96        17.03        14.56 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.99              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           153.86            210.97 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            22.39             20.45 
[1] "1.0 - 153.9 (22.4)" "0.1 - 211.0 (20.4)"
[1] "hr=" "1"  
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  4P LOSS MUTATED        13       23        32        98         5         1
  4P LOSS WILD-TYPE      14       53        50       155         7         0
D48V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                13                14
  STAGE II               23                53
  STAGE III              32                50
  STAGE IVA              98               155
  STAGE IVB               5                 7
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4P LOSS MUTATED      21  44  48  63
  4P LOSS WILD-TYPE    29  93  52 110
D48V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1              21                29
  T2                 44                93
  T3                 48                52
  T4                 63               110
[1] 4 2
[1] 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
  4P LOSS MUTATED    65  27  68   5
  4P LOSS WILD-TYPE 114  41 100   3
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              65               114
  N1              27                41
  N2              68               100
  N3               5                 3
[1] 4 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
  4P LOSS MUTATED    61   1
  4P LOSS WILD-TYPE 128   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     61    1
  4P LOSS WILD-TYPE  128    0
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              61               128
  1               1                 0
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    45 149
  4P LOSS WILD-TYPE  95 233
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     45  149
  4P LOSS WILD-TYPE   95  233
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              45                95
  MALE               149               233
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    54 110
  4P LOSS WILD-TYPE  97 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     54  110
  4P LOSS WILD-TYPE   97  173
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               54                97
  YES             110               173
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  4P LOSS MUTATED                                     189
  4P LOSS WILD-TYPE                                   322
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  4P LOSS MUTATED                                                             0
  4P LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  4P LOSS MUTATED                                                     5
  4P LOSS WILD-TYPE                                                   5
D48V9, multiclass
                                                             clus
vv                                                            4P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   189
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       5
                                                             clus
vv                                                            4P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     322
  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"
D48V10, continuous
D48V11, continuous
D48V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     2
  4P LOSS WILD-TYPE                                2     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                          25   161
  4P LOSS WILD-TYPE                        23   285
D48V13, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                     25                23
  WHITE                                        161               285
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V14, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    11 170
  4P LOSS WILD-TYPE  15 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     11  170
  4P LOSS WILD-TYPE   15  289
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                15
  NOT HISPANIC OR LATINO             170               289
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    84  67
  4Q LOSS WILD-TYPE 219 151
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              151               370 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               67               151 
$`4Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-6870 TCGA-BA-6873 
        9.30         9.07        17.10        20.48        14.83         4.01 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DI TCGA-BA-A8YP 
       29.42        28.11        27.95         7.10        11.05        16.41 
TCGA-BB-4227 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
        4.41        66.28        24.66        71.05        20.52        10.55 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 
        6.28        12.69        38.04        56.68        12.89        57.11 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-6010 
       20.55        45.83        13.05        12.39        71.31        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6989 
       30.67        48.00        19.07        34.13         9.07        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       38.89         3.68        32.48        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A6V7 
       23.57        29.72         7.40        31.69        12.39        19.53 
TCGA-CQ-5323 TCGA-CQ-6220 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7064 
       48.20        32.38        56.58        13.25        14.99        64.87 
TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-6472 
       16.73        77.56        23.24        31.23        54.67        34.52 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 
       11.64         7.69        12.46        39.16        47.34         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7392 
        3.09        24.95        29.23         0.99        17.13        46.85 
TCGA-CR-7398 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
        5.13        48.39        17.16       129.21       108.95        76.24 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5976 TCGA-CV-6003 TCGA-CV-6441 
       17.95       107.51        80.12        48.59        54.74         9.60 
TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6962 
        9.70        11.24       140.78        65.82         7.13         4.14 
TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7180 
      111.16        12.66         5.26        52.31        12.92        10.75 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7413 TCGA-CV-7418 
       18.97        17.13        36.13        35.54         9.67        25.94 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7435 
       34.09       100.57        14.89         3.52        16.27       153.86 
TCGA-CV-7440 TCGA-CV-A45U TCGA-CV-A460 TCGA-CV-A465 TCGA-CX-7086 TCGA-CX-7219 
       22.19        35.47        60.43         7.07        18.84        34.36 
TCGA-D6-6823 TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7588 
       23.05         7.63        13.94        11.11        30.94        14.04 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-A50G TCGA-F7-A61S TCGA-H7-A6C5 TCGA-HD-7831 
       46.32        37.58        20.25        18.94        21.11        21.93 
TCGA-HD-8634 TCGA-HD-A6HZ TCGA-IQ-A61H TCGA-IQ-A61J TCGA-MT-A67G TCGA-P3-A5Q6 
       12.66         3.65        37.41        33.57         6.25        15.78 
TCGA-P3-A5QA TCGA-P3-A6SX TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6VB TCGA-QK-A8Z7 
       71.74        47.01        23.15         7.30        21.07         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-T3-A92M TCGA-T3-A92N 
        5.62        12.20         8.32        15.91        13.71         3.12 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO 
       17.95        24.30        55.43        29.46        13.94        20.75 
TCGA-WA-A7GZ 
       20.55 

$`4Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
        3.35        15.19        13.64        37.28        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
       42.35        57.93        23.84        65.59        68.48        15.52 
TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A4II 
       21.17         3.55        12.62        41.85        20.45        30.18 
TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ 
       11.54         5.69        14.47         7.82         2.27        13.38 
TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 
       20.48         6.15       105.90         9.14         4.60        18.38 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7872 
       22.42        36.72        33.70        50.20        44.98        38.40 
TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4722 TCGA-CN-4723 
       25.71        27.19        12.92         8.81        48.76        55.86 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
        4.67        51.29        26.86        32.81        52.14        12.99 
TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       14.33        27.58        73.61        42.02        46.32         8.58 
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-6013 TCGA-CN-6016 TCGA-CN-6017 
        8.52        52.08        56.94        23.90        47.44        28.04 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
        6.74         9.24        52.08        11.08        10.45        35.05 
TCGA-CN-6996 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       17.42        17.29        21.21        22.32        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        23.44        19.82        24.39        20.88 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
       45.99        10.42        11.21         4.24        41.19        32.88 
TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 
       46.95         4.24        38.76        70.13        53.52        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       41.88        43.10        44.48        11.61        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 
       29.49        14.14        12.46        84.23        11.77        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
       26.27        58.42        50.01        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6491 
       16.90         6.02        11.90        10.22        11.34        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7376 
       15.75         9.27        47.18        40.93        35.84        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
        9.17        34.06        19.92        26.17        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 
       27.06        12.89        29.82        30.02        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 
       30.58         7.10         5.95        35.41        29.95       139.43 
TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 
       19.20        87.55        76.50        91.53        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 
       23.05        86.83        60.49         7.07        43.23        21.07 
TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       62.43        90.12         2.14         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       21.90        26.43        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6960 
       30.08         6.08        53.95        10.98         8.42        28.34 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 
        2.50        64.83       126.15        18.81         7.99         9.01 
TCGA-CV-7102 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
        1.84        21.80        71.21       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7252 
       47.47        36.00        31.36        26.20        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 
       11.87        47.97         2.10        18.41        57.47        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 
      210.97        89.33         0.46        22.85        25.08         0.07 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
       56.48       156.49        54.94        84.49        19.76         7.17 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       16.64         6.38        27.98        21.01       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-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
       67.86         0.76        56.61        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
       23.47        19.92        22.52        10.42        10.42        10.55 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
       51.12        13.25        25.41         9.60         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-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 
       28.77        22.59        24.95        12.10        12.79        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 
       37.25        33.86        18.02        46.45        20.45        40.24 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       40.04        39.12        41.59        37.18        32.71        21.63 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
        3.02        31.13        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
       20.25        12.43        13.38        15.16        15.06        13.61 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 
       20.94         0.07        28.47        25.74        27.48        27.48 
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-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
       11.84         0.07         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       15.48        13.35        18.15        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI 
        7.96        30.05         1.84        12.62        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       16.08        17.98        29.92        51.25        10.85        36.82 
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-A6IH TCGA-QK-A6II 
       16.01        13.15        21.07        21.21        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J 
       12.72        18.64        19.73        14.76        17.82        15.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI 
       12.72        16.96         6.87         7.10        32.45        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.25        20.35        64.80        54.67         2.83        49.51 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JJ TCGA-UF-A7JS 
       48.03        49.45        44.65        74.47        18.05        22.36 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
       32.65         2.96        17.03        14.56 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.99              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           153.86            210.97 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            20.55             21.04 
[1] "1.0 - 153.9 (20.6)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1.1"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  4Q LOSS MUTATED         9       17        30        74         1         1
  4Q LOSS WILD-TYPE      18       59        52       179        11         0
D49V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 9                18
  STAGE II               17                59
  STAGE III              30                52
  STAGE IVA              74               179
  STAGE IVB               1                11
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4Q LOSS MUTATED      15  35  39  47
  4Q LOSS WILD-TYPE    35 102  61 126
D49V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1              15                35
  T2                 35               102
  T3                 39                61
  T4                 47               126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4Q LOSS MUTATED    44  23  56   1
  4Q LOSS WILD-TYPE 135  45 112   7
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              44               135
  N1              23                45
  N2              56               112
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    44   1
  4Q LOSS WILD-TYPE 145   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     44    1
  4Q LOSS WILD-TYPE  145    0
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              44               145
  1               1                 0
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    38 113
  4Q LOSS WILD-TYPE 102 269
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     38  113
  4Q LOSS WILD-TYPE  102  269
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              38               102
  MALE               113               269
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    40  91
  4Q LOSS WILD-TYPE 111 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     40   91
  4Q LOSS WILD-TYPE  111  192
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               40               111
  YES              91               192
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  4Q LOSS MUTATED                                     149
  4Q LOSS WILD-TYPE                                   362
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  4Q LOSS MUTATED                                                             0
  4Q LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  4Q LOSS MUTATED                                                     2
  4Q LOSS WILD-TYPE                                                   8
D49V9, multiclass
                                                             clus
vv                                                            4Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   149
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            4Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     362
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V10, continuous
D49V11, continuous
D49V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  1     4
  4Q LOSS WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                          21   119
  4Q LOSS WILD-TYPE                        27   327
D49V13, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          4                 7
  BLACK OR AFRICAN AMERICAN                     21                27
  WHITE                                        119               327
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V14, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     9 132
  4Q LOSS WILD-TYPE  17 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9  132
  4Q LOSS WILD-TYPE   17  327
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   9                17
  NOT HISPANIC OR LATINO             132               327
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    29  22
  5P LOSS WILD-TYPE 274 196
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               51               470 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               22               196 
$`5P LOSS MUTATED`
TCGA-BA-6871 TCGA-BA-A6DA TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-7871 TCGA-BB-A5HY 
        3.55        11.54        16.41         9.14        24.66        10.55 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-6988 TCGA-CN-A499 TCGA-CN-A63U TCGA-CQ-5326 
       42.02        46.32        10.45        23.57        31.69         2.93 
TCGA-CQ-5332 TCGA-CQ-7069 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CR-6493 TCGA-CR-7364 
       10.42        41.88        23.24        29.49         9.27        47.18 
TCGA-CR-7372 TCGA-CV-5432 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 
       24.95       129.21        48.59        60.49        43.23        54.74 
TCGA-CV-6933 TCGA-CV-6940 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6962 TCGA-CV-7242 
       90.12        26.43        15.09        30.08         4.14        36.00 
TCGA-CV-7248 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7435 TCGA-CV-7438 
       17.13        18.41        35.54         0.46       153.86         6.38 
TCGA-D6-A6EQ TCGA-F7-A50G TCGA-IQ-A61G TCGA-IQ-A61H TCGA-P3-A5QF TCGA-P3-A6T5 
       12.10        20.25        11.84        37.41        10.85        29.00 
TCGA-QK-A6IH TCGA-QK-A6VB TCGA-QK-AA3J TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC 
       21.47        21.07        15.32        49.45        44.65        17.95 
TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JO 
       24.30        29.46        20.75 

$`5P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       20.48        65.59        68.48        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-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       105.90 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       50.20        44.98        66.28        38.40        71.05        20.52 
TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       25.71        27.19        12.92         8.81         6.28        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
       48.76        55.86        38.04         4.67        51.29        56.68 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       12.89        26.86        32.81        52.14        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        45.83        27.58        73.61        13.05 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
        8.58        12.39        71.31         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.84        11.57        12.49         8.52        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        34.13         6.74         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       11.08        32.22        35.05        38.89         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B 
       32.48        11.74        35.01        25.41        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
       21.21         7.40        22.32        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        23.44        19.82        24.39        20.88 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
       19.53        48.20        52.37        21.50        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       62.37        45.99        11.21         4.24        41.19        32.38 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       32.88        46.95        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       38.76        70.13        64.87        53.52        16.73        43.04 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        77.56        44.48        11.61        29.36        33.60 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       14.14        12.46        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
       37.87        26.27        58.42        50.01        39.52        34.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
       36.99        18.54        16.90         6.02        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       11.34        11.64         7.69        12.46        22.78        15.75 
TCGA-CR-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-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       29.23         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       26.17        17.13        32.78        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       29.82        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         5.13         5.95        35.41        29.95        48.39 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
      139.43        17.16       108.95        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        87.55        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 
       13.35        23.05        86.83         7.07        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
        9.60         2.14         9.70         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       21.90        11.24       140.78        19.79        12.03        42.38 
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-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
       28.34         2.50        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-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 
        4.73        47.47        31.36        26.20        18.97        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7406 
        4.96        11.87        47.97         2.10        36.13        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-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
      156.49        54.94         3.52        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
        7.17        16.64        22.19        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
        7.07        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
       22.52        10.42        10.42        10.55        18.84        34.36 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       16.14        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       12.36        28.77         7.63        22.59        24.95        13.94 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
       12.79        11.11        58.45        37.25        30.94        33.86 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       18.02        14.04        46.32        46.45        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       40.24        40.04        39.12        41.59        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       21.63         3.02        31.13        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       17.85        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       15.06        13.61        21.11        20.94         0.07        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       25.74        21.93        27.48        27.48        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        38.53        14.50        37.71 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
        0.07        33.57         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       15.48        13.35        18.15        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       51.25        36.82        47.01        19.00        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        2.04        12.99        16.01        13.15        21.07        21.21 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC 
       23.15         7.30         9.34        12.72        18.64        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K 
        6.51         5.62        14.76        12.20        17.82         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.72        16.96         6.87        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       13.71         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JF 
       54.67         2.83        49.51        48.03        74.47        55.43 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       18.05        13.94        22.36        32.65         2.96        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.46              0.07 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           153.86            210.97 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           23.570            20.535 
[1] "0.5 - 153.9 (23.6)" "0.1 - 211.0 (20.5)"
[1] "hr=" "1"  
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  5P LOSS MUTATED         3        7         9        29         2         0
  5P LOSS WILD-TYPE      24       69        73       224        10         1
D50V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 3                24
  STAGE II                7                69
  STAGE III               9                73
  STAGE IVA              29               224
  STAGE IVB               2                10
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5P LOSS MUTATED       3  12  13  22
  5P LOSS WILD-TYPE    47 125  87 151
D50V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1               3                47
  T2                 12               125
  T3                 13                87
  T4                 22               151
[1] 4 2
[1] 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
  5P LOSS MUTATED    18   6  21   1
  5P LOSS WILD-TYPE 161  62 147   7
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              18               161
  N1               6                62
  N2              21               147
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    19   0
  5P LOSS WILD-TYPE 170   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     19    0
  5P LOSS WILD-TYPE  170    1
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              19               170
  1               0                 1
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    15  36
  5P LOSS WILD-TYPE 125 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     15   36
  5P LOSS WILD-TYPE  125  346
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              15               125
  MALE                36               346
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    15  27
  5P LOSS WILD-TYPE 136 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     15   27
  5P LOSS WILD-TYPE  136  256
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               15               136
  YES              27               256
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  5P LOSS MUTATED                                      49
  5P LOSS WILD-TYPE                                   462
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  5P LOSS MUTATED                                                             0
  5P LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  5P LOSS MUTATED                                                     2
  5P LOSS WILD-TYPE                                                   8
D50V9, multiclass
                                                             clus
vv                                                            5P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    49
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            5P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     462
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, continuous
D50V11, continuous
D50V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     0
  5P LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           7    41
  5P LOSS WILD-TYPE                        41   405
D50V13, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      7                41
  WHITE                                         41               405
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V14, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3  38
  5P LOSS WILD-TYPE  23 421
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3   38
  5P LOSS WILD-TYPE   23  421
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                23
  NOT HISPANIC OR LATINO              38               421
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED   101  63
  5Q LOSS WILD-TYPE 202 155
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              164               357 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               63               155 
$`5Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
        9.30         9.07        17.10         3.55        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
       41.85        28.11        27.95        11.54         7.10        14.47 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 
       16.41         6.15         9.14        66.28        24.66        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4729 
       20.52        10.55         6.28        38.04        51.29        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 
       26.86        32.81        20.55        45.83        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6019 
       46.32        71.31        11.84        50.07        48.00        34.13 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-A499 TCGA-CN-A63U TCGA-CN-A63W 
       11.08        10.45        35.05        23.57        31.69        12.39 
TCGA-CN-A641 TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6229 
       12.07         2.93        10.42        13.25         4.24        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CE 
       64.87        53.52        41.88        77.56        23.24        29.49 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 
       12.46        31.23        11.77        18.54        16.90        12.46 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        9.27        47.18        39.16        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7379 TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7404 
        3.09        24.95        34.06        29.82         5.13        48.39 
TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-5976 
      129.21        76.24       107.51        87.55        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6940 
       60.49         7.07        43.23        54.74        90.12        26.43 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7090 
       15.09        30.08         8.42        28.34         4.14       126.15 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7180 
      111.16        18.81         5.26        52.31        21.80        10.75 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 
       36.00        31.36        17.13        47.97        36.13        18.41 
TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7421 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7435 
       35.54         0.46         0.07        14.89         3.52       153.86 
TCGA-CV-7438 TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A465 
        6.38       180.16        45.96         6.51        48.20         7.07 
TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-A6EQ TCGA-D6-A74Q 
       35.34        10.42        18.84        23.05        12.10        11.11 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 
       18.02        14.04        46.32        37.58        40.04        39.12 
TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A61W TCGA-F7-A622 TCGA-H7-A6C4 TCGA-HD-7753 
       37.18        20.25         0.46        11.80        13.61        28.47 
TCGA-HD-7917 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66T 
       27.48        11.84        37.41        19.04        15.48        18.15 
TCGA-MT-A67D TCGA-MT-A7BN TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T5 
        1.84        15.42        10.85        47.01        18.97        29.00 
TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
       21.21        21.47        12.72        21.07        19.73         6.51 
TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-T2-A6WZ TCGA-UF-A71B TCGA-UF-A71D 
       14.76        17.82        15.32        15.91        49.51        48.03 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.45        44.65        74.47        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JO 
       29.46        20.75 

$`5Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
        3.35        15.19        13.64        37.28        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       42.35        57.93        23.84        20.48        65.59        68.48 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A4II 
       15.52        21.17        14.83        29.42        20.45        30.18 
TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
        5.69         7.82         2.27        11.05        13.38        20.48 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
      105.90         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7872 TCGA-BB-A5HU TCGA-BB-A5HZ 
       33.70        50.20        44.98        38.40        25.71        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 
       12.92         8.81        12.69        48.76        55.86         4.67 
TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 
       56.68        52.14        57.11        12.99        14.33        27.58 
TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       73.61         8.58        12.39         8.32        16.21        11.54 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 
       11.57        12.49         8.52        52.08        56.94        30.67 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 
       23.90        47.44        28.04        19.07         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
        9.24        52.08        32.22        38.89         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B 
       32.48        11.74        35.01        25.41        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 
       21.21         7.40        22.32        16.57         4.41         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       23.44        19.82        24.39        20.88        19.53        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       52.37        21.50        54.58        70.45        62.37        45.99 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 
       11.21         4.24        41.19        32.38        32.88        46.95 
TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 
       56.58        14.99        70.13        16.73        43.04        43.10 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-5243 
       44.48        11.61        29.36        33.60        14.14        84.23 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       34.52        36.99         6.02        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7367 TCGA-CR-7373 
       11.64         7.69        22.78        15.75        47.34        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
        0.99        31.96         9.17        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
       32.78        47.01        27.06        12.89        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 
       32.65        44.25        30.58         7.10         5.95        35.41 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 
       29.95       139.43        17.16       108.95        19.20        17.95 
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-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       21.07        62.43         9.60         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
       20.52         4.73        21.90        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       12.03        42.38         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        7.13         2.50        64.83        12.66         7.99         9.01 
TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
        1.84        12.92        71.21       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       47.47        26.20        18.97        95.34         4.96        11.87 
TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
        2.10        57.47        17.85       210.97        89.33         9.67 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7425 
       22.85        25.08        25.94        34.09       100.57        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
      156.49        54.94        16.27        84.49        19.76         7.17 
TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T 
       16.64        22.19        27.98        21.01       169.38       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
       35.47         1.05        88.87        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       56.61        15.25         5.98         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        34.36        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
        9.60         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN 
       25.32        17.72        12.36        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
       24.95        13.94        12.79        58.45        37.25        30.94 
TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7596 TCGA-F7-8298 
       33.86        46.45        20.45        40.24        41.59        32.71 
TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 
       21.63         3.02        31.13        18.94        24.95        17.85 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C5 
       20.25        12.43        13.38        15.16        15.06        21.11 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
       20.94         0.07        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       22.03        12.66        22.85         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        3.65         6.90        34.75        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       37.71         0.07        33.57         5.29        13.68        13.84 
TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       13.35        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
       12.62         6.25         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
       15.78        71.74        51.25        36.82        19.00        75.55 
TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF 
        2.04        12.99        16.01        13.15        21.07        23.15 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-AA3K 
        7.30         9.34        18.64         5.62        12.20         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       12.72        16.96         6.87         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        3.12        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
        2.83        18.05        13.94        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.07              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           180.16            210.97 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           21.635            20.520 
[1] "0.1 - 180.2 (21.6)" "0.1 - 211.0 (20.5)"
[1] "hr=" "1.2"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  5Q LOSS MUTATED         6       26        31        82         3         0
  5Q LOSS WILD-TYPE      21       50        51       171         9         1
D51V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 6                21
  STAGE II               26                50
  STAGE III              31                51
  STAGE IVA              82               171
  STAGE IVB               3                 9
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5Q LOSS MUTATED       9  46  32  62
  5Q LOSS WILD-TYPE    41  91  68 111
D51V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1               9                41
  T2                 46                91
  T3                 32                68
  T4                 62               111
[1] 4 2
[1] 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
  5Q LOSS MUTATED    54  26  54   2
  5Q LOSS WILD-TYPE 125  42 114   6
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              54               125
  N1              26                42
  N2              54               114
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    62   0
  5Q LOSS WILD-TYPE 127   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     62    0
  5Q LOSS WILD-TYPE  127    1
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              62               127
  1               0                 1
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    39 125
  5Q LOSS WILD-TYPE 101 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     39  125
  5Q LOSS WILD-TYPE  101  257
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              39               101
  MALE               125               257
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    46  87
  5Q LOSS WILD-TYPE 105 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     46   87
  5Q LOSS WILD-TYPE  105  196
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               46               105
  YES              87               196
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  5Q LOSS MUTATED                                     160
  5Q LOSS WILD-TYPE                                   351
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  5Q LOSS MUTATED                                                             0
  5Q LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  5Q LOSS MUTATED                                                     4
  5Q LOSS WILD-TYPE                                                   6
D51V9, multiclass
                                                             clus
vv                                                            5Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   160
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       4
                                                             clus
vv                                                            5Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     351
  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"
D51V10, continuous
D51V11, continuous
D51V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  1     5
  5Q LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                          22   132
  5Q LOSS WILD-TYPE                        26   314
D51V13, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          5                 6
  BLACK OR AFRICAN AMERICAN                     22                26
  WHITE                                        132               314
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V14, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     8 139
  5Q LOSS WILD-TYPE  18 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      8  139
  5Q LOSS WILD-TYPE   18  320
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   8                18
  NOT HISPANIC OR LATINO             139               320
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    37  31
  6P LOSS WILD-TYPE 266 187
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               68               453 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               31               187 
$`6P LOSS MUTATED`
TCGA-BA-5152 TCGA-BA-5559 TCGA-BB-4225 TCGA-BB-7862 TCGA-CN-4725 TCGA-CN-4728 
       42.35        68.48         4.60        36.72        38.04        56.68 
TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-5359 TCGA-CN-6010 TCGA-CN-6024 
       12.89        57.11        27.58        12.39        50.07        11.08 
TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A63T TCGA-CN-A640 TCGA-CN-A6V7 TCGA-CQ-5332 
       38.89        32.48         7.40         4.41        19.53        10.42 
TCGA-CQ-6223 TCGA-CQ-A4C9 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7371 
       46.95        23.24        12.46         9.27        39.16         3.09 
TCGA-CR-7373 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5443 
       29.23         5.95        48.39       108.95        19.20        91.53 
TCGA-CV-5444 TCGA-CV-6441 TCGA-CV-6940 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7095 
       80.12         9.60        26.43        28.34         4.14        18.81 
TCGA-CV-7101 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7263 
        5.26        18.97        17.13        11.87        47.97        18.41 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-A465 TCGA-CV-A6JT TCGA-D6-6823 TCGA-D6-6826 
       25.08        25.94         7.07        28.01        23.05        11.44 
TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 
       12.10        11.11        58.45        14.04        46.32        20.45 
TCGA-F7-A623 TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61I TCGA-MT-A67G TCGA-MT-A7BN 
       20.25         3.65        11.84         0.07         6.25        15.42 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-T3-A92N TCGA-UF-A71E 
       17.98        15.78        71.74        19.00         3.12        49.45 
TCGA-UF-A7JF TCGA-UP-A6WW 
       55.43        17.03 

$`6P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       26.50        23.74        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       65.59        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        4.01        41.85        29.42        28.11        20.45        30.18 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       27.95        11.54         7.10         5.69        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
        2.27        11.05        13.38        20.48        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 
      105.90         9.14         4.41        18.38        22.42        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       50.20        44.98        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-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 
        6.28        12.69        48.76        55.86         4.67        51.29 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       26.86        32.81        52.14        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       45.83        73.61        13.05        42.02        46.32         8.58 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       71.31         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 
       12.49         8.52        52.08        56.94        30.67        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       23.90        47.44        28.04        19.07        34.13         6.74 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        9.07         9.24        52.08        10.45        32.22        35.05 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       17.29        29.72        21.21        31.69        22.32        12.39 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
       16.57        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        48.20        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       70.45        62.37        45.99        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       32.38        32.88        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       38.76        70.13        64.87        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        11.61        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
       39.52        34.52        36.99        18.54        16.90         6.02 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 
       11.90        10.22        11.34        11.64         7.69        22.78 
TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       15.75        47.18        47.34        40.93        35.84         3.45 
TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       24.95         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       26.17        17.13        32.78        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       29.82        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 
        7.10         5.13        35.41        29.95       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
      129.21        76.24        17.95       107.51        87.55        76.50 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 
        7.07        43.23        54.74        21.07        62.43        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       140.78        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 
        8.42         2.50        64.83       126.15       111.16        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        7.99         9.01         1.84        52.31        12.92        21.80 
TCGA-CV-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-7250 TCGA-CV-7252 TCGA-CV-7255 
       36.00        31.36        26.20        95.34         4.96         2.10 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       36.13        57.47        35.54        17.85       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
        9.67         0.46        22.85         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
       14.89        56.48       156.49        54.94         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-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
       22.19        27.98        21.01       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
       35.47         1.05        45.96         6.51        88.87        48.20 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
       60.43        67.86         0.76        56.61        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-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       18.84        34.36        51.12        13.25        25.41         9.60 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
        2.53        16.14        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       12.36        28.77         7.63        22.59        24.95        13.94 
TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 
       12.79        37.25        30.94        33.86        18.02        46.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       37.58        40.24        40.04        39.12        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 
       24.95         0.46        17.85        11.80        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       15.16        15.06        13.61        21.11        20.94         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       28.47        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       22.03        12.66        22.85         0.36        13.84         4.27 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        38.53        14.50        37.71 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
       37.41        33.57         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       15.48        13.35        18.15        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A5BI TCGA-MZ-A6I9 
        7.96        30.05         1.84        12.62         7.13        16.08 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
       29.92        51.25        10.85        36.82        47.01        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       18.97         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        18.64        21.07        19.73         6.51         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       16.96         6.87        15.91         7.10        32.45        13.71 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        48.03        44.65        74.47        17.95        24.30 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       29.46        18.05        13.94        20.75        22.36        32.65 
TCGA-UF-A7JV TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        20.55        14.56 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.07              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           108.95            210.97 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            19.10             21.07 
[1] "0.1 - 109.0 (19.1)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.2"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  6P LOSS MUTATED         1        9        11        39         0         0
  6P LOSS WILD-TYPE      26       67        71       214        12         1
D52V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 1                26
  STAGE II                9                67
  STAGE III              11                71
  STAGE IVA              39               214
  STAGE IVB               0                12
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6P LOSS MUTATED       4  16  16  23
  6P LOSS WILD-TYPE    46 121  84 150
D52V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1               4                46
  T2                 16               121
  T3                 16                84
  T4                 23               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
  6P LOSS MUTATED    19   8  25   0
  6P LOSS WILD-TYPE 160  60 143   8
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              19               160
  N1               8                60
  N2              25               143
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    17   0
  6P LOSS WILD-TYPE 172   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     17    0
  6P LOSS WILD-TYPE  172    1
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              17               172
  1               0                 1
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    14  54
  6P LOSS WILD-TYPE 126 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     14   54
  6P LOSS WILD-TYPE  126  328
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              14               126
  MALE                54               328
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    21  36
  6P LOSS WILD-TYPE 130 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     21   36
  6P LOSS WILD-TYPE  130  247
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               21               130
  YES              36               247
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  6P LOSS MUTATED                                      67
  6P LOSS WILD-TYPE                                   444
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  6P LOSS MUTATED                                                             0
  6P LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  6P LOSS MUTATED                                                     1
  6P LOSS WILD-TYPE                                                   9
D52V9, multiclass
                                                             clus
vv                                                            6P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    67
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            6P LOSS 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                         9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V10, continuous
D52V11, continuous
D52V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     0
  6P LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                          11    53
  6P LOSS WILD-TYPE                        37   393
D52V13, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                     11                37
  WHITE                                         53               393
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V14, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     7  53
  6P LOSS WILD-TYPE  19 406
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      7   53
  6P LOSS WILD-TYPE   19  406
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                19
  NOT HISPANIC OR LATINO              53               406
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    42  26
  6Q LOSS WILD-TYPE 261 192
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               68               453 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               26               192 
$`6Q LOSS MUTATED`
TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5559 TCGA-BB-4225 TCGA-CN-4725 TCGA-CN-4728 
       42.35        17.10        68.48         4.60        38.04        56.68 
TCGA-CN-4729 TCGA-CN-4740 TCGA-CN-5359 TCGA-CN-6010 TCGA-CN-6024 TCGA-CN-6988 
       12.89        27.58        12.39        50.07        11.08        10.45 
TCGA-CN-6994 TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A6V7 TCGA-CQ-6223 TCGA-CQ-A4C7 
       38.89         4.41        12.07        19.53        46.95        11.61 
TCGA-CQ-A4C9 TCGA-CR-5248 TCGA-CR-6473 TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7373 
       23.24        54.67        36.99        22.78        39.16        29.23 
TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5443 TCGA-CV-5444 
        5.95        48.39       108.95       107.51        91.53        80.12 
TCGA-CV-6441 TCGA-CV-6940 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7095 
        9.60        26.43        53.95        65.82       111.16        18.81 
TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7247 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7263 
        5.26        77.16        18.97        11.87        47.97        18.41 
TCGA-CV-7416 TCGA-CV-A45U TCGA-D6-6823 TCGA-D6-6826 TCGA-DQ-5624 TCGA-DQ-5631 
       25.08        35.47        23.05        11.44        58.45        18.02 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-F7-A50G TCGA-F7-A623 TCGA-HD-A633 
       14.04        46.32        20.45        20.25        20.25        13.84 
TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61I TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A6SW 
        3.65        11.84         0.07         6.25        17.98        36.82 
TCGA-P3-A6T0 TCGA-RS-A6TP TCGA-T3-A92N TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK 
       19.00        16.96         3.12        55.43        29.46        13.94 
TCGA-UP-A6WW TCGA-WA-A7GZ 
       17.03        20.55 

$`6Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       26.50        23.74        57.93        23.84        20.48        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
       15.52        21.17        14.83         3.55        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
       41.85        29.42        28.11        20.45        30.18        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        9.14         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       50.20        44.98        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-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 
        6.28        12.69        48.76        55.86         4.67        51.29 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       26.86        32.81        52.14        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       14.33        45.83        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
        8.58        71.31         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-6011 
       11.57        12.49         8.52        52.08        56.94        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       48.00        23.90        47.44        28.04        19.07        34.13 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6992 
        6.74         9.07         9.24        52.08        32.22        35.05 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        3.68        17.42        32.48        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       23.57        17.29        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
       22.32        12.39        16.57         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       24.39        20.88        48.20        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6225 
        4.24        41.19        32.38        32.88        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        4.24        14.99        38.76        70.13        64.87        53.52 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       16.73        43.04        41.88        43.10        77.56        44.48 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       84.23        11.77        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       39.52        34.52        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-6492 
       10.22        11.34        11.64         7.69        12.46        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        9.27        47.18        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        3.09        24.95         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        29.82        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 
       30.58         7.10         5.13        35.41        29.95       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 
       17.16       129.21        76.24        19.20        17.95        87.55 
TCGA-CV-5442 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       76.50        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       60.49         7.07        43.23        54.74        21.07        62.43 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       90.12         2.14         9.70         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       21.90        11.24       140.78        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
       15.09        30.08         6.08        10.98         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7097 
       28.34         2.50         4.14        64.83       126.15        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        7.99         9.01         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       71.21        10.75       130.88         4.73        47.47        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7255 
       31.36        26.20        17.13        95.34         4.96         2.10 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       36.13        57.47        35.54        17.85       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        9.67         0.46        22.85        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 
      100.57        14.89        56.48       156.49        54.94         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-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
        6.38        22.19        27.98        21.01       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-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       60.43        67.86         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 
       10.42        10.55        18.84        34.36        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 
       25.41         9.60         2.53        16.14        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN 
       25.32        17.72        12.36        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 
       24.95        13.94        12.10        12.79        11.11        37.25 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       30.94        33.86        46.45        37.58        40.24        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I 
       39.12        41.59        37.18        32.71        21.63         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       31.13        18.94        24.95         0.46        17.85        11.80 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
       12.43        13.38        15.16        15.06        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       20.94         0.07        28.47        25.74        21.93        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
       27.48        14.66        22.03        12.66        22.85         0.36 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         6.90        34.75        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       37.71        37.41        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       19.04        15.48        13.35        18.15        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN 
       14.37         7.96        30.05         1.84        12.62        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
        7.13        16.08        29.92        15.78        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       10.85        47.01        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        21.47         9.34        12.72        18.64        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       19.73         6.51         5.62        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       15.32         8.32        12.72         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       32.45        13.71        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        49.51        48.03        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS 
       74.47        17.95        24.30        18.05        20.75        22.36 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-WA-A7H4 
       32.65         2.96        14.56 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.07              0.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           111.16            210.97 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            20.50             21.01 
[1] "0.1 - 111.2 (20.5)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1.2"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  6Q LOSS MUTATED         1        9        10        35         1         0
  6Q LOSS WILD-TYPE      26       67        72       218        11         1
D53V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 1                26
  STAGE II                9                67
  STAGE III              10                72
  STAGE IVA              35               218
  STAGE IVB               1                11
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6Q LOSS MUTATED       4  17  11  25
  6Q LOSS WILD-TYPE    46 120  89 148
D53V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1               4                46
  T2                 17               120
  T3                 11                89
  T4                 25               148
[1] 4 2
[1] 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
  6Q LOSS MUTATED    19   8  23   1
  6Q LOSS WILD-TYPE 160  60 145   7
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              19               160
  N1               8                60
  N2              23               145
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    18   0
  6Q LOSS WILD-TYPE 171   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     18    0
  6Q LOSS WILD-TYPE  171    1
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              18               171
  1               0                 1
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    12  56
  6Q LOSS WILD-TYPE 128 326
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     12   56
  6Q LOSS WILD-TYPE  128  326
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              12               128
  MALE                56               326
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    21  37
  6Q LOSS WILD-TYPE 130 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     21   37
  6Q LOSS WILD-TYPE  130  246
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               21               130
  YES              37               246
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  6Q LOSS MUTATED                                      67
  6Q LOSS WILD-TYPE                                   444
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  6Q LOSS MUTATED                                                             0
  6Q LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  6Q LOSS MUTATED                                                     1
  6Q LOSS WILD-TYPE                                                   9
D53V9, multiclass
                                                             clus
vv                                                            6Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    67
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            6Q LOSS 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                         9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V10, continuous
D53V11, continuous
D53V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0     0
  6Q LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                          11    54
  6Q LOSS WILD-TYPE                        37   392
D53V13, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                     11                37
  WHITE                                         54               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"
D53V14, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     4  57
  6Q LOSS WILD-TYPE  22 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4   57
  6Q LOSS WILD-TYPE   22  402
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              57               402
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    18  11
  7P LOSS WILD-TYPE 285 207
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               29               492 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               11               207 
$`7P LOSS MUTATED`
TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A6DE TCGA-CN-5374 TCGA-CN-6992 TCGA-CN-6998 
       68.48        28.11        14.47        56.94        35.05        11.74 
TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A6V7 TCGA-CR-6473 TCGA-CV-5435 
       29.72        31.69        12.39        19.53        36.99        76.24 
TCGA-CV-6003 TCGA-CV-7242 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 TCGA-CX-7082 
       54.74        36.00         3.52        16.27        19.76        10.42 
TCGA-D6-A6EQ TCGA-F7-A50G TCGA-F7-A623 TCGA-HD-A6HZ TCGA-KU-A6H7 TCGA-MZ-A5BI 
       12.10        20.25        20.25         3.65        19.27         7.13 
TCGA-MZ-A6I9 TCGA-QK-A6IH TCGA-QK-A8Z8 TCGA-QK-AA3J TCGA-UF-A719 
       16.08        21.47         5.62        15.32        54.67 

$`7P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       20.48        65.59        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A4II 
       12.62         4.01        41.85        29.42        20.45        30.18 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG 
       27.95        11.54         7.10         5.69         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       33.70        50.20        44.98        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-4722 TCGA-CN-4723 TCGA-CN-4725 
        8.81         6.28        12.69        48.76        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
        4.67        51.29        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       52.14        57.11        12.99        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        73.61        13.05        42.02        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       12.39        71.31         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 
       11.57        12.49         8.52        52.08        50.07        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       48.00        23.90        47.44        28.04        19.07        34.13 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A497 
       32.22        38.89         3.68        17.42        32.48        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V 
       25.41        23.57        17.29        21.21         7.40        22.32 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
       16.57         4.41        12.07         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       24.39        20.88        48.20        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
        4.24        41.19        32.38        32.88        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       13.25         4.24        14.99        38.76        70.13        64.87 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       53.52        16.73        43.04        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       14.14        12.46        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
       37.87        26.27        58.42        50.01        39.52        34.52 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       18.54        16.90         6.02        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       47.18        39.16        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.09        24.95        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        29.82        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58         7.10         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       29.95        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        87.55        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
       60.49         7.07        43.23        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       90.12         2.14         9.70         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       21.90        26.43        11.24       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-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-7428 TCGA-CV-7432 TCGA-CV-7434 
       14.89        56.48       156.49        54.94        84.49         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
      153.86        16.64         6.38        22.19        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
      169.38       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       56.61         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
       19.92        22.52        10.42        10.55        18.84        34.36 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       16.14        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       12.36        28.77         7.63        22.59        24.95        13.94 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
       12.79        11.11        58.45        37.25        30.94        33.86 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       18.02        14.04        46.32        46.45        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       40.24        40.04        39.12        41.59        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       21.63         3.02        31.13        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       17.85        11.80        12.43        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.61        21.11        20.94         0.07        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
       21.93        27.48        27.48        14.66        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       22.85         0.36        13.84         4.27         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
        0.07        33.57         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       15.48        13.35        18.15        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A7D7 
       30.05         1.84        12.62         6.25        15.42        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        71.74        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
        7.30         9.34        12.72        18.64        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO 
        6.51        14.76        12.20        17.82         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       16.96         6.87        15.91         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A 
        3.12        13.55        13.25        20.35        64.80         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       49.51        48.03        49.45        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36        32.65         2.96        17.03        20.55        14.56 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             3.52              0.07 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            76.24            210.97 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            19.76             21.07 
[1] "3.5 - 76.2 (19.8)"  "0.1 - 211.0 (21.1)"
[1] "hr=" "1"  
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  7P LOSS MUTATED         1        3         4        14         1         1
  7P LOSS WILD-TYPE      26       73        78       239        11         0
D54V3, multiclass
           clus
vv          7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                 1                26
  STAGE II                3                73
  STAGE III               4                78
  STAGE IVA              14               239
  STAGE IVB               1                11
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7P LOSS MUTATED       3   9   6   7
  7P LOSS WILD-TYPE    47 128  94 166
D54V4, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1               3                47
  T2                  9               128
  T3                  6                94
  T4                  7               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
  7P LOSS MUTATED     5   6  13   0
  7P LOSS WILD-TYPE 174  62 155   8
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               5               174
  N1               6                62
  N2              13               155
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     9   1
  7P LOSS WILD-TYPE 180   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      9    1
  7P LOSS WILD-TYPE  180    0
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               9               180
  1               1                 0
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     9  20
  7P LOSS WILD-TYPE 131 362
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      9   20
  7P LOSS WILD-TYPE  131  362
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               9               131
  MALE                20               362
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     7  16
  7P LOSS WILD-TYPE 144 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      7   16
  7P LOSS WILD-TYPE  144  267
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                7               144
  YES              16               267
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  7P LOSS MUTATED                                      28
  7P LOSS WILD-TYPE                                   483
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  7P LOSS MUTATED                                                             0
  7P LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  7P LOSS MUTATED                                                     1
  7P LOSS WILD-TYPE                                                   9
D54V9, multiclass
                                                             clus
vv                                                            7P LOSS 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                       1
                                                             clus
vv                                                            7P LOSS 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                         9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V10, continuous
D54V11, continuous
D54V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     0
  7P LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                           2    26
  7P LOSS WILD-TYPE                        46   420
D54V13, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      2                46
  WHITE                                         26               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"
D54V14, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1  27
  7P LOSS WILD-TYPE  25 432
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   27
  7P LOSS WILD-TYPE   25  432
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO              27               432
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    21  19
  7Q LOSS WILD-TYPE 282 199
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               40               481 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               19               199 
$`7Q LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5559 TCGA-BA-A4IH TCGA-BA-A6DE 
       15.19        13.64        42.35        68.48        20.45        14.47 
TCGA-BB-4224 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-5359 TCGA-CN-5374 
        9.14        26.86        32.81        20.55        12.39        56.94 
TCGA-CN-6998 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-6220 TCGA-CR-6474 
       11.74        29.72        31.69        12.39        32.38        18.54 
TCGA-CR-7374 TCGA-CR-7398 TCGA-CV-5444 TCGA-CV-6003 TCGA-CV-6954 TCGA-CV-7180 
        0.99         5.13        80.12        54.74        65.82        10.75 
TCGA-CV-7429 TCGA-CV-7433 TCGA-CV-7438 TCGA-CX-7082 TCGA-D6-6823 TCGA-F7-8489 
        3.52        19.76         6.38        10.42        23.05        21.63 
TCGA-F7-A50G TCGA-HD-A6HZ TCGA-IQ-7632 TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MZ-A5BI 
       20.25         3.65        14.50        18.15        19.27         7.13 
TCGA-MZ-A6I9 TCGA-P3-A5QE TCGA-QK-A8Z9 TCGA-UF-A7JK 
       16.08        51.25        14.76        13.94 

$`7Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
        3.35         9.30        37.28         9.07        26.50        23.74 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 
       57.93        17.10        23.84        20.48        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       21.17        14.83         3.55        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       29.42        28.11        30.18        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
        5.69         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
       16.41         6.15       105.90         4.60         4.41        18.38 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
       22.42        36.72        33.70        50.20        44.98        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-4722 
       27.19        12.92         8.81         6.28        12.69        48.76 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       55.86        38.04         4.67        51.29        56.68        12.89 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       52.14        57.11        12.99        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 
       73.61        13.05        42.02        46.32         8.58        71.31 
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-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
        8.52        52.08        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
       47.44        28.04        19.07        34.13         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        9.24        52.08        11.08        10.45        32.22        35.05 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A498 
       38.89         3.68        17.42        32.48        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y 
       23.57        17.29        21.21         7.40        22.32        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
        4.24        41.19        32.88        46.95        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        4.24        14.99        38.76        70.13        64.87        53.52 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       16.73        43.04        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       11.61        23.24        29.36        33.60        29.49        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       12.46        31.23        84.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
       26.27        58.42        50.01        39.52        34.52        36.99 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       16.90         6.02        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        22.78        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       39.16        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       24.95        29.23        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       26.17        17.13        32.78        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       29.82        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        7.10         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-5966 TCGA-CV-5970 
      107.51        87.55        76.50        91.53        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      140.78        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
        6.08        53.95        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-7183 TCGA-CV-7235 TCGA-CV-7236 
       12.92        21.80        71.21       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-7428 
       34.09       100.57        14.89        56.48       156.49        54.94 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 
       16.27        84.49         7.17       153.86        16.64        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        21.01       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
        1.05        45.96         6.51        88.87        48.20        60.43 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       67.86         0.76        56.61         7.07        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       35.34         6.38        29.79         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       18.84        34.36        51.12        13.25        25.41         9.60 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
        2.53        16.14        11.44        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        11.11        58.45        37.25 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       30.94        33.86        18.02        14.04        46.32        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45        37.58        40.24        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       37.18        32.71         3.02        31.13        18.94        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
        0.46        17.85        11.80        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       15.16        15.06        13.61        21.11        20.94         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       28.47        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       22.03        12.66        22.85         0.36        13.84         4.27 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61G 
        6.90        34.75        15.95        38.53        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       37.41         0.07        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       19.04        15.48        13.35        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A7D7 
       30.05         1.84        12.62         6.25        15.42        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       29.92        15.78        71.74        10.85        36.82        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       19.00        75.55        18.97         2.04        29.00        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       16.01        13.15        21.07        21.21        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       21.47         9.34        12.72        18.64        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        6.51         5.62        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.72        16.96         6.87        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       13.71         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        49.51        48.03        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       74.47        17.95        24.30        55.43        29.46        18.05 
TCGA-UF-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 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.99              0.07 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            80.12            210.97 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           18.345            21.170 
[1] "1.0 - 80.1 (18.3)"  "0.1 - 211.0 (21.2)"
[1] "hr=" "1.4"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  7Q LOSS MUTATED         1        5         6        23         0         0
  7Q LOSS WILD-TYPE      26       71        76       230        12         1
D55V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                 1                26
  STAGE II                5                71
  STAGE III               6                76
  STAGE IVA              23               230
  STAGE IVB               0                12
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7Q LOSS MUTATED       1  16   5  13
  7Q LOSS WILD-TYPE    49 121  95 160
D55V4, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1               1                49
  T2                 16               121
  T3                  5                95
  T4                 13               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
  7Q LOSS MUTATED     8   8  16   0
  7Q LOSS WILD-TYPE 171  60 152   8
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               8               171
  N1               8                60
  N2              16               152
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    13   0
  7Q LOSS WILD-TYPE 176   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     13    0
  7Q LOSS WILD-TYPE  176    1
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              13               176
  1               0                 1
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    12  28
  7Q LOSS WILD-TYPE 128 354
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     12   28
  7Q LOSS WILD-TYPE  128  354
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              12               128
  MALE                28               354
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    13  20
  7Q LOSS WILD-TYPE 138 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     13   20
  7Q LOSS WILD-TYPE  138  263
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               13               138
  YES              20               263
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  7Q LOSS MUTATED                                      38
  7Q LOSS WILD-TYPE                                   473
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  7Q LOSS MUTATED                                                             0
  7Q LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  7Q LOSS MUTATED                                                     2
  7Q LOSS WILD-TYPE                                                   8
D55V9, multiclass
                                                             clus
vv                                                            7Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    38
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            7Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     473
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V10, continuous
D55V11, continuous
D55V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     0
  7Q LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           3    36
  7Q LOSS WILD-TYPE                        45   410
D55V13, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      3                45
  WHITE                                         36               410
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V14, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  37
  7Q LOSS WILD-TYPE  25 422
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   37
  7Q LOSS WILD-TYPE   25  422
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO              37               422
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    96  91
  8P LOSS WILD-TYPE 207 127
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              187               334 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               91               127 
$`8P LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5558 TCGA-BA-6870 
       15.19        13.64        26.50        23.74        65.59        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DI 
       12.62         4.01        41.85        27.95        14.47        11.05 
TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7871 TCGA-BB-A5HU TCGA-BB-A5HY 
        4.41        36.72        33.70        24.66        25.71        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 
       27.19         8.81         6.28        12.69        38.04         4.67 
TCGA-CN-4736 TCGA-CN-4742 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 
       12.99        13.05        71.31         8.32        11.54        11.57 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
        8.52        52.08        56.94        30.67        23.90        47.44 
TCGA-CN-6020 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49A 
        6.74        35.05        17.42        32.48        25.41        17.29 
TCGA-CN-A49B TCGA-CN-A640 TCGA-CN-A641 TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-5334 
       29.72         4.41        12.07         2.93        10.42         4.24 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       13.25         4.24        14.99        38.76        70.13        64.87 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB 
       53.52        16.73        41.88        77.56        44.48        29.36 
TCGA-CR-5247 TCGA-CR-6471 TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7364 
       11.77        39.52        18.54        11.64        12.46        47.18 
TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7380 
       35.84        24.95        29.23         0.99         9.17        19.92 
TCGA-CR-7388 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5441 
       27.06         5.95        35.41       129.21       108.95        87.55 
TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6940 
       17.92        86.83        62.43        90.12         9.70        26.43 
TCGA-CV-6942 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
      140.78         6.08        65.82         7.13         8.42        28.34 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7104 
        4.14        64.83       126.15         9.01         1.84        12.92 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7247 TCGA-CV-7248 
       77.16         4.73        47.47        36.00        18.97        17.13 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
        2.10        36.13        35.54         0.46        22.85        25.08 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7427 TCGA-CV-7434 TCGA-CV-7438 
        0.07        34.09       100.57       156.49         7.17         6.38 
TCGA-CV-7440 TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A460 TCGA-CV-A464 TCGA-CV-A465 
       22.19        35.47        45.96        60.43        56.61         7.07 
TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JZ TCGA-CX-7219 TCGA-D6-6517 
        5.98         6.48        28.01        23.47        34.36         9.60 
TCGA-D6-6825 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 
       16.14        17.72         7.63        12.79        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-A50I 
       33.86        18.02        46.32        37.58        32.71         3.02 
TCGA-F7-A50J TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-H7-8501 TCGA-H7-8502 
       31.13         0.46        17.85        11.80        15.16        15.06 
TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A633 TCGA-IQ-7630 TCGA-IQ-A61E 
       28.47        14.66        22.85        13.84        15.95        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        37.41         0.07        33.57         5.29        13.68 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A7BN TCGA-MZ-A6I9 
       19.04        15.48        18.15         7.96        15.42        16.08 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       15.78        71.74        47.01        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       21.21        21.47        21.07        19.73         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-TN-A7HJ 
       12.20        17.82        15.32         8.32        15.91        13.25 
TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JV 
        2.83        48.03        49.45        44.65        24.30         2.96 
TCGA-WA-A7H4 
       14.56 

$`8P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5153 
        3.35         9.30        37.28         9.07        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
       17.10        23.84        20.48        68.48        15.52        21.17 
TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA 
        3.55        29.42        28.11        20.45        30.18        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
        7.10         5.69         7.82         2.27        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 
       16.41         6.15       105.90         9.14         4.60        18.38 
TCGA-BB-7861 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 
       22.42        50.20        44.98        66.28        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A6UM TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4728 
       20.52        12.92        48.76        55.86        51.29        56.68 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 
       12.89        26.86        32.81        52.14        57.11        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 
       14.33        45.83        27.58        73.61        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-6010 
        8.58        12.39        16.21        11.84        12.49        50.07 
TCGA-CN-6012 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 
       48.00        28.04        19.07        34.13         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 
       52.08        11.08        10.45        32.22        38.89         3.68 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       11.74        35.01        23.57        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
       22.32        12.39        16.57         2.70        23.44        19.82 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       24.39        20.88        19.53        48.20        52.37        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-6218 
       54.58        70.45        62.37        45.99        11.21        41.19 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-7068 TCGA-CQ-7071 
       32.38        32.88        46.95        56.58        43.04        43.10 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       11.61        23.24        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       31.23        84.23        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       50.01        34.52        36.99        16.90         6.02        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       10.22        11.34         7.69        22.78        15.75         9.27 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7376 
       39.16        47.34        40.93         3.45         3.09        31.96 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 
       34.06        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        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        7.10         5.13        29.95        48.39       139.43        17.16 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 
       76.24        19.20        17.95       107.51        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       80.12        13.35        23.05        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 
       43.23        54.74        21.07         9.60         2.14         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6945 
       20.52         4.73        21.90        11.24        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6961 
       42.38        15.09        30.08        53.95        10.98         2.50 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7103 
      111.16        18.81        12.66         7.99         5.26        52.31 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7243 TCGA-CV-7245 
       21.80        71.21        10.75       130.88        31.36        26.20 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7263 TCGA-CV-7406 
       95.34         4.96        11.87        47.97        18.41        57.47 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7418 TCGA-CV-7424 
       17.85       210.97        89.33         9.67        25.94        14.89 
TCGA-CV-7425 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       56.48        54.94         3.52        16.27        84.49        19.76 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
      153.86        16.64        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 
      159.65         1.05         6.51        88.87        48.20        67.86 
TCGA-CV-A463 TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JU 
        0.76        15.25        35.34         6.38        29.79         3.62 
TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
       21.24        19.92        22.52        10.42        10.42        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6824 
       18.84        51.12        13.25        25.41        23.05         2.53 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK 
       11.44        18.67        24.95        25.32        12.36        28.77 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5629 
       22.59        24.95        13.94        12.10        11.11        30.94 
TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       14.04        46.45        20.45        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61S TCGA-F7-A61V 
       41.59        37.18        21.63        20.25        18.94        24.95 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       20.25        12.43        13.38        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8314 
        0.07        25.74        21.93        27.48        27.48        22.03 
TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
       12.66         0.36         4.27         3.65         6.90        34.75 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 
       38.53        14.50        13.84        13.35        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI 
       14.37        30.05         1.84        12.62         6.25         7.13 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 
       17.98        29.92        51.25        10.85        36.82        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-QK-A6IF 
       75.55        18.97         2.04        29.00        12.99        23.15 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-RS-A6TO 
        7.30         9.34        12.72        18.64         6.51        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
       16.96         6.87         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7JA 
       13.55        20.35        64.80        54.67        49.51        74.47 
TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       17.95        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       22.36        32.65        17.03        20.55 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.07              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           156.49            210.97 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           18.150            21.225 
[1] "0.1 - 156.5 (18.1)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.4"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  8P LOSS MUTATED        11       25        35        91         5         1
  8P LOSS WILD-TYPE      16       51        47       162         7         0
D56V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                11                16
  STAGE II               25                51
  STAGE III              35                47
  STAGE IVA              91               162
  STAGE IVB               5                 7
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  8P LOSS MUTATED      19  42  45  64
  8P LOSS WILD-TYPE    31  95  55 109
D56V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1              19                31
  T2                 42                95
  T3                 45                55
  T4                 64               109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8P LOSS MUTATED    60  28  65   2
  8P LOSS WILD-TYPE 119  40 103   6
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              60               119
  N1              28                40
  N2              65               103
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    72   1
  8P LOSS WILD-TYPE 117   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     72    1
  8P LOSS WILD-TYPE  117    0
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              72               117
  1               1                 0
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    59 128
  8P LOSS WILD-TYPE  81 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     59  128
  8P LOSS WILD-TYPE   81  254
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              59                81
  MALE               128               254
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    53 103
  8P LOSS WILD-TYPE  98 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     53  103
  8P LOSS WILD-TYPE   98  180
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               53                98
  YES             103               180
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  8P LOSS MUTATED                                     185
  8P LOSS WILD-TYPE                                   326
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  8P LOSS MUTATED                                                             0
  8P LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  8P LOSS MUTATED                                                     2
  8P LOSS WILD-TYPE                                                   8
D56V9, multiclass
                                                             clus
vv                                                            8P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   185
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            8P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     326
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V10, continuous
D56V11, continuous
D56V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  1     6
  8P LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                          21   156
  8P LOSS WILD-TYPE                        27   290
D56V13, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          6                 5
  BLACK OR AFRICAN AMERICAN                     21                27
  WHITE                                        156               290
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V14, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    11 162
  8P LOSS WILD-TYPE  15 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     11  162
  8P LOSS WILD-TYPE   15  297
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                15
  NOT HISPANIC OR LATINO             162               297
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    15  15
  8Q LOSS WILD-TYPE 288 203
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               30               491 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               15               203 
$`8Q LOSS MUTATED`
TCGA-BA-4076 TCGA-BA-A6D8 TCGA-BB-A6UO TCGA-CN-4726 TCGA-CN-5360 TCGA-CN-5367 
       13.64        27.95         8.81         4.67        71.31        11.57 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-A641 TCGA-CQ-6225 TCGA-CQ-7063 
       30.67        23.90        47.44        12.07        13.25        70.13 
TCGA-CQ-7064 TCGA-CR-6471 TCGA-CV-6956 TCGA-CV-7242 TCGA-CV-7261 TCGA-CV-7415 
       64.87        39.52         7.13        36.00        36.13        22.85 
TCGA-CV-7440 TCGA-CV-A45W TCGA-CV-A6JD TCGA-CV-A6JT TCGA-D6-A6EM TCGA-F7-A622 
       22.19        45.96         5.98        28.01         7.63        11.80 
TCGA-H7-8502 TCGA-IQ-7630 TCGA-MZ-A6I9 TCGA-P3-A6T7 TCGA-QK-A6VB TCGA-QK-AA3J 
       15.06        15.95        16.08        16.01        21.07        15.32 

$`8Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19         9.30        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       65.59        68.48        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-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-BA-A8YP TCGA-BB-4217 
        2.27        11.05        13.38        20.48        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
       36.72        33.70        50.20        44.98        66.28        24.66 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ 
       38.40        71.05        20.52        25.71        10.55        27.19 
TCGA-BB-A6UM TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
       12.92         6.28        12.69        48.76        55.86        38.04 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       51.29        56.68        12.89        26.86        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       57.11        12.99        20.55        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       73.61        13.05        42.02        46.32         8.58        12.39 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 
        8.32        16.21        11.54        11.84        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6017 TCGA-CN-6018 
       52.08        56.94        50.07        48.00        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       34.13         6.74         9.07         9.24        52.08        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        32.22        35.05        38.89         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       32.48        11.74        35.01        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       29.72        21.21         7.40        31.69        22.32        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
       16.57         4.41         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
        4.24        41.19        32.38        32.88        46.95        56.58 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        4.24        14.99        38.76        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
       50.01        34.52        36.99        18.54        16.90         6.02 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       22.78        15.75         9.27        47.18        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       40.93        35.84         3.45         3.09        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
        0.99        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       17.13        32.78        47.01        27.06        12.89        29.82 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58         7.10 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       17.16       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        87.55        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       140.78        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       15.09        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-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-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-7253 TCGA-CV-7254 
       18.97        17.13        95.34         4.96        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
        2.10        18.41        57.47        35.54        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
       89.33         9.67         0.46        25.08        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       34.09       100.57        14.89        56.48       156.49        54.94 
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-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       16.64         6.38        27.98        21.01       169.38       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-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-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       18.84        34.36        51.12        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
       23.05         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EO 
       25.32        17.72        12.36        28.77        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        11.11        58.45        37.25 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       30.94        33.86        18.02        14.04        46.32        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45        37.58        40.24        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       37.18        32.71        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 
       18.94        24.95         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        20.94         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       28.47        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       22.03        12.66        22.85         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        3.65         6.90        34.75        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        37.41         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
       13.84        19.04        15.48        13.35        18.15        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
        6.25        15.42         7.13        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T8 
       75.55        18.97         2.04        29.00        12.99        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       12.72        18.64        19.73         6.51         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       12.20        17.82         8.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
       15.91         7.10        32.45        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.25        20.35        64.80        54.67         2.83        49.51 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       48.03        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       32.65         2.96        17.03        20.55        14.56 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             4.67              0.07 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            71.31            210.97 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           18.575            20.940 
[1] "4.7 - 71.3 (18.6)"  "0.1 - 211.0 (20.9)"
[1] "hr=" "1.3"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  8Q LOSS MUTATED         2        5         5        15         0         0
  8Q LOSS WILD-TYPE      25       71        77       238        12         1
D57V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 2                25
  STAGE II                5                71
  STAGE III               5                77
  STAGE IVA              15               238
  STAGE IVB               0                12
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  8Q LOSS MUTATED       2   6   6  13
  8Q LOSS WILD-TYPE    48 131  94 160
D57V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1               2                48
  T2                  6               131
  T3                  6                94
  T4                 13               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
  8Q LOSS MUTATED    10   5   9   0
  8Q LOSS WILD-TYPE 169  63 159   8
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              10               169
  N1               5                63
  N2               9               159
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    14   0
  8Q LOSS WILD-TYPE 175   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     14    0
  8Q LOSS WILD-TYPE  175    1
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              14               175
  1               0                 1
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     7  23
  8Q LOSS WILD-TYPE 133 359
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      7   23
  8Q LOSS WILD-TYPE  133  359
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               7               133
  MALE                23               359
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     6  18
  8Q LOSS WILD-TYPE 145 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6   18
  8Q LOSS WILD-TYPE  145  265
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                6               145
  YES              18               265
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  8Q LOSS MUTATED                                      29
  8Q LOSS WILD-TYPE                                   482
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  8Q LOSS MUTATED                                                             0
  8Q LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  8Q LOSS MUTATED                                                     1
  8Q LOSS WILD-TYPE                                                   9
D57V9, multiclass
                                                             clus
vv                                                            8Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    29
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            8Q LOSS 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                         9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V10, continuous
D57V11, continuous
D57V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     0
  8Q LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           2    28
  8Q LOSS WILD-TYPE                        46   418
D57V13, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      2                46
  WHITE                                         28               418
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V14, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     2  27
  8Q LOSS WILD-TYPE  24 432
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2   27
  8Q LOSS WILD-TYPE   24  432
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                24
  NOT HISPANIC OR LATINO              27               432
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   107  79
  9P LOSS WILD-TYPE 196 139
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              186               335 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               79               139 
$`9P LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6869 
       15.19        13.64         9.07        17.10        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 
       14.83         3.55        12.62        41.85        29.42        27.95 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-7862 
        5.69        14.47        20.48        16.41         9.14        36.72 
TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HU TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 
       38.40        20.52        25.71        55.86         4.67        51.29 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4740 
       12.89        26.86        32.81        57.11        20.55        27.58 
TCGA-CN-5360 TCGA-CN-5373 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6024 
       71.31        52.08        19.07         6.74         9.07        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A63W 
       10.45        32.22        35.05        32.48        35.01        12.39 
TCGA-CN-A641 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6225 
       12.07        21.50         2.93        10.42        32.88        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 
        4.24        14.99        64.87        53.52        16.73        41.88 
TCGA-CQ-7072 TCGA-CQ-A4CB TCGA-CR-5247 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6477 
       77.56        29.36        11.77        34.52        18.54        16.90 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7372 
       12.46        22.78        47.18        39.16        40.93        24.95 
TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7401 
        0.99        17.13        27.06        29.82         5.13        35.41 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5444 
      139.43       129.21        76.24        19.20        17.95        80.12 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       86.83        48.59        43.23         9.60        90.12         2.14 
TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6960 TCGA-CV-7091 
       20.52        26.43        12.03        42.38        28.34       111.16 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 
       12.66         5.26        52.31        12.92        21.80        10.75 
TCGA-CV-7236 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7252 TCGA-CV-7255 
        4.73        36.00        31.36        26.20         4.96         2.10 
TCGA-CV-7263 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
       18.41         9.67        22.85         0.07        34.09       100.57 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45Y 
       16.27        84.49         7.17       153.86        22.19        88.87 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A6JU TCGA-CX-7082 TCGA-CX-7086 
       60.43        67.86        56.61         3.62        10.42        18.84 
TCGA-CX-A4AQ TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       51.12        23.05        11.44        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5629 
       12.36        24.95        13.94        12.79        11.11        30.94 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A61W 
       18.02        14.04        39.12        37.18         3.02         0.46 
TCGA-F7-A623 TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8635 TCGA-HD-A633 
       20.25        21.11        28.47        25.74        22.85        13.84 
TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A6SG TCGA-IQ-A6SH 
        3.65        15.95        11.84        33.57        19.04        15.48 
TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       18.15         7.96         1.84         7.13        17.98        15.78 
TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IH 
       47.01        18.97         2.04        13.15        21.07        21.47 
TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA 
       12.72        21.07        19.73         6.51         5.62        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-T3-A92M TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       17.82        15.32        13.71        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF 
       49.51        48.03        49.45        74.47        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ 
       29.46        18.05        13.94        22.36        17.03        20.55 

$`9P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
        3.35         9.30        37.28        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6873 
       57.93        23.84        20.48        65.59        68.48         4.01 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DF 
       28.11        20.45        30.18        11.54         7.10         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 
        2.27        11.05        13.38         6.15       105.90         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
        4.41        18.38        22.42        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       66.28        24.66        71.05        10.55        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4728 
        8.81         6.28        12.69        48.76        38.04        56.68 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 
       52.14        12.99        14.33        45.83        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5364 
       42.02        46.32         8.58        12.39         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5374 
       11.54        11.84        11.57        12.49         8.52        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       34.13         9.24        52.08        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       11.74        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 
        7.40        31.69        22.32        16.57         4.41         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       23.44        19.82        24.39        20.88        19.53        48.20 
TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
       52.37        54.58        70.45        62.37        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6229 
        4.24        41.19        32.38        46.95        56.58        38.76 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       70.13        43.04        43.10        44.48        11.61        23.24 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       36.99         6.02        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 
        7.69        15.75         9.27        47.34        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
        3.09        29.23        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
       26.17        32.78        47.01        12.89        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7402 
       32.65        44.25        30.58         7.10         5.95        29.95 
TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       48.39        17.16       108.95       107.51        87.55        76.50 
TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5977 TCGA-CV-5978 
       91.53        17.92        13.35        23.05        60.49         7.07 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 
       54.74        21.07        62.43         9.70         5.46         4.73 
TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 
       21.90        11.24       140.78        19.79        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-7095 TCGA-CV-7099 
        2.50         4.14        64.83       126.15        18.81         7.99 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        9.01         1.84        71.21       130.88        77.16        47.47 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 
       18.97        17.13        95.34        11.87        47.97        36.13 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 
       57.47        35.54        17.85       210.97        89.33         0.46 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       25.08        25.94        14.89        56.48       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7433 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P 
        3.52        19.76        16.64         6.38        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
      169.38       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
        6.51        48.20         0.76         7.07        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY 
       35.34         6.38        29.79         6.48        28.01        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7219 
       23.47        19.92        22.52        10.42        10.55        34.36 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 
       13.25        25.41         9.60         2.53        16.14        18.67 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EQ TCGA-DQ-5624 TCGA-DQ-5625 
       28.77         7.63        22.59        12.10        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       33.86        46.32        46.45        20.45        37.58        40.24 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J 
       40.04        41.59        32.71        21.63        20.25        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 
       18.94        24.95        17.85        11.80        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7831 
       15.16        15.06        13.61        20.94         0.07        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 
       27.48        27.48        14.66        22.03        12.66         0.36 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        4.27         6.90        34.75        38.53        14.50        37.71 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
       37.41         0.07         5.29        13.68        13.84        13.35 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G 
       19.27        10.75        14.37        30.05        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       15.42        16.08        29.92        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       36.82        19.00        75.55        29.00        12.99        16.01 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z9 
       21.21        23.15         7.30         9.34        18.64        14.76 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
        8.32        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A7J9 
       32.45         3.12        13.55        13.25        20.35        44.65 
TCGA-UF-A7JC TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UF-A7JV TCGA-WA-A7H4 
       17.95        20.75        32.65         2.96        14.56 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.07              0.07 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           153.86            210.97 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            20.50             21.21 
[1] "0.1 - 153.9 (20.5)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.1"
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  9P LOSS MUTATED        10       25        28        94         4         1
  9P LOSS WILD-TYPE      17       51        54       159         8         0
D58V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                10                17
  STAGE II               25                51
  STAGE III              28                54
  STAGE IVA              94               159
  STAGE IVB               4                 8
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9P LOSS MUTATED      18  49  32  67
  9P LOSS WILD-TYPE    32  88  68 106
D58V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1              18                32
  T2                 49                88
  T3                 32                68
  T4                 67               106
[1] 4 2
[1] 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
  9P LOSS MUTATED    67  27  61   2
  9P LOSS WILD-TYPE 112  41 107   6
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              67               112
  N1              27                41
  N2              61               107
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    67   1
  9P LOSS WILD-TYPE 122   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     67    1
  9P LOSS WILD-TYPE  122    0
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              67               122
  1               1                 0
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    43 143
  9P LOSS WILD-TYPE  97 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     43  143
  9P LOSS WILD-TYPE   97  239
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              43                97
  MALE               143               239
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    52  96
  9P LOSS WILD-TYPE  99 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     52   96
  9P LOSS WILD-TYPE   99  187
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               52                99
  YES              96               187
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  9P LOSS MUTATED                                     183
  9P LOSS WILD-TYPE                                   328
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  9P LOSS MUTATED                                                             0
  9P LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  9P LOSS MUTATED                                                     3
  9P LOSS WILD-TYPE                                                   7
D58V9, multiclass
                                                             clus
vv                                                            9P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   183
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       3
                                                             clus
vv                                                            9P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     328
  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"
D58V10, continuous
D58V11, continuous
D58V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  1     3
  9P LOSS WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                          25   150
  9P LOSS WILD-TYPE                        23   296
D58V13, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                     25                23
  WHITE                                        150               296
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V14, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    10 156
  9P LOSS WILD-TYPE  16 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     10  156
  9P LOSS WILD-TYPE   16  303
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                  10                16
  NOT HISPANIC OR LATINO             156               303
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    50  37
  9Q LOSS WILD-TYPE 253 181
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               87               434 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               37               181 
$`9Q LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 
       15.19        14.83         3.55        41.85        29.42        27.95 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-6018 TCGA-CN-6020 
       20.52        25.71        20.55        27.58        19.07         6.74 
TCGA-CN-6024 TCGA-CN-A63W TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7067 
       11.08        12.39        32.88         4.24        14.99        16.73 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CR-5247 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-7364 
       41.88        77.56        11.77        34.52        18.54        47.18 
TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5435 
       39.16        24.95         0.99        29.82       139.43        76.24 
TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6933 
       19.20        87.55        86.83        43.23         9.60        90.12 
TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6945 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
       20.52        26.43        12.03       111.16        18.81        12.66 
TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7243 TCGA-CV-7252 TCGA-CV-7255 TCGA-CV-7413 
        5.26        10.75        31.36         4.96         2.10         9.67 
TCGA-CV-7423 TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A464 TCGA-CV-A6JU 
      100.57        16.27       153.86        22.19        56.61         3.62 
TCGA-CX-7082 TCGA-D6-6823 TCGA-D6-A6EP TCGA-DQ-5631 TCGA-F7-7848 TCGA-F7-A50I 
       10.42        23.05        13.94        18.02        37.18         3.02 
TCGA-F7-A623 TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-A61G 
       20.25        21.11        28.47        22.85         3.65        11.84 
TCGA-IQ-A61J TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66T TCGA-MT-A67D TCGA-MZ-A5BI 
       33.57        19.04        15.48        18.15         1.84         7.13 
TCGA-P3-A5Q6 TCGA-P3-A6T3 TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 
       15.78        18.97        12.72        21.07        19.73         5.62 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7JD TCGA-UF-A7JF 
       12.20        17.82        54.67        49.51        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       29.46        18.05        13.94 

$`9Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35         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-6872 TCGA-BA-6873 
       65.59        68.48        15.52        21.17        12.62         4.01 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       28.11        20.45        30.18        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.60         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
       18.38        22.42        36.72        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A5HY TCGA-BB-A5HZ 
       66.28        24.66        38.40        71.05        10.55        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
       12.92         8.81         6.28        12.69        48.76        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       38.04         4.67        51.29        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 
       32.81        52.14        57.11        12.99        14.33        45.83 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       73.61        13.05        42.02        46.32         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       71.31         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
       12.49         8.52        52.08        56.94        50.07        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6021 
       48.00        23.90        47.44        28.04        34.13         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
        9.24        52.08        10.45        32.22        35.05        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        3.68        17.42        32.48        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       23.57        17.29        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       22.32        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       19.82        24.39        20.88        19.53        48.20        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 
       10.42        11.21         4.24        41.19        32.38        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
       56.58        13.25        38.76        70.13        64.87        53.52 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       43.04        43.10        44.48        11.61        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        16.90         6.02        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 
       47.34        40.93        35.84         3.45         3.09        29.23 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
       32.78        47.01        27.06        12.89        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58         7.10         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       35.41        29.95        48.39        17.16       129.21       108.95 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       17.95       107.51        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 
       13.35        23.05        48.59        60.49         7.07        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 
       21.07        62.43         2.14         9.70         5.46         4.73 
TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6950 
       21.90        11.24       140.78        19.79        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-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        7.99         9.01         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       71.21       130.88        77.16         4.73        47.47        36.00 
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-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-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
       89.33         0.46        22.85        25.08        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 
       34.09        14.89        56.48       156.49        54.94         3.52 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O 
       84.49        19.76         7.17        16.64         6.38        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       21.01       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
       45.96         6.51        88.87        48.20        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
        0.76         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
       29.79         6.48        28.01        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ 
       22.52        10.42        10.55        18.84        34.36        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       13.25        25.41         9.60         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        22.59        24.95        12.10        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 
       58.45        37.25        30.94        33.86        14.04        46.32 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       46.45        20.45        37.58        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S 
       41.59        32.71        21.63        20.25        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 
       24.95         0.46        17.85        11.80        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 
       15.16        15.06        13.61        20.94         0.07        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
       21.93        27.48        27.48        14.66        22.03        12.66 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-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-A61H TCGA-IQ-A61I TCGA-IQ-A61K 
       38.53        14.50        37.71        37.41         0.07         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       13.68        13.84        13.35        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 
        7.96        30.05        12.62         6.25        15.42        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       17.98        29.92        71.74        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       47.01        19.00        75.55         2.04        29.00        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       16.01        13.15        21.07        21.21        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-AA3J 
       21.47         9.34        18.64         6.51        14.76        15.32 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
        8.32        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       32.45        13.71         3.12        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       64.80         2.83        48.03        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       17.95        20.75        22.36        32.65         2.96        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.99              0.07 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           153.86            210.97 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            19.20             21.21 
[1] "1.0 - 153.9 (19.2)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1"  
D59V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  9Q LOSS MUTATED         4       14        16        41         1         1
  9Q LOSS WILD-TYPE      23       62        66       212        11         0
D59V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 4                23
  STAGE II               14                62
  STAGE III              16                66
  STAGE IVA              41               212
  STAGE IVB               1                11
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9Q LOSS MUTATED       7  29  13  30
  9Q LOSS WILD-TYPE    43 108  87 143
D59V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1               7                43
  T2                 29               108
  T3                 13                87
  T4                 30               143
[1] 4 2
[1] 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
  9Q LOSS MUTATED    31  14  27   0
  9Q LOSS WILD-TYPE 148  54 141   8
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              31               148
  N1              14                54
  N2              27               141
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    34   1
  9Q LOSS WILD-TYPE 155   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     34    1
  9Q LOSS WILD-TYPE  155    0
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              34               155
  1               1                 0
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    22  65
  9Q LOSS WILD-TYPE 118 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     22   65
  9Q LOSS WILD-TYPE  118  317
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              22               118
  MALE                65               317
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    24  45
  9Q LOSS WILD-TYPE 127 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     24   45
  9Q LOSS WILD-TYPE  127  238
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               24               127
  YES              45               238
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  9Q LOSS MUTATED                                      87
  9Q LOSS WILD-TYPE                                   424
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  9Q LOSS MUTATED                                                             0
  9Q LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  9Q LOSS MUTATED                                                     0
  9Q LOSS WILD-TYPE                                                  10
D59V9, multiclass
                                                             clus
vv                                                            9Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    87
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            9Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     424
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, continuous
D59V11, continuous
D59V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     0
  9Q LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                          13    68
  9Q LOSS WILD-TYPE                        35   378
D59V13, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                     13                35
  WHITE                                         68               378
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V14, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     7  69
  9Q LOSS WILD-TYPE  19 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      7   69
  9Q LOSS WILD-TYPE   19  390
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                19
  NOT HISPANIC OR LATINO              69               390
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    81  75
  10P LOSS WILD-TYPE 222 143
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               156                365 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                75                143 
$`10P LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 
        9.30         9.07        42.35        68.48        15.52        14.83 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DI TCGA-BA-A8YP TCGA-BB-7870 
        4.01        29.42        27.95        11.05        16.41        66.28 
TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4723 
       38.40        20.52        25.71        10.55         6.28        55.86 
TCGA-CN-4725 TCGA-CN-4737 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
       38.04        20.55        42.02        12.39        71.31         8.32 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       56.94        30.67        48.00        19.07        34.13         6.74 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A49A TCGA-CN-A63U 
       11.08        10.45        17.42        11.74        17.29        31.69 
TCGA-CN-A63W TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5326 TCGA-CQ-6223 TCGA-CQ-6224 
       12.39        19.53        48.20         2.93        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C7 
       13.25        14.99        64.87        41.88        77.56        11.61 
TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       18.54        11.64        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
        3.45        24.95        29.23        19.92        26.17        17.13 
TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7398 TCGA-CV-5435 TCGA-CV-5444 TCGA-CV-5966 
       47.01        12.89         5.13        76.24        80.12        17.92 
TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       60.49        43.23         5.46        26.43        11.24       140.78 
TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7090 
       15.09         6.08        65.82         2.50         4.14       126.15 
TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7242 
       12.66         9.01         5.26         1.84        71.21        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7263 
       31.36        26.20        18.97        17.13         4.96        18.41 
TCGA-CV-7406 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 
       57.47         0.46        25.94       100.57        14.89        54.94 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A465 
       84.49         7.17         6.38        45.96         6.51         7.07 
TCGA-CV-A6JD TCGA-CV-A6JT TCGA-CV-A6K1 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 
        5.98        28.01        22.52        34.36         9.60        23.05 
TCGA-D6-6826 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5629 TCGA-DQ-5631 
       11.44        12.36        13.94        12.10        30.94        18.02 
TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       14.04        46.45        40.24        21.63        20.25         3.02 
TCGA-F7-A61V TCGA-F7-A620 TCGA-HD-7831 TCGA-HD-8635 TCGA-HD-A633 TCGA-IQ-A61G 
       24.95        17.85        21.93        22.85        13.84        11.84 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51X 
       37.41        33.57         5.29        18.15        19.27         7.96 
TCGA-MZ-A6I9 TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       16.08        47.01        75.55        18.97         2.04        29.00 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A8Z9 
       13.15        21.07        23.15        21.47        18.64        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-T2-A6X0 TCGA-TN-A7HJ TCGA-UF-A718 
       12.20        17.82         8.32         7.10        13.25        64.80 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7JC TCGA-UF-A7JD TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.83        49.51        17.95        24.30        20.55        14.56 

$`10P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
        3.35        15.19        13.64        37.28        26.50        23.74 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 
       57.93        17.10        23.84        20.48        65.59        21.17 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        3.55        12.62        41.85        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-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       13.38        20.48         6.15       105.90         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.41        18.38        22.42        36.72        33.70        50.20 
TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       44.98        24.66        71.05        27.19        12.92         8.81 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       12.69        48.76         4.67        51.29        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
       26.86        32.81        52.14        57.11        12.99        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 
       45.83        27.58        73.61        13.05        46.32         8.58 
TCGA-CN-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-6010 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6021 
       52.08        50.07        23.90        47.44        28.04         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
        9.24        52.08        32.22        35.05        38.89         3.68 
TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C 
       32.48        35.01        25.41        23.57        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
        7.40        22.32        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 
       23.44        19.82        24.39        20.88        52.37        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6229 
        4.24        41.19        32.38        32.88         4.24        38.76 
TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 
       70.13        53.52        16.73        43.04        43.10        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 
       58.42        50.01        39.52        34.52        36.99        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-7371 TCGA-CR-7374 
       22.78        15.75         9.27        47.18         3.09         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7390 
       31.96         9.17        34.06        32.78        27.06        29.82 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58         7.10 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-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-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      129.21       108.95        19.20        17.95       107.51        87.55 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       76.50        91.53        13.35        23.05        86.83        48.59 
TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
        7.07        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6943 
        2.14         9.70        20.52         4.73        21.90        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 
       12.03        42.38        30.08        53.95        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 
        8.42        28.34        64.83       111.16        18.81         7.99 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
       52.31        12.92        21.80        10.75       130.88        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
        4.73        47.47        95.34        11.87        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       36.13        35.54        17.85       210.97        89.33         9.67 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7427 
       22.85        25.08         0.07        34.09        56.48       156.49 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 
        3.52        16.27        19.76       153.86        16.64        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        21.01       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        1.05        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       56.61        15.25        35.34         6.38        29.79         6.48 
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-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6824 
       10.55        18.84        51.12        13.25        25.41         2.53 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK 
       16.14        18.67        24.95        25.32        17.72        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
        7.63        22.59        24.95        12.79        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       37.25        33.86        46.32        20.45        37.58        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50J TCGA-F7-A61S 
       39.12        41.59        37.18        32.71        31.13        18.94 
TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
        0.46        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       15.06        13.61        21.11        20.94         0.07        28.47 
TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
       25.74        27.48        27.48        14.66        22.03        12.66 
TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
        0.36         4.27         3.65         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61L TCGA-IQ-A61O 
       38.53        14.50        37.71         0.07        13.68        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A 
       19.04        15.48        13.35        10.75        14.37        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A7D7 
        1.84        12.62         6.25        15.42         7.13        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        71.74        51.25        10.85        36.82 
TCGA-P3-A6T0 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6II 
       19.00        12.99        16.01        21.21         7.30         9.34 
TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-AA3J 
       12.72        21.07        19.73         6.51         5.62        15.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-T3-A92M 
       12.72        16.96         6.87        15.91        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A71E 
        3.12        13.55        20.35        54.67        48.03        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       44.65        74.47        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       20.75        22.36        32.65         2.96        17.03 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.46               0.07 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            140.78             210.97 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             19.02              21.24 
[1] "0.5 - 140.8 (19.0)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.4"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  10P LOSS MUTATED         5       23        20        84         5         0
  10P LOSS WILD-TYPE      22       53        62       169         7         1
D60V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  5                 22
  STAGE II                23                 53
  STAGE III               20                 62
  STAGE IVA               84                169
  STAGE IVB                5                  7
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10P LOSS MUTATED       8  42  28  61
  10P LOSS WILD-TYPE    42  95  72 112
D60V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1                8                 42
  T2                  42                 95
  T3                  28                 72
  T4                  61                112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10P LOSS MUTATED    49  20  57   2
  10P LOSS WILD-TYPE 130  48 111   6
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               49                130
  N1               20                 48
  N2               57                111
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    55   0
  10P LOSS WILD-TYPE 134   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     55    0
  10P LOSS WILD-TYPE  134    1
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               55                134
  1                0                  1
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    32 124
  10P LOSS WILD-TYPE 108 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     32  124
  10P LOSS WILD-TYPE  108  258
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               32                108
  MALE                124                258
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    45  89
  10P LOSS WILD-TYPE 106 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     45   89
  10P LOSS WILD-TYPE  106  194
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                45                106
  YES               89                194
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  10P LOSS MUTATED                                     156
  10P LOSS WILD-TYPE                                   355
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  10P LOSS MUTATED                                                             0
  10P LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  10P LOSS MUTATED                                                     0
  10P LOSS WILD-TYPE                                                  10
D60V9, multiclass
                                                             clus
vv                                                            10P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    156
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            10P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      355
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V10, continuous
D60V11, continuous
D60V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     4
  10P LOSS WILD-TYPE                                2     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                          22   129
  10P LOSS WILD-TYPE                        26   317
D60V13, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           4                  7
  BLACK OR AFRICAN AMERICAN                      22                 26
  WHITE                                         129                317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V14, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     7 138
  10P LOSS WILD-TYPE  19 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      7  138
  10P LOSS WILD-TYPE   19  321
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                 19
  NOT HISPANIC OR LATINO              138                321
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    62  51
  10Q LOSS WILD-TYPE 241 167
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               113                408 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                51                167 
$`10Q LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5559 
       15.19         9.30         9.07        42.35        17.10        68.48 
TCGA-BA-A6D8 TCGA-BA-A6DI TCGA-BA-A8YP TCGA-BB-7870 TCGA-BB-8601 TCGA-C9-A47Z 
       27.95        11.05        16.41        66.28        20.52         6.28 
TCGA-CN-4725 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6012 
       38.04        42.02        12.39        71.31        56.94        48.00 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6024 TCGA-CN-6998 TCGA-CN-A49A 
       19.07        34.13         6.74        11.08        11.74        17.29 
TCGA-CN-A63U TCGA-CN-A6V7 TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 
       31.69        19.53        10.42        56.58        13.25        14.99 
TCGA-CQ-7064 TCGA-CQ-7072 TCGA-CR-6470 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6484 
       64.87        77.56        50.01        18.54        16.90        11.64 
TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 
       39.16        40.93        35.84         3.45        24.95        29.23 
TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7398 TCGA-CV-5431 TCGA-CV-5432 
       17.13        47.01        12.89         5.13        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6936 TCGA-CV-6940 
      108.95        76.24        60.49        43.23         5.46        26.43 
TCGA-CV-6941 TCGA-CV-6950 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7097 
       11.24        15.09         2.50         4.14       126.15        12.66 
TCGA-CV-7101 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7263 TCGA-CV-7406 
        5.26        36.00        26.20        17.13        18.41        57.47 
TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-7438 
        0.46        25.94       100.57        14.89        84.49         6.38 
TCGA-CV-A45W TCGA-CV-A465 TCGA-D6-6823 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-D6-A6EQ 
       45.96         7.07        23.05        12.36        13.94        12.10 
TCGA-D6-A6ES TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7593 
       12.79        18.02        14.04        46.32        46.45        40.24 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A6SG TCGA-KU-A66T 
       11.84        37.41        33.57         5.29        19.04        18.15 
TCGA-KU-A6H7 TCGA-MT-A51X TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A6T0 
       19.27         7.96        15.42        16.08        17.98        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z9 
       75.55        29.00        21.47        18.64        21.07        14.76 
TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-TN-A7HJ TCGA-UF-A718 
       12.20         8.32        15.91         7.10        13.25        64.80 
TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-WA-A7GZ TCGA-WA-A7H4 
       49.51        44.65        17.95        20.55        14.56 

$`10Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 
        3.35        13.64        37.28        26.50        23.74        57.93 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       23.84        20.48        65.59        15.52        21.17        14.83 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG 
        3.55        12.62         4.01        41.85        29.42        28.11 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       20.45        30.18        11.54         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 
        7.82         2.27        13.38        20.48         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       33.70        50.20        44.98        24.66        38.40        71.05 
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-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       48.76        55.86         4.67        51.29        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       26.86        32.81        52.14        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 
       14.33        45.83        27.58        73.61        13.05        46.32 
TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        8.58         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 
       12.49         8.52        52.08        50.07        30.67        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 
       47.44        28.04         9.07         9.24        52.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       32.22        35.05        38.89         3.68        17.42        32.48 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       35.01        25.41        23.57        29.72        21.21         7.40 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5323 TCGA-CQ-5324 
       23.44        19.82        24.39        20.88        48.20        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 
       11.21         4.24        41.19        32.38        32.88        46.95 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        4.24        38.76        70.13        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        44.48        11.61        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6471 
       11.77        54.67        37.87        26.27        58.42        39.52 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       34.52        36.99         6.02        11.90        10.22        11.34 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        22.78        15.75         9.27        47.18 
TCGA-CR-7367 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       47.34         3.09         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 
       19.92        26.17        32.78        27.06        29.82        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 
       46.85        32.65        44.25        30.58         7.10         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5436 TCGA-CV-5439 
       35.41        29.95        48.39       139.43        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      107.51        87.55        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-6003 
       13.35        23.05        86.83        48.59         7.07        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-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       20.52         4.73        21.90       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       42.38        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 
        7.13         8.42        28.34        64.83       111.16        18.81 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        7.99         9.01         1.84        52.31        12.92        21.80 
TCGA-CV-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-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       31.36        18.97        95.34         4.96        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
        2.10        36.13        35.54        17.85       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7425 
        9.67        22.85        25.08         0.07        34.09        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 
      156.49        54.94         3.52        16.27        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
      153.86        16.64        22.19        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y 
      180.16       159.65        35.47         1.05         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 
       48.20        60.43        67.86         0.76        56.61        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 
       10.42        10.55        18.84        34.36        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
       25.41         9.60         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN 
       24.95        25.32        17.72        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
       24.95        11.11        58.45        37.25        30.94        33.86 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       20.45        37.58        40.04        39.12        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       24.95         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
        4.27         3.65         6.90        34.75        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SH 
       14.50        37.71         0.07        13.68        13.84        15.48 
TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       13.35        10.75        14.37        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MZ-A5BI TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
        6.25         7.13        29.92        15.78        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 
       10.85        36.82        47.01        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        21.21        23.15         7.30 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB 
        9.34        12.72        19.73         6.51         5.62        17.82 
TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-T3-A92M 
       15.32        12.72        16.96         6.87        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71D 
        3.12        13.55        20.35        54.67         2.83        48.03 
TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       49.45        74.47        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       13.94        20.75        22.36        32.65         2.96        17.03 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.46               0.07 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            129.21             210.97 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             18.54              21.37 
[1] "0.5 - 129.2 (18.5)" "0.1 - 211.0 (21.4)"
[1] "hr=" "1.1"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  10Q LOSS MUTATED         3       18        14        59         3         0
  10Q LOSS WILD-TYPE      24       58        68       194         9         1
D61V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  3                 24
  STAGE II                18                 58
  STAGE III               14                 68
  STAGE IVA               59                194
  STAGE IVB                3                  9
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10Q LOSS MUTATED       5  31  25  38
  10Q LOSS WILD-TYPE    45 106  75 135
D61V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1                5                 45
  T2                  31                106
  T3                  25                 75
  T4                  38                135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10Q LOSS MUTATED    40   8  42   1
  10Q LOSS WILD-TYPE 139  60 126   7
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               40                139
  N1                8                 60
  N2               42                126
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    43   0
  10Q LOSS WILD-TYPE 146   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     43    0
  10Q LOSS WILD-TYPE  146    1
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               43                146
  1                0                  1
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    21  92
  10Q LOSS WILD-TYPE 119 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     21   92
  10Q LOSS WILD-TYPE  119  290
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               21                119
  MALE                 92                290
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    29  68
  10Q LOSS WILD-TYPE 122 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     29   68
  10Q LOSS WILD-TYPE  122  215
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                29                122
  YES               68                215
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  10Q LOSS MUTATED                                     113
  10Q LOSS WILD-TYPE                                   398
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  10Q LOSS MUTATED                                                             0
  10Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  10Q LOSS MUTATED                                                     0
  10Q LOSS WILD-TYPE                                                  10
D61V9, multiclass
                                                             clus
vv                                                            10Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    113
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            10Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      398
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, continuous
D61V11, continuous
D61V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     3
  10Q LOSS WILD-TYPE                                2     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                          16    94
  10Q LOSS WILD-TYPE                        32   352
D61V13, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                      16                 32
  WHITE                                          94                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"
D61V14, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     7  98
  10Q LOSS WILD-TYPE  19 361
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      7   98
  10Q LOSS WILD-TYPE   19  361
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                 19
  NOT HISPANIC OR LATINO               98                361
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    80  61
  11P LOSS WILD-TYPE 223 157
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               141                380 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                61                157 
$`11P LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       15.19         9.07         3.55        12.62         4.01        41.85 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BB-4227 
       28.11        20.45        30.18         5.69        14.47         4.41 
TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-A6UO TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 
       66.28        71.05         8.81        56.68        12.89        57.11 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 
       45.83        27.58        46.32        12.39         8.32        11.54 
TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6021 
       11.84        56.94        30.67        48.00         6.74         9.07 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 
       10.45        32.22        35.05        38.89         3.68        11.74 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63Y TCGA-CN-A6V7 
       25.41        17.29        21.21        31.69        16.57        19.53 
TCGA-CQ-5332 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-A4CB TCGA-CQ-A4CI TCGA-CR-5247 
       10.42         4.24        14.99        29.36        31.23        11.77 
TCGA-CR-5248 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-7370 TCGA-CR-7374 
       54.67        16.90         6.02        10.22         3.45         0.99 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 
       17.13        32.78        27.06         5.95        48.39        17.16 
TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6441 
      129.21        17.95       107.51        60.49         7.07         9.60 
TCGA-CV-6933 TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6948 
       90.12         5.46        26.43       140.78        12.03        42.38 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 
      111.16        18.81        12.66         5.26         1.84        77.16 
TCGA-CV-7245 TCGA-CV-7253 TCGA-CV-7263 TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7423 
       26.20        11.87        18.41        22.85         0.07       100.57 
TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A6JU 
       16.27        19.76       153.86       180.16        88.87         3.62 
TCGA-CX-7082 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6ES TCGA-DQ-5624 
       10.42        24.95        17.72        12.36        12.79        58.45 
TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       30.94        46.32        40.04        41.59        37.18        32.71 
TCGA-F7-A50I TCGA-F7-A623 TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 
        3.02        20.25        13.61        28.47        21.93        27.48 
TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61J TCGA-KU-A66T TCGA-MT-A51W 
       22.85         3.65        11.84        33.57        18.15        14.37 
TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q6 
        1.84         6.25        15.42         7.13        16.08        15.78 
TCGA-P3-A6SW TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A6IH TCGA-QK-A8Z7 TCGA-QK-A8Z9 
       36.82         2.04        13.15        21.47         6.51        14.76 
TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-T3-A92N TCGA-TN-A7HJ 
       12.20        15.32         8.32        15.91         3.12        13.25 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       64.80        54.67         2.83        49.51        48.03        49.45 
TCGA-UF-A7JA TCGA-UF-A7JH TCGA-UF-A7JS 
       74.47        29.46        22.36 

$`11P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
        3.35         9.30        13.64        37.28        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       42.35        57.93        17.10        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A6D8 
       68.48        15.52        21.17        14.83        29.42        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
       11.54         7.10         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       20.48        16.41         6.15       105.90         9.14         4.60 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
       18.38        22.42        36.72        33.70        50.20        44.98 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ 
       24.66        38.40        20.52        25.71        10.55        27.19 
TCGA-BB-A6UM TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
       12.92         6.28        12.69        48.76        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
        4.67        51.29        26.86        32.81        52.14        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
       20.55        14.33        73.61        13.05        42.02         8.58 
TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       71.31        16.21        11.57        12.49         8.52        52.08 
TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       50.07        23.90        47.44        28.04        19.07        34.13 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A497 
        9.24        52.08        11.08        17.42        32.48        35.01 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 
       23.57        29.72         7.40        22.32        12.39         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        23.44        19.82        24.39        20.88 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       62.37        45.99        11.21         4.24        41.19        32.38 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7063 
       32.88        46.95        56.58        13.25        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
       64.87        53.52        16.73        43.04        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE 
       77.56        44.48        11.61        23.24        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       14.14        12.46        84.23        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 
       50.01        39.52        34.52        36.99        18.54        11.90 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       11.34        11.64         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        3.09        24.95        29.23        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       19.92        26.17        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 
       46.85        32.65        44.25        30.58         7.10         5.13 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
       35.41        29.95       139.43       108.95        76.24        19.20 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       87.55        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       23.05        86.83        48.59        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
       62.43         2.14         9.70        20.52         4.73        21.90 
TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       11.24        19.79        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-7099 TCGA-CV-7100 TCGA-CV-7103 
        4.14        64.83       126.15         7.99         9.01        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 
       12.92        21.80        71.21        10.75       130.88         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-7252 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 
        4.96        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-7416 
       17.85       210.97        89.33         9.67         0.46        25.08 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       25.94        34.09        14.89        56.48       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
        3.52        84.49         7.17        16.64         6.38        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       27.98        21.01       169.38       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
       45.96         6.51        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       56.61         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
       29.79         6.48        28.01        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ 
       22.52        10.42        10.55        18.84        34.36        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN 
       11.44        18.67        25.32        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5630 
       24.95        13.94        12.10        11.11        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       18.02        14.04        46.45        20.45        37.58        40.24 
TCGA-DQ-7595 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       39.12        21.63        20.25        31.13        18.94        24.95 
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-H7-8502 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 
       15.06        21.11        20.94         0.07        25.74        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       14.66        22.03        12.66         0.36        13.84         4.27 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        38.53        14.50        37.71 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
       37.41         0.07         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A 
       15.48        13.35        19.27        10.75         7.96        30.05 
TCGA-MT-A67F TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       12.62        17.98        29.92        71.74        51.25        10.85 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T6 
       47.01        19.00        75.55        18.97        29.00        12.99 
TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
       16.01        21.07        21.21        23.15         7.30         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8ZB 
       12.72        18.64        21.07        19.73         5.62        17.82 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       12.72        16.96         6.87         7.10        32.45        13.71 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       13.55        20.35        44.65        17.95        24.30        55.43 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       18.05        13.94        20.75        32.65         2.96        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.07               0.07 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            180.16             210.97 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            17.950             21.225 
[1] "0.1 - 180.2 (17.9)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.1"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  11P LOSS MUTATED         6       14        16        72         8         0
  11P LOSS WILD-TYPE      21       62        66       181         4         1
D62V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  6                 21
  STAGE II                14                 62
  STAGE III               16                 66
  STAGE IVA               72                181
  STAGE IVB                8                  4
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11P LOSS MUTATED      13  33  24  49
  11P LOSS WILD-TYPE    37 104  76 124
D62V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1               13                 37
  T2                  33                104
  T3                  24                 76
  T4                  49                124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11P LOSS MUTATED    41  14  50   5
  11P LOSS WILD-TYPE 138  54 118   3
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               41                138
  N1               14                 54
  N2               50                118
  N3                5                  3
[1] 4 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
  11P LOSS MUTATED    45   0
  11P LOSS WILD-TYPE 144   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     45    0
  11P LOSS WILD-TYPE  144    1
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               45                144
  1                0                  1
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    33 108
  11P LOSS WILD-TYPE 107 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     33  108
  11P LOSS WILD-TYPE  107  274
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               33                107
  MALE                108                274
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    32  83
  11P LOSS WILD-TYPE 119 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     32   83
  11P LOSS WILD-TYPE  119  200
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                32                119
  YES               83                200
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  11P LOSS MUTATED                                     135
  11P LOSS WILD-TYPE                                   376
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  11P LOSS MUTATED                                                             0
  11P LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  11P LOSS MUTATED                                                     6
  11P LOSS WILD-TYPE                                                   4
D62V9, multiclass
                                                             clus
vv                                                            11P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    135
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        6
                                                             clus
vv                                                            11P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      376
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V10, continuous
D62V11, continuous
D62V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  1     0
  11P LOSS WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                          15   122
  11P LOSS WILD-TYPE                        33   324
D62V13, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                      15                 33
  WHITE                                         122                324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V14, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    10 116
  11P LOSS WILD-TYPE  16 343
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     10  116
  11P LOSS WILD-TYPE   16  343
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                   10                 16
  NOT HISPANIC OR LATINO              116                343
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED   101  71
  11Q LOSS WILD-TYPE 202 147
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               172                349 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                71                147 
$`11Q LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-6868 
       15.19        13.64        37.28         9.07        26.50        15.52 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
       12.62         4.01        41.85        28.11        20.45        30.18 
TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-A5HU 
       11.54         5.69        44.98        66.28        71.05        25.71 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 
       12.92         8.81        51.29        56.68        12.89        57.11 
TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
       45.83        73.61        12.39        71.31         8.32        11.54 
TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 
       11.84        56.94        30.67        48.00        23.90         6.74 
TCGA-CN-6021 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 
        9.07        32.22        35.05        38.89         3.68        11.74 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63Y 
       25.41        17.29        29.72        21.21         7.40        16.57 
TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5332 
       12.07        23.44        20.88        19.53        48.20        10.42 
TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-A4CB 
       32.88        56.58         4.24        14.99        38.76        29.36 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-6470 TCGA-CR-6477 TCGA-CR-6478 
       84.23        54.67        37.87        50.01        16.90         6.02 
TCGA-CR-6481 TCGA-CR-6487 TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7380 
       10.22         7.69         3.45         0.99         9.17        19.92 
TCGA-CR-7388 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5439 
       27.06         5.95        48.39        17.16       129.21        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6441 
      107.51        87.55        13.35        60.49        21.07         9.60 
TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6942 
       90.12         9.70         5.46        21.90        26.43       140.78 
TCGA-CV-6945 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 
       12.03         2.50       111.16        18.81        12.66         5.26 
TCGA-CV-7102 TCGA-CV-7247 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7414 TCGA-CV-7415 
        1.84        18.97        18.41        57.47         0.46        22.85 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45Y 
        0.07        34.09        19.76       153.86       180.16        88.87 
TCGA-CV-A460 TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-A4AQ TCGA-D6-6825 TCGA-D6-A4Z9 
       60.43        35.34        10.42        51.12        16.14        17.72 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       12.79        11.11        58.45        14.04        46.32        46.45 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G 
       40.24        40.04        41.59        37.18        32.71        20.25 
TCGA-F7-A50I TCGA-F7-A623 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
        3.02        20.25        15.06        13.61        21.11        20.94 
TCGA-HD-7753 TCGA-HD-8314 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-A61G TCGA-IQ-A61H 
       28.47        22.03         3.65        34.75        11.84        37.41 
TCGA-IQ-A61J TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67G 
       33.57        18.15        14.37         7.96         1.84         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5QF TCGA-P3-A6SW 
       15.42         7.13        16.08        17.98        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A6IG TCGA-QK-A6IH 
       47.01         2.04        16.01        13.15         7.30        21.47 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K 
       18.64         6.51        14.76        12.20        15.32         8.32 
TCGA-T2-A6WZ TCGA-T3-A92M TCGA-T3-A92N TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       15.91        13.71         3.12         2.83        49.51        49.45 
TCGA-UF-A7JA TCGA-UF-A7JH TCGA-UF-A7JS TCGA-UP-A6WW 
       74.47        29.46        22.36        17.03 

$`11Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        3.35         9.30        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 
       23.84        20.48        65.59        68.48        21.17        14.83 
TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DF 
        3.55        29.42        27.95         7.10        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
        2.27        11.05        13.38        20.48        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
      105.90         9.14         4.60         4.41        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 
       36.72        33.70        50.20        24.66        38.40        20.52 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
       10.55        27.19         6.28        12.69        48.76        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
       38.04         4.67        26.86        32.81        52.14        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       20.55        14.33        27.58        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5364 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
        8.58        16.21        11.57        12.49         8.52        52.08 
TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6022 
       50.07        47.44        28.04        19.07        34.13         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A497 
       52.08        11.08        10.45        17.42        32.48        35.01 
TCGA-CN-A499 TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A642 
       23.57        31.69        22.32        12.39         4.41         2.70 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       19.82        24.39        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       70.45        62.37        45.99        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
       32.38        46.95        13.25        70.13        64.87        53.52 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       16.73        43.04        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       11.61        23.24        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6472 
       31.23        11.77        26.27        58.42        39.52        34.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 
       36.99        18.54        11.90        11.34        11.64        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       22.78        15.75         9.27        47.18        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 
       40.93        35.84         3.09        24.95        29.23        31.96 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 
       34.06        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        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5434 
        7.10         5.13        35.41        29.95       139.43       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       76.24        19.20        76.50        91.53        80.12        17.92 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       23.05        86.83        48.59         7.07        43.23        54.74 
TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6941 TCGA-CV-6943 
       62.43         2.14        20.52         4.73        11.24        19.79 
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-7099 TCGA-CV-7100 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
      126.15         7.99         9.01        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-7248 TCGA-CV-7250 TCGA-CV-7252 
       36.00        31.36        26.20        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 
       11.87        47.97         2.10        36.13        35.54        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7423 
      210.97        89.33         9.67        25.08        25.94       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
       14.89        56.48       156.49        54.94         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
       84.49         7.17        16.64         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
       21.01       169.38       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
        6.51        48.20        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
       15.25         5.98         6.38        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-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-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
       23.05         2.53        11.44        18.67        24.95        25.32 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       12.36        28.77         7.63        22.59        24.95        13.94 
TCGA-D6-A6EQ TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 
       12.10        37.25        30.94        33.86        18.02        20.45 
TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       37.58        39.12        21.63        31.13        18.94        24.95 
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-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
        0.07        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
       12.66        22.85         0.36        13.84         4.27         6.90 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61K 
       15.95        38.53        14.50        37.71         0.07         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A6H7 
       13.68        13.84        19.04        15.48        13.35        19.27 
TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
       10.75        30.05        12.62        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T6 
       51.25        19.00        75.55        18.97        29.00        12.99 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB 
       21.07        21.21        23.15         9.34        12.72        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       19.73         5.62        17.82        12.72        16.96         6.87 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
        7.10        32.45        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       54.67        48.03        44.65        17.95        24.30        55.43 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UF-A7JV TCGA-WA-A7GZ 
       18.05        13.94        20.75        32.65         2.96        20.55 
TCGA-WA-A7H4 
       14.56 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.07               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            180.16             210.97 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             19.25              21.63 
[1] "0.1 - 180.2 (19.2)" "0.1 - 211.0 (21.6)"
[1] "hr=" "1"  
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  11Q LOSS MUTATED         8       18        19        88         6         0
  11Q LOSS WILD-TYPE      19       58        63       165         6         1
D63V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  8                 19
  STAGE II                18                 58
  STAGE III               19                 63
  STAGE IVA               88                165
  STAGE IVB                6                  6
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11Q LOSS MUTATED      17  40  30  55
  11Q LOSS WILD-TYPE    33  97  70 118
D63V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1               17                 33
  T2                  40                 97
  T3                  30                 70
  T4                  55                118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11Q LOSS MUTATED    44  18  69   3
  11Q LOSS WILD-TYPE 135  50  99   5
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               44                135
  N1               18                 50
  N2               69                 99
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    51   0
  11Q LOSS WILD-TYPE 138   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     51    0
  11Q LOSS WILD-TYPE  138    1
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               51                138
  1                0                  1
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    29 143
  11Q LOSS WILD-TYPE 111 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     29  143
  11Q LOSS WILD-TYPE  111  239
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               29                111
  MALE                143                239
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    35 111
  11Q LOSS WILD-TYPE 116 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     35  111
  11Q LOSS WILD-TYPE  116  172
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                35                116
  YES              111                172
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  11Q LOSS MUTATED                                     166
  11Q LOSS WILD-TYPE                                   345
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  11Q LOSS MUTATED                                                             0
  11Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  11Q LOSS MUTATED                                                     6
  11Q LOSS WILD-TYPE                                                   4
D63V9, multiclass
                                                             clus
vv                                                            11Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    166
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        6
                                                             clus
vv                                                            11Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      345
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V10, continuous
D63V11, continuous
D63V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  1     0
  11Q LOSS WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                          14   155
  11Q LOSS WILD-TYPE                        34   291
D63V13, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                      14                 34
  WHITE                                         155                291
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V14, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    12 148
  11Q LOSS WILD-TYPE  14 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     12  148
  11Q LOSS WILD-TYPE   14  311
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   12                 14
  NOT HISPANIC OR LATINO              148                311
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    15  22
  12P LOSS WILD-TYPE 288 196
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                37                484 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                22                196 
$`12P LOSS MUTATED`
TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       37.28        26.50        15.52        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BB-8596 TCGA-CN-5355 TCGA-CN-5365 
       41.85        11.54        14.47        71.05        42.02        11.54 
TCGA-CN-5374 TCGA-CR-6484 TCGA-CR-7377 TCGA-CR-7389 TCGA-CV-6441 TCGA-CV-7090 
       56.94        11.64         9.17        12.89         9.60       126.15 
TCGA-CV-7100 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7432 TCGA-CV-A460 TCGA-CV-A6JY 
        9.01         2.10        18.41        84.49        60.43        21.24 
TCGA-D6-6826 TCGA-D6-A6EP TCGA-DQ-5631 TCGA-HD-8224 TCGA-IQ-A61E TCGA-MZ-A5BI 
       11.44        13.94        18.02        14.66        37.71         7.13 
TCGA-MZ-A6I9 TCGA-P3-A6T5 TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-UF-A719 
       16.08        29.00        16.96        15.91         7.10        54.67 
TCGA-WA-A7GZ 
       20.55 

$`12P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 
        3.35        15.19         9.30        13.64         9.07        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       42.35        57.93        17.10        23.84        20.48        65.59 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       68.48        21.17         3.55        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG 
       30.18        27.95         7.10         5.69         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       33.70        50.20        44.98        66.28        24.66        38.40 
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-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        6.28        12.69        48.76        55.86        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       51.29        56.68        12.89        26.86        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       57.11        12.99        20.55        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       73.61        13.05        46.32         8.58        12.39        71.31 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
        8.32        16.21        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       52.08        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       28.04        19.07        34.13         6.74         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
       52.08        11.08        10.45        32.22        35.05        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        3.68        17.42        32.48        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       23.57        17.29        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       23.44        19.82        24.39        20.88        19.53        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       45.99        10.42        11.21         4.24        41.19        32.38 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       32.88        46.95        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       38.76        70.13        64.87        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       50.01        39.52        34.52        36.99        18.54        16.90 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-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-7365 TCGA-CR-7367 
       22.78        15.75         9.27        47.18        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       40.93        35.84         3.45         3.09        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
        0.99        31.96        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       32.78        47.01        27.06        29.82        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58         7.10         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      108.95        76.24        19.20        17.95       107.51        87.55 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       21.07        62.43        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        2.50         4.14        64.83       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        7.99         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-7261 TCGA-CV-7406 TCGA-CV-7407 
        4.96        11.87        47.97        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-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 
       56.48       156.49        54.94         3.52        16.27        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
        7.17       153.86        16.64         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       21.01       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 
       45.96         6.51        88.87        48.20        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       56.61         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 
       29.79         6.48        28.01         3.62        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
       22.52        10.42        10.42        10.55        18.84        34.36 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6827 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-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES 
       28.77         7.63        22.59        24.95        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 
       11.11        58.45        37.25        30.94        33.86        14.04 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       46.32        46.45        20.45        37.58        40.24        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       39.12        41.59        37.18        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.61        21.11        20.94         0.07        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       21.93        27.48        27.48        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-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       15.95        38.53        14.50        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
       33.57         5.29        13.68        13.84        19.04        15.48 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        19.27        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A7D7 
       30.05         1.84        12.62         6.25        15.42        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        71.74        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-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        21.21        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       21.47         9.34        12.72        18.64        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
        6.51         5.62        14.76        12.20        17.82        15.32 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        8.32        12.72         6.87        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B 
       13.55        13.25        20.35        64.80         2.83        49.51 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       48.03        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
       32.65         2.96        17.03        14.56 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              2.10               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            126.15             210.97 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             15.91              21.14 
[1] "2.1 - 126.2 (15.9)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.6"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  12P LOSS MUTATED         0        7         5        14         1         0
  12P LOSS WILD-TYPE      27       69        77       239        11         1
D64V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  0                 27
  STAGE II                 7                 69
  STAGE III                5                 77
  STAGE IVA               14                239
  STAGE IVB                1                 11
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12P LOSS MUTATED       1  11   6  11
  12P LOSS WILD-TYPE    49 126  94 162
D64V4, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1                1                 49
  T2                  11                126
  T3                   6                 94
  T4                  11                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
  12P LOSS MUTATED    13   2  10   1
  12P LOSS WILD-TYPE 166  66 158   7
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               13                166
  N1                2                 66
  N2               10                158
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    12   0
  12P LOSS WILD-TYPE 177   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     12    0
  12P LOSS WILD-TYPE  177    1
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               12                177
  1                0                  1
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    11  26
  12P LOSS WILD-TYPE 129 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     11   26
  12P LOSS WILD-TYPE  129  356
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               11                129
  MALE                 26                356
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    15  16
  12P LOSS WILD-TYPE 136 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     15   16
  12P LOSS WILD-TYPE  136  267
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                15                136
  YES               16                267
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  12P LOSS MUTATED                                      37
  12P LOSS WILD-TYPE                                   474
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  12P LOSS MUTATED                                                             0
  12P LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  12P LOSS MUTATED                                                     0
  12P LOSS WILD-TYPE                                                  10
D64V9, multiclass
                                                             clus
vv                                                            12P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     37
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            12P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      474
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V10, continuous
D64V11, continuous
D64V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     1
  12P LOSS WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                           5    30
  12P LOSS WILD-TYPE                        43   416
D64V13, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       5                 43
  WHITE                                          30                416
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V14, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     3  31
  12P LOSS WILD-TYPE  23 428
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3   31
  12P LOSS WILD-TYPE   23  428
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               31                428
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    19  14
  12Q LOSS WILD-TYPE 284 204
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                33                488 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                14                204 
$`12Q LOSS MUTATED`
TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DE 
       15.52        14.83         4.01        41.85        20.45        14.47 
TCGA-BB-8596 TCGA-CN-5355 TCGA-CN-5374 TCGA-CN-6024 TCGA-CN-6994 TCGA-CR-6493 
       71.05        42.02        56.94        11.08        38.89         9.27 
TCGA-CR-7390 TCGA-CV-6003 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7254 TCGA-CV-7255 
       29.82        54.74       126.15       111.16        47.97         2.10 
TCGA-CV-7263 TCGA-CV-7432 TCGA-CV-A6JY TCGA-CX-7219 TCGA-D6-A6EP TCGA-F7-7848 
       18.41        84.49        21.24        34.36        13.94        37.18 
TCGA-IQ-A61G TCGA-IQ-A6SG TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A6T5 TCGA-T2-A6WZ 
       11.84        19.04         7.13        16.08        29.00        15.91 
TCGA-T2-A6X0 TCGA-UF-A719 TCGA-WA-A7GZ 
        7.10        54.67        20.55 

$`12Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 
       20.48        65.59        68.48        21.17         3.55        12.62 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       29.42        28.11        30.18        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
        5.69         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.60         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
       18.38        22.42        36.72        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY 
       66.28        24.66        38.40        20.52        25.71        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
       27.19        12.92         8.81         6.28        12.69        48.76 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       55.86        38.04         4.67        51.29        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       26.86        32.81        52.14        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 
       14.33        45.83        27.58        73.61        13.05        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
        8.58        12.39        71.31         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
       11.84        11.57        12.49         8.52        52.08        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        48.00        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 
       34.13         6.74         9.07         9.24        52.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       32.22        35.05         3.68        17.42        32.48        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        31.69        22.32        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        23.44        19.82        24.39        20.88 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       19.53        48.20        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       70.45        62.37        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       41.19        32.38        32.88        46.95        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        4.24        14.99        38.76        70.13        64.87        53.52 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       16.73        43.04        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       11.61        23.24        29.36        33.60        29.49        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       12.46        31.23        84.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
       26.27        58.42        50.01        39.52        34.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       18.54        16.90         6.02        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 
       11.64         7.69        12.46        22.78        15.75        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-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       12.89        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         5.13         5.95        35.41        29.95        48.39 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
      139.43        17.16       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       17.95       107.51        87.55        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-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       140.78        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       15.09        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
        7.13         8.42        28.34         2.50         4.14        64.83 
TCGA-CV-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-7261 
       18.97        17.13        95.34         4.96        11.87        36.13 
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-7428 TCGA-CV-7429 
      100.57        14.89        56.48       156.49        54.94         3.52 
TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       16.27        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
       22.19        27.98        21.01       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
       35.47         1.05        45.96         6.51        88.87        48.20 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       60.43        67.86         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
        3.62        23.47        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        51.12        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
       23.05         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN 
       25.32        17.72        12.36        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       24.95        12.10        12.79        11.11        58.45        37.25 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       30.94        33.86        18.02        14.04        46.32        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45        37.58        40.24        40.04        39.12        41.59 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       24.95         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
        4.27         3.65         6.90        34.75        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       14.50        37.71        37.41         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
       13.68        13.84        15.48        13.35        18.15        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        6.25        15.42        17.98        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       18.97         2.04        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.21        23.15         7.30        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       18.64        21.07        19.73         6.51         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ 
        6.87        32.45        13.71         3.12        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       20.35        64.80         2.83        49.51        48.03        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       18.05        13.94        20.75        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7H4 
       17.03        14.56 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              2.10               0.07 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            126.15             210.97 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            20.550             20.975 
[1] "2.1 - 126.2 (20.6)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1.1"
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  12Q LOSS MUTATED         1        6         4        15         0         0
  12Q LOSS WILD-TYPE      26       70        78       238        12         1
D65V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  1                 26
  STAGE II                 6                 70
  STAGE III                4                 78
  STAGE IVA               15                238
  STAGE IVB                0                 12
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12Q LOSS MUTATED       1  11   4  12
  12Q LOSS WILD-TYPE    49 126  96 161
D65V4, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1                1                 49
  T2                  11                126
  T3                   4                 96
  T4                  12                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
  12Q LOSS MUTATED    13   4   7   0
  12Q LOSS WILD-TYPE 166  64 161   8
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               13                166
  N1                4                 64
  N2                7                161
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    10   0
  12Q LOSS WILD-TYPE 179   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     10    0
  12Q LOSS WILD-TYPE  179    1
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               10                179
  1                0                  1
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     8  25
  12Q LOSS WILD-TYPE 132 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      8   25
  12Q LOSS WILD-TYPE  132  357
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                8                132
  MALE                 25                357
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    12  13
  12Q LOSS WILD-TYPE 139 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     12   13
  12Q LOSS WILD-TYPE  139  270
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                12                139
  YES               13                270
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  12Q LOSS MUTATED                                      32
  12Q LOSS WILD-TYPE                                   479
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  12Q LOSS MUTATED                                                             0
  12Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  12Q LOSS MUTATED                                                     1
  12Q LOSS WILD-TYPE                                                   9
D65V9, multiclass
                                                             clus
vv                                                            12Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     32
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            12Q LOSS 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                          9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V10, continuous
D65V11, continuous
D65V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     0
  12Q LOSS WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                           6    26
  12Q LOSS WILD-TYPE                        42   420
D65V13, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       6                 42
  WHITE                                          26                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"
D65V14, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     4  27
  12Q LOSS WILD-TYPE  22 432
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      4   27
  12Q LOSS WILD-TYPE   22  432
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 22
  NOT HISPANIC OR LATINO               27                432
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    97  69
  13Q LOSS WILD-TYPE 206 149
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               166                355 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                69                149 
$`13Q LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6869 
       15.19         9.07        42.35        17.10        68.48        21.17 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
        3.55         4.01        41.85        20.45        30.18        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4224 
       11.54         7.10         5.69        11.05        20.48         9.14 
TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 
        4.41        36.72        50.20        66.28        24.66        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 
       20.52        10.55        27.19         6.28        55.86        38.04 
TCGA-CN-4730 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5367 
       26.86        45.83        27.58        71.31         8.32        11.57 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 
       52.08        56.94        50.07        30.67        48.00        19.07 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6998 
        6.74         9.07        11.08        10.45        38.89        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T 
       35.01        25.41        23.57        17.29        21.21         7.40 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5330 TCGA-CQ-6220 TCGA-CQ-6224 TCGA-CQ-6225 
       19.53        48.20        62.37        32.38        56.58        13.25 
TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-A4CE TCGA-CR-5249 TCGA-CR-6472 TCGA-CR-6477 
       64.87        16.73        29.49        37.87        34.52        16.90 
TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7372 TCGA-CR-7374 
        6.02        10.22         7.69        47.18        24.95         0.99 
TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7397 TCGA-CR-7402 TCGA-CR-7404 
       34.06        17.13        32.78         7.10        29.95        48.39 
TCGA-CV-5434 TCGA-CV-5441 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6940 TCGA-CV-6941 
      108.95        87.55        60.49         7.07        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6950 TCGA-CV-6954 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7091 
      140.78        15.09        65.82         4.14        64.83       111.16 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7235 
        7.99         9.01        52.31        12.92        21.80        77.16 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7415 
       36.00        26.20        17.13        18.41        57.47        22.85 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7429 TCGA-CV-7435 TCGA-CV-7440 
       25.94         0.07        34.09         3.52       153.86        22.19 
TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 
      180.16        45.96        88.87        67.86        56.61         7.07 
TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-7219 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-A4Z9 
       35.34        10.42        34.36        16.14        24.95        17.72 
TCGA-D6-A6EP TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7595 TCGA-DQ-7596 
       13.94        33.86        14.04        46.32        39.12        41.59 
TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A623 TCGA-HD-7753 TCGA-HD-7831 
       37.18        20.25         3.02        20.25        28.47        21.93 
TCGA-HD-7917 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
       27.48        22.85         3.65        13.84        19.04        15.48 
TCGA-KU-A66T TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q6 TCGA-P3-A5QA 
       18.15         6.25         7.13        16.08        15.78        71.74 
TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T7 TCGA-QK-A6IG TCGA-QK-A6V9 TCGA-QK-A8Z7 
       47.01         2.04        16.01         7.30        18.64         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-AA3K TCGA-T2-A6X0 TCGA-T3-A92M TCGA-T3-A92N 
        5.62        14.76         8.32         7.10        13.71         3.12 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       20.35        64.80         2.83        48.03        49.45        44.65 
TCGA-UF-A7JC TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UP-A6WW 
       17.95        13.94        20.75        17.03 

$`13Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
        3.35         9.30        13.64        37.28        26.50        23.74 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 
       57.93        23.84        20.48        65.59        15.52        14.83 
TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       12.62        29.42        28.11        14.47         7.82         2.27 
TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 
       13.38        16.41         6.15       105.90         4.60        18.38 
TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7872 TCGA-BB-A5HU TCGA-BB-A6UM 
       22.42        33.70        44.98        38.40        25.71        12.92 
TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
        8.81        12.69        48.76         4.67        51.29        56.68 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       12.89        32.81        52.14        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       14.33        73.61        13.05        42.02        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 
       12.39        16.21        11.54        11.84        12.49         8.52 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6023 
       23.90        47.44        28.04        34.13         9.24        52.08 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A49B 
       32.22        35.05         3.68        17.42        32.48        29.72 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5324 
        2.70        23.44        19.82        24.39        20.88        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 
       21.50         2.93        54.58        70.45        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 
       11.21         4.24        41.19        32.88        46.95         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
       14.99        38.76        70.13        53.52        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       43.10        77.56        44.48        11.61        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       33.60        14.14        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       54.67        26.27        58.42        50.01        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 
       18.54        11.90        11.34        11.64        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       15.75         9.27        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7380 
        3.45         3.09        29.23        31.96         9.17        19.92 
TCGA-CR-7382 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       26.17        47.01        27.06        12.89        29.82        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 
       46.85        32.65        44.25        30.58         5.13         5.95 
TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 
       35.41       139.43        17.16       129.21        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       17.95       107.51        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6003 
       13.35        23.05        86.83        48.59        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-6943 TCGA-CV-6945 
        5.46        20.52         4.73        21.90        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 
       42.38        30.08         6.08        53.95        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 
        8.42        28.34         2.50       126.15        18.81        12.66 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 
        5.26         1.84        71.21        10.75       130.88         4.73 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       47.47        31.36        18.97        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
       47.97         2.10        36.13        35.54        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7424 
       89.33         9.67         0.46        25.08       100.57        14.89 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       56.48       156.49        54.94        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
        7.17        16.64         6.38        27.98        21.01       169.38 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A460 
      159.65        35.47         1.05         6.51        48.20        60.43 
TCGA-CV-A463 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
        0.76        15.25         5.98         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 
        9.60        23.05         2.53        11.44        18.67        25.32 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ 
       12.36        28.77         7.63        22.59        24.95        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        37.25        30.94        18.02 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-F7-8298 
       46.45        20.45        37.58        40.24        40.04        32.71 
TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
       21.63        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
       11.80        12.43        13.38        15.16        15.06        13.61 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8224 
       21.11        20.94         0.07        25.74        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
       22.03        12.66         0.36        13.84         4.27         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
       34.75        15.95        38.53        14.50        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A66S 
       37.41         0.07        33.57         5.29        13.68        13.35 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.27        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF 
       12.62        15.42        17.98        29.92        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T6 
       36.82        19.00        75.55        18.97        29.00        12.99 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
       13.15        21.07        21.21        23.15        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       12.72        21.07        19.73        12.20        17.82        15.32 
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-UF-A719 TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF 
       13.25        54.67        49.51        74.47        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-WA-A7GZ 
       29.46        18.05        22.36        32.65         2.96        20.55 
TCGA-WA-A7H4 
       14.56 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.07               0.07 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            180.16             210.97 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             21.19              20.88 
[1] "0.1 - 180.2 (21.2)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1"  
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  13Q LOSS MUTATED        11       18        25        83         3         1
  13Q LOSS WILD-TYPE      16       58        57       170         9         0
D66V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                 11                 16
  STAGE II                18                 58
  STAGE III               25                 57
  STAGE IVA               83                170
  STAGE IVB                3                  9
  STAGE IVC                1                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  13Q LOSS MUTATED      17  42  29  55
  13Q LOSS WILD-TYPE    33  95  71 118
D66V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1               17                 33
  T2                  42                 95
  T3                  29                 71
  T4                  55                118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  13Q LOSS MUTATED    52  22  56   2
  13Q LOSS WILD-TYPE 127  46 112   6
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               52                127
  N1               22                 46
  N2               56                112
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    58   1
  13Q LOSS WILD-TYPE 131   0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     58    1
  13Q LOSS WILD-TYPE  131    0
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               58                131
  1                1                  0
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    41 126
  13Q LOSS WILD-TYPE  99 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     41  126
  13Q LOSS WILD-TYPE   99  256
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               41                 99
  MALE                126                256
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    48  91
  13Q LOSS WILD-TYPE 103 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     48   91
  13Q LOSS WILD-TYPE  103  192
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                48                103
  YES               91                192
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  13Q LOSS MUTATED                                     163
  13Q LOSS WILD-TYPE                                   348
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  13Q LOSS MUTATED                                                             1
  13Q LOSS WILD-TYPE                                                           0
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  13Q LOSS MUTATED                                                     3
  13Q LOSS WILD-TYPE                                                   7
D66V9, multiclass
                                                             clus
vv                                                            13Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    163
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        3
                                                             clus
vv                                                            13Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      348
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  0
  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"
D66V10, continuous
D66V11, continuous
D66V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  1     1
  13Q LOSS WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                          22   138
  13Q LOSS WILD-TYPE                        26   308
D66V13, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                      22                 26
  WHITE                                         138                308
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V14, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    11 137
  13Q LOSS WILD-TYPE  15 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     11  137
  13Q LOSS WILD-TYPE   15  322
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   11                 15
  NOT HISPANIC OR LATINO              137                322
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    34  24
  14Q LOSS WILD-TYPE 269 194
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                58                463 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                24                194 
$`14Q LOSS MUTATED`
TCGA-4P-AA8J TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        3.35         9.07        42.35        21.17        14.83         3.55 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A8YP TCGA-BB-7862 TCGA-BB-A6UM TCGA-CN-6019 
       20.45        27.95        16.41        36.72        12.92        34.13 
TCGA-CN-6020 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-A63U TCGA-CQ-5332 TCGA-CQ-6221 
        6.74        35.05         3.68        31.69        10.42        32.88 
TCGA-CR-5247 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-7365 TCGA-CR-7398 TCGA-CV-5966 
       11.77        50.01        34.52        39.16         5.13        17.92 
TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6939 TCGA-CV-6962 TCGA-CV-7263 TCGA-CV-7406 
       90.12         9.70        21.90         4.14        18.41        57.47 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7435 TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A6JY 
       34.09       100.57       153.86        48.20        60.43        21.24 
TCGA-CV-A6K1 TCGA-CX-A4AQ TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A6EM TCGA-DQ-5631 
       22.52        51.12        11.44        25.32         7.63        18.02 
TCGA-DQ-7590 TCGA-F7-7848 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-8224 TCGA-MT-A7BN 
       46.45        37.18        21.11        20.94        14.66        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A6T0 TCGA-QK-A8Z7 TCGA-T2-A6X0 TCGA-TN-A7HL 
        7.13        16.08        19.00         6.51         7.10        20.35 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       48.03        49.45        44.65        74.47 

$`14Q LOSS 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-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       57.93        17.10        23.84        20.48        65.59        68.48 
TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG 
       15.52        12.62         4.01        41.85        29.42        28.11 
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       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 
        9.14         4.60         4.41        18.38        22.42        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       50.20        44.98        66.28        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        25.71        10.55        27.19         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
       12.69        48.76        55.86        38.04         4.67        51.29 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       56.68        12.89        26.86        32.81        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        42.02        46.32         8.58        12.39        71.31 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
        8.32        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        8.52        52.08        56.94        50.07        30.67        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6022 
       23.90        47.44        28.04        19.07         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 
       52.08        11.08        10.45        32.22        38.89        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       32.48        11.74        35.01        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       29.72        21.21         7.40        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        70.45        62.37        45.99        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       41.19        32.38        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
       14.99        38.76        70.13        64.87        53.52        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       43.04        41.88        43.10        77.56        44.48        11.61 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       31.23        84.23        54.67        37.87        26.27        58.42 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       39.52        36.99        18.54        16.90         6.02        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       15.75         9.27        47.18        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        29.82        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 
       32.65        44.25        30.58         7.10         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       29.95        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       76.24        19.20        17.95       107.51        87.55        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       91.53        80.12        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-6934 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6940 
        9.60         2.14         5.46        20.52         4.73        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       140.78        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-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-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
        2.10        36.13        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-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
       14.89        56.48       156.49        54.94         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       84.49        19.76         7.17        16.64         6.38        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        21.01       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A463 
        1.05        45.96         6.51        88.87        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       56.61         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 
       29.79         6.48        28.01         3.62        23.47        19.92 
TCGA-CV-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-D6-6827 
       25.41         9.60        23.05         2.53        16.14        18.67 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EO 
       24.95        17.72        12.36        28.77        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        11.11        58.45        37.25 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 
       30.94        33.86        14.04        46.32        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
       40.24        40.04        39.12        41.59        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       17.85        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.06        13.61         0.07        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
       27.48        27.48        22.03        12.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
       13.84         4.27         3.65         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
       33.57         5.29        13.68        13.84        19.04        15.48 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        19.27        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q5 
       30.05         1.84        12.62         6.25        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       15.78        71.74        51.25        10.85        36.82        47.01 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 
        9.34        12.72        18.64        21.07        19.73         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
       16.96         6.87        15.91        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.55        13.25        64.80        54.67         2.83        49.51 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              3.35               0.07 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            153.86             210.97 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             21.14              20.75 
[1] "3.4 - 153.9 (21.1)" "0.1 - 211.0 (20.8)"
[1] "hr=" "1"  
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  14Q LOSS MUTATED         0        9         6        30         1         0
  14Q LOSS WILD-TYPE      27       67        76       223        11         1
D67V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  0                 27
  STAGE II                 9                 67
  STAGE III                6                 76
  STAGE IVA               30                223
  STAGE IVB                1                 11
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  14Q LOSS MUTATED       3  13  10  20
  14Q LOSS WILD-TYPE    47 124  90 153
D67V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1                3                 47
  T2                  13                124
  T3                  10                 90
  T4                  20                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
  14Q LOSS MUTATED    18   8  16   1
  14Q LOSS WILD-TYPE 161  60 152   7
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               18                161
  N1                8                 60
  N2               16                152
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    22   0
  14Q LOSS WILD-TYPE 167   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     22    0
  14Q LOSS WILD-TYPE  167    1
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               22                167
  1                0                  1
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    10  48
  14Q LOSS WILD-TYPE 130 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     10   48
  14Q LOSS WILD-TYPE  130  334
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               10                130
  MALE                 48                334
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    10  40
  14Q LOSS WILD-TYPE 141 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     10   40
  14Q LOSS WILD-TYPE  141  243
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                10                141
  YES               40                243
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  14Q LOSS MUTATED                                      55
  14Q LOSS WILD-TYPE                                   456
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  14Q LOSS MUTATED                                                             0
  14Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  14Q LOSS MUTATED                                                     3
  14Q LOSS WILD-TYPE                                                   7
D67V9, multiclass
                                                             clus
vv                                                            14Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     55
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        3
                                                             clus
vv                                                            14Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      456
  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"
D67V10, continuous
D67V11, continuous
D67V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0     0
  14Q LOSS WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                           8    50
  14Q LOSS WILD-TYPE                        40   396
D67V13, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       8                 40
  WHITE                                          50                396
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V14, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     2  47
  14Q LOSS WILD-TYPE  24 412
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2   47
  14Q LOSS WILD-TYPE   24  412
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 24
  NOT HISPANIC OR LATINO               47                412
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    50  53
  15Q LOSS WILD-TYPE 253 165
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               103                418 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                53                165 
$`15Q LOSS MUTATED`
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-7269 
       42.35        57.93        17.10        68.48        15.52        41.85 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A8YP 
       29.42        28.11        30.18        14.47        11.05        16.41 
TCGA-BB-4225 TCGA-BB-7870 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-5359 
        4.60        66.28        38.04        56.68        26.86        12.39 
TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-6012 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6996 
        8.32         8.52        48.00         9.07        11.08        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A63W TCGA-CN-A6UY TCGA-CQ-5326 
       32.48        11.74        23.57        12.39        23.44         2.93 
TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7067 
       62.37        10.42        56.58         4.24        38.76        16.73 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CE TCGA-CR-6478 TCGA-CR-7402 
       77.56        44.48        11.61        29.49         6.02        29.95 
TCGA-CV-5435 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 
       76.24        87.55        17.92        13.35        48.59        60.49 
TCGA-CV-6441 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6948 TCGA-CV-6954 TCGA-CV-6962 
        9.60        20.52        26.43        42.38        65.82         4.14 
TCGA-CV-7095 TCGA-CV-7104 TCGA-CV-7242 TCGA-CV-7247 TCGA-CV-7407 TCGA-CV-7424 
       18.81        12.92        36.00        18.97        35.54        14.89 
TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-A45R TCGA-CV-A460 TCGA-CV-A465 
       84.49       153.86         6.38       180.16        60.43         7.07 
TCGA-CV-A6JM TCGA-CV-A6JZ TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 
        6.38        23.47        34.36         9.60        23.05        11.44 
TCGA-D6-A6EO TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-A50I 
       24.95        11.11        58.45        18.02        37.58         3.02 
TCGA-F7-A61S TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-A76A TCGA-IQ-A61E TCGA-IQ-A61O 
       18.94        20.25        12.43        20.94        37.71        13.84 
TCGA-KU-A66T TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-P3-A5QA TCGA-P3-A6T3 TCGA-P3-A6T4 
       18.15        15.42         7.13        71.74        18.97         2.04 
TCGA-P3-A6T5 TCGA-QK-A6IG TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-RS-A6TO 
       29.00         7.30        19.73        14.76        12.20        12.72 
TCGA-T2-A6WZ TCGA-T3-A92M TCGA-T3-A92N TCGA-UF-A718 TCGA-UF-A7JA TCGA-UF-A7JD 
       15.91        13.71         3.12        64.80        74.47        24.30 
TCGA-UF-A7JO 
       20.75 

$`15Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 
       26.50        23.74        23.84        20.48        65.59        21.17 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IH TCGA-BA-A6D8 
       14.83         3.55        12.62         4.01        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ 
       11.54         7.10         5.69         7.82         2.27        13.38 
TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 
       20.48         6.15       105.90         9.14         4.41        18.38 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 
       22.42        36.72        33.70        50.20        44.98        24.66 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ 
       38.40        71.05        20.52        25.71        10.55        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
       12.92         8.81         6.28        12.69        48.76        55.86 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        4.67        51.29        12.89        32.81        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 
       13.05        42.02        46.32         8.58        71.31        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-5374 
       11.54        11.84        11.57        12.49        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       50.07        30.67        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 
       34.13         6.74         9.24        52.08        10.45        32.22 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A 
       35.05        38.89         3.68        35.01        25.41        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
       29.72        21.21         7.40        31.69        22.32        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
        4.41        12.07         2.70        19.82        24.39        20.88 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
       19.53        48.20        52.37        21.50        54.58        70.45 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 
       45.99        11.21         4.24        41.19        32.38        32.88 
TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
       46.95        13.25        14.99        70.13        64.87        53.52 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.04        41.88        43.10        23.24        29.36        33.60 
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-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       47.18        39.16        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.09        24.95        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        29.82        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58         7.10         5.13         5.95        35.41 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 
       48.39       139.43        17.16       129.21       108.95        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5971 
       17.95       107.51        76.50        91.53        80.12        23.05 
TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       86.83         7.07        43.23        54.74        21.07        62.43 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 
       90.12         2.14         9.70         5.46         4.73        21.90 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 
       11.24       140.78        19.79        12.03        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
        6.08        53.95        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 
        2.50        64.83       126.15       111.16        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7178 
        9.01         5.26         1.84        52.31        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 
       10.75       130.88        77.16         4.73        47.47        31.36 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       26.20        17.13        95.34         4.96        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 
        2.10        36.13        18.41        57.47        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-7425 TCGA-CV-7427 TCGA-CV-7428 
        0.07        34.09       100.57        56.48       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7440 
        3.52        16.27        19.76         7.17        16.64        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       27.98        21.01       169.38       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 
       45.96         6.51        88.87        48.20        67.86         0.76 
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-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
       28.01         3.62        21.24        19.92        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
        2.53        16.14        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EP TCGA-D6-A6EQ 
       12.36        28.77         7.63        22.59        13.94        12.10 
TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 
       12.79        37.25        30.94        33.86        14.04        46.32 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       46.45        20.45        40.24        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V 
       37.18        32.71        21.63        20.25        31.13        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
        0.46        17.85        11.80        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       13.61        21.11         0.07        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       27.48        27.48        14.66        22.03        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
        0.36        13.84         4.27         3.65         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       15.95        38.53        14.50        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S 
       33.57         5.29        13.68        19.04        15.48        13.35 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.27        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       12.62         6.25        16.08        17.98        29.92        15.78 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 
       21.47         9.34        12.72        18.64        21.07         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX 
        5.62        17.82        15.32         8.32        16.96         6.87 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A719 
        7.10        32.45        13.55        13.25        20.35        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC 
        2.83        49.51        48.03        49.45        44.65        17.95 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT 
       55.43        29.46        18.05        13.94        22.36        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        17.03        20.55        14.56 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              2.04               0.07 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            180.16             210.97 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             19.73              21.09 
[1] "2.0 - 180.2 (19.7)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.3"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  15Q LOSS MUTATED         3       17        13        49         3         0
  15Q LOSS WILD-TYPE      24       59        69       204         9         1
D68V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  3                 24
  STAGE II                17                 59
  STAGE III               13                 69
  STAGE IVA               49                204
  STAGE IVB                3                  9
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  15Q LOSS MUTATED       6  26  23  33
  15Q LOSS WILD-TYPE    44 111  77 140
D68V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1                6                 44
  T2                  26                111
  T3                  23                 77
  T4                  33                140
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  15Q LOSS MUTATED    30  11  36   3
  15Q LOSS WILD-TYPE 149  57 132   5
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               30                149
  N1               11                 57
  N2               36                132
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    31   0
  15Q LOSS WILD-TYPE 158   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     31    0
  15Q LOSS WILD-TYPE  158    1
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               31                158
  1                0                  1
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    27  76
  15Q LOSS WILD-TYPE 113 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     27   76
  15Q LOSS WILD-TYPE  113  306
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               27                113
  MALE                 76                306
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    27  59
  15Q LOSS WILD-TYPE 124 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     27   59
  15Q LOSS WILD-TYPE  124  224
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                27                124
  YES               59                224
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  15Q LOSS MUTATED                                     102
  15Q LOSS WILD-TYPE                                   409
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  15Q LOSS MUTATED                                                             1
  15Q LOSS WILD-TYPE                                                           0
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  15Q LOSS MUTATED                                                     0
  15Q LOSS WILD-TYPE                                                  10
D68V9, multiclass
                                                             clus
vv                                                            15Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    102
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            15Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      409
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V10, continuous
D68V11, continuous
D68V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  1     2
  15Q LOSS WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                          12    84
  15Q LOSS WILD-TYPE                        36   362
D68V13, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                      12                 36
  WHITE                                          84                362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V14, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     8  86
  15Q LOSS WILD-TYPE  18 373
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      8   86
  15Q LOSS WILD-TYPE   18  373
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                 18
  NOT HISPANIC OR LATINO               86                373
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    37  26
  16P LOSS WILD-TYPE 266 192
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                63                458 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                26                192 
$`16P LOSS MUTATED`
TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DE 
        3.35        13.64         9.07        41.85        20.45        14.47 
TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-CN-4729 TCGA-CN-5363 
       66.28        71.05        20.52        10.55        12.89         8.32 
TCGA-CN-5374 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A63T TCGA-CQ-5330 TCGA-CQ-6224 
       56.94        35.01        23.57         7.40        62.37        56.58 
TCGA-CQ-A4C7 TCGA-CR-6473 TCGA-CR-7368 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7398 
       11.61        36.99        40.93         0.99        17.13         5.13 
TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5436 TCGA-CV-6940 TCGA-CV-6950 TCGA-CV-6962 
        5.95        29.95        19.20        26.43        15.09         4.14 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7407 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7424 
       77.16         4.73        35.54        25.08        25.94        14.89 
TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7438 TCGA-CX-7082 TCGA-D6-A4Z9 TCGA-D6-A6EM 
        3.52        84.49         6.38        10.42        17.72         7.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-HD-7753 TCGA-HD-8224 TCGA-IQ-A61E TCGA-IQ-A61G 
       20.25         3.02        28.47        14.66        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61K TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       37.41         5.29        19.04        19.27        16.08        17.98 
TCGA-P3-A5Q6 TCGA-P3-A6SW TCGA-QK-A6IG TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-T3-A92N 
       15.78        36.82         7.30        12.20         8.32         3.12 
TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UP-A6WW 
       13.25        54.67        17.03 

$`16P LOSS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
       15.19         9.30        37.28        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       57.93        17.10        23.84        20.48        65.59        68.48 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
       15.52        21.17        14.83         3.55        12.62         4.01 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       29.42        28.11        30.18        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
        5.69         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.60         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
       18.38        22.42        36.72        33.70        50.20        44.98 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       24.66        38.40        25.71        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        6.28        12.69        48.76        55.86        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       51.29        56.68        26.86        32.81        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        42.02        46.32         8.58        12.39        71.31 
TCGA-CN-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-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       52.08        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       28.04        19.07        34.13         6.74         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
       52.08        11.08        10.45        32.22        35.05        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A 
        3.68        17.42        32.48        11.74        25.41        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       29.72        21.21        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        70.45        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 
       41.19        32.38        32.88        46.95        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
       14.99        38.76        70.13        64.87        53.52        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       43.04        41.88        43.10        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
       50.01        39.52        34.52        18.54        16.90         6.02 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       22.78        15.75         9.27        47.18        39.16        47.34 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 
       35.84         3.45         3.09        24.95        29.23        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
        9.17        34.06        19.92        26.17        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        29.82        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 
       44.25        30.58         7.10        35.41        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 
       17.16       129.21       108.95        76.24        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       87.55        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       54.74        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 
        9.70         5.46        20.52         4.73        21.90        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 
      140.78        19.79        12.03        42.38        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        2.50        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-7238 TCGA-CV-7242 
       21.80        71.21        10.75       130.88        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-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
        0.07        34.09       100.57        56.48       156.49        54.94 
TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 
       16.27        19.76         7.17       153.86        16.64        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        21.01       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
        1.05        45.96         6.51        88.87        48.20        60.43 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       67.86         0.76        56.61         7.07        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       35.34         6.38        29.79         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       18.84        34.36        51.12        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
       23.05         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       25.32        12.36        28.77        22.59        24.95        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
       12.10        12.79        11.11        58.45        37.25        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
       33.86        18.02        14.04        46.32        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       37.58        40.24        40.04        39.12        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       32.71        21.63        31.13        18.94        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       17.85        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 
       15.06        13.61        21.11        20.94         0.07        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       21.93        27.48        27.48        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-A61I TCGA-IQ-A61J TCGA-IQ-A61L 
       15.95        38.53        14.50         0.07        33.57        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H8 TCGA-MT-A51W 
       13.84        15.48        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         6.25        15.42 
TCGA-MZ-A5BI TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SX 
        7.13        29.92        71.74        51.25        10.85        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-A6IH 
       16.01        13.15        21.07        21.21        23.15        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        18.64        21.07        19.73         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP 
        5.62        14.76        17.82        15.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HI 
        6.87        15.91         7.10        32.45        13.71        13.55 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       20.35        64.80         2.83        49.51        48.03        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       18.05        13.94        20.75        22.36        32.65         2.96 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.99               0.07 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             84.49             210.97 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            17.030             21.355 
[1] "1.0 - 84.5 (17.0)"  "0.1 - 211.0 (21.4)"
[1] "hr=" "1.2"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  16P LOSS MUTATED         3        8        11        31         2         0
  16P LOSS WILD-TYPE      24       68        71       222        10         1
D69V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  3                 24
  STAGE II                 8                 68
  STAGE III               11                 71
  STAGE IVA               31                222
  STAGE IVB                2                 10
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16P LOSS MUTATED       4  22  18  12
  16P LOSS WILD-TYPE    46 115  82 161
D69V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1                4                 46
  T2                  22                115
  T3                  18                 82
  T4                  12                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
  16P LOSS MUTATED    13  11  25   2
  16P LOSS WILD-TYPE 166  57 143   6
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               13                166
  N1               11                 57
  N2               25                143
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    20   0
  16P LOSS WILD-TYPE 169   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     20    0
  16P LOSS WILD-TYPE  169    1
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               20                169
  1                0                  1
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    19  44
  16P LOSS WILD-TYPE 121 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     19   44
  16P LOSS WILD-TYPE  121  338
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               19                121
  MALE                 44                338
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    16  37
  16P LOSS WILD-TYPE 135 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     16   37
  16P LOSS WILD-TYPE  135  246
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                16                135
  YES               37                246
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  16P LOSS MUTATED                                      61
  16P LOSS WILD-TYPE                                   450
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  16P LOSS MUTATED                                                             0
  16P LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  16P LOSS MUTATED                                                     2
  16P LOSS WILD-TYPE                                                   8
D69V9, multiclass
                                                             clus
vv                                                            16P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     61
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            16P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      450
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V10, continuous
D69V11, continuous
D69V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     1
  16P LOSS WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           8    51
  16P LOSS WILD-TYPE                        40   395
D69V13, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       8                 40
  WHITE                                          51                395
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V14, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     6  55
  16P LOSS WILD-TYPE  20 404
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      6   55
  16P LOSS WILD-TYPE   20  404
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 20
  NOT HISPANIC OR LATINO               55                404
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    51  30
  16Q LOSS WILD-TYPE 252 188
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                81                440 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                30                188 
$`16Q LOSS MUTATED`
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5153 TCGA-BA-5559 TCGA-BA-A4IH TCGA-BB-4225 
       13.64         9.07        57.93        68.48        20.45         4.60 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 
       22.42        36.72        44.98        66.28        71.05        20.52 
TCGA-BB-A5HY TCGA-CN-4729 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5374 
       10.55        12.89        46.32        71.31         8.32        56.94 
TCGA-CN-6012 TCGA-CN-6021 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A63T TCGA-CN-A63U 
       48.00         9.07        35.01        23.57         7.40        31.69 
TCGA-CN-A6UY TCGA-CQ-6224 TCGA-CQ-A4C7 TCGA-CR-5243 TCGA-CR-6467 TCGA-CR-6473 
       23.44        56.58        11.61        84.23        58.42        36.99 
TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7398 TCGA-CR-7402 
       10.22        11.64        40.93         3.45         5.13        29.95 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-6940 TCGA-CV-6962 TCGA-CV-7235 TCGA-CV-7236 
       91.53        80.12        26.43         4.14        77.16         4.73 
TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7429 
       35.54         0.46        25.94        14.89        54.94         3.52 
TCGA-CV-7432 TCGA-CV-7438 TCGA-CV-A45W TCGA-CV-A460 TCGA-CX-7082 TCGA-CX-A4AQ 
       84.49         6.38        45.96        60.43        10.42        51.12 
TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
       18.67        17.72         7.63        46.32        46.45        20.45 
TCGA-F7-A50I TCGA-HD-8224 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A6SG 
        3.02        14.66        37.71        37.41         0.07        19.04 
TCGA-KU-A6H7 TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-QK-A6IF 
       19.27         7.13        16.08        51.25        36.82        23.15 
TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A719 
       12.20         8.32        12.72         3.12        13.25        54.67 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UP-A6WW 
       49.45        44.65        17.03 

$`16Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
        3.35        15.19         9.30        37.28        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 
       42.35        17.10        23.84        20.48        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       21.17        14.83         3.55        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       29.42        28.11        30.18        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 
       20.48        16.41         6.15       105.90         9.14         4.41 
TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HU 
       18.38        33.70        50.20        24.66        38.40        25.71 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
       27.19        12.92         8.81         6.28        12.69        48.76 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 
       55.86        38.04         4.67        51.29        56.68        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       32.81        52.14        57.11        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
       45.83        27.58        73.61        13.05        42.02         8.58 
TCGA-CN-5359 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
       12.39        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
        8.52        52.08        50.07        30.67        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 
       28.04        19.07        34.13         6.74         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       11.08        10.45        32.22        35.05        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B 
       17.42        32.48        11.74        25.41        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       21.21        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
        2.70        19.82        24.39        20.88        19.53        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       45.99        10.42        11.21         4.24        41.19        32.38 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       32.88        46.95        13.25         4.24        14.99        38.76 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
       70.13        64.87        53.52        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        77.56        44.48        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 
       29.49        14.14        12.46        31.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6474 
       37.87        26.27        50.01        39.52        34.52        18.54 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
       16.90         6.02        11.90        11.34         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       22.78        15.75         9.27        47.18        39.16        47.34 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
       35.84         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        29.82        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 
       32.65        44.25        30.58         7.10         5.95        35.41 
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-5966 
       19.20        17.95       107.51        87.55        76.50        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-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       140.78        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-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-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-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       18.41        57.47        17.85       210.97        89.33         9.67 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7425 
       22.85        25.08         0.07        34.09       100.57        56.48 
TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 
      156.49        16.27        19.76         7.17       153.86        16.64 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
       22.19        27.98        21.01       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 
       35.47         1.05         6.51        88.87        48.20        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        0.76        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       23.47        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-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-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK 
       16.14        11.44        24.95        25.32        12.36        28.77 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       58.45        37.25        30.94        33.86        18.02        14.04 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       37.58        40.24        40.04        39.12        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       32.71        21.63        20.25        31.13        18.94        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
        0.46        17.85        11.80        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       15.16        15.06        13.61        21.11        20.94         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        27.48        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G 
        6.90        34.75        15.95        38.53        14.50        11.84 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-KU-A66S 
       33.57         5.29        13.68        13.84        15.48        13.35 
TCGA-KU-A66T TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       18.15        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       12.62         6.25        15.42        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       71.74        10.85        47.01        19.00        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
        2.04        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.21         7.30        21.47         9.34        12.72        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB 
       21.07        19.73         6.51         5.62        14.76        17.82 
TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       15.32        16.96         6.87        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B 
       13.71        13.55        20.35        64.80         2.83        49.51 
TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       48.03        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       18.05        13.94        20.75        22.36        32.65         2.96 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.07               0.07 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             91.53             210.97 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            23.150             20.815 
[1] "0.1 - 91.5 (23.1)"  "0.1 - 211.0 (20.8)"
[1] "hr=" "1.2"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  16Q LOSS MUTATED         2        9        13        35         2         0
  16Q LOSS WILD-TYPE      25       67        69       218        10         1
D70V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  2                 25
  STAGE II                 9                 67
  STAGE III               13                 69
  STAGE IVA               35                218
  STAGE IVB                2                 10
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16Q LOSS MUTATED       6  23  17  17
  16Q LOSS WILD-TYPE    44 114  83 156
D70V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1                6                 44
  T2                  23                114
  T3                  17                 83
  T4                  17                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
  16Q LOSS MUTATED    17  12  27   2
  16Q LOSS WILD-TYPE 162  56 141   6
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               17                162
  N1               12                 56
  N2               27                141
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    24   0
  16Q LOSS WILD-TYPE 165   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     24    0
  16Q LOSS WILD-TYPE  165    1
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               24                165
  1                0                  1
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    17  64
  16Q LOSS WILD-TYPE 123 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     17   64
  16Q LOSS WILD-TYPE  123  318
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               17                123
  MALE                 64                318
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    21  47
  16Q LOSS WILD-TYPE 130 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     21   47
  16Q LOSS WILD-TYPE  130  236
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                21                130
  YES               47                236
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  16Q LOSS MUTATED                                      77
  16Q LOSS WILD-TYPE                                   434
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  16Q LOSS MUTATED                                                             0
  16Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  16Q LOSS MUTATED                                                     4
  16Q LOSS WILD-TYPE                                                   6
D70V9, multiclass
                                                             clus
vv                                                            16Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     77
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        4
                                                             clus
vv                                                            16Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      434
  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"
D70V10, continuous
D70V11, continuous
D70V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     2
  16Q LOSS WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           9    68
  16Q LOSS WILD-TYPE                        39   378
D70V13, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       9                 39
  WHITE                                          68                378
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V14, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     5  72
  16Q LOSS WILD-TYPE  21 387
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5   72
  16Q LOSS WILD-TYPE   21  387
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 21
  NOT HISPANIC OR LATINO               72                387
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    58  49
  17P LOSS WILD-TYPE 245 169
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               107                414 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                49                169 
$`17P LOSS MUTATED`
TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 
       26.50        42.35        20.48        68.48        15.52        14.83 
TCGA-BA-6871 TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A8YP 
        3.55        20.45        30.18        27.95        14.47        16.41 
TCGA-BB-4223 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-CN-4725 
      105.90        36.72        44.98        66.28        24.66        38.04 
TCGA-CN-4730 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5360 TCGA-CN-5364 
       26.86        57.11        45.83        13.05        71.31        16.21 
TCGA-CN-5374 TCGA-CN-6988 TCGA-CN-A49A TCGA-CN-A63W TCGA-CQ-6220 TCGA-CQ-6221 
       56.94        10.45        17.29        12.39        32.38        32.88 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7067 TCGA-CQ-7069 
       46.95        56.58        13.25        14.99        16.73        41.88 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CR-6472 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-7364 
       11.61        23.24        34.52        10.22        11.64        47.18 
TCGA-CR-7371 TCGA-CR-7390 TCGA-CR-7398 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5444 
        3.09        29.82         5.13        17.16        17.95        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6953 TCGA-CV-6961 
       17.92        13.35         7.07         9.60        53.95         2.50 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7253 TCGA-CV-7263 
        1.84        10.75        26.20        18.97        11.87        18.41 
TCGA-CV-7406 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7435 
       57.47         0.07       100.57        14.89        54.94       153.86 
TCGA-CV-7440 TCGA-CV-A460 TCGA-CV-A465 TCGA-CV-A6JU TCGA-CX-7086 TCGA-CX-7219 
       22.19        60.43         7.07         3.62        18.84        34.36 
TCGA-CX-A4AQ TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A6EM TCGA-DQ-5629 
       51.12        23.05        11.44        25.32         7.63        30.94 
TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7595 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A620 
       14.04        20.45        39.12        20.25        31.13        17.85 
TCGA-F7-A623 TCGA-H7-A6C5 TCGA-HD-7831 TCGA-HD-8635 TCGA-IQ-7630 TCGA-IQ-A61G 
       20.25        21.11        21.93        22.85        15.95        11.84 
TCGA-IQ-A61H TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN TCGA-P3-A5Q6 TCGA-P3-A5QA 
       37.41         1.84         6.25        15.42        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6VC 
       51.25        47.01        16.01        13.15        21.07        19.73 
TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-T2-A6WZ TCGA-T3-A92N TCGA-TN-A7HL 
        5.62        12.20        15.91         3.12        20.35 

$`17P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 
       23.74        57.93        17.10        23.84        65.59        21.17 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A6DA 
       12.62         4.01        41.85        29.42        28.11        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        7.10         5.69         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
       20.48         6.15         9.14         4.60         4.41        18.38 
TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       22.42        33.70        50.20        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-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
       12.69        48.76        55.86         4.67        51.29        56.68 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       12.89        32.81        52.14        12.99        20.55        14.33 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       27.58        73.61        42.02        46.32         8.58        12.39 
TCGA-CN-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-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       52.08        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       28.04        19.07        34.13         6.74         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       52.08        11.08        32.22        35.05        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        32.48        11.74        35.01        25.41        23.57 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
       29.72        21.21         7.40        31.69        22.32        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
        4.24        41.19         4.24        38.76        70.13        64.87 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB 
       53.52        43.04        43.10        77.56        44.48        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       39.52        36.99        18.54        16.90         6.02        11.90 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.34         7.69        12.46        22.78        15.75         9.27 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 
       39.16        47.34        40.93        35.84         3.45        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-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58         7.10 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 
        5.95        35.41        29.95        48.39       139.43       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
      108.95        76.24        19.20       107.51        87.55        76.50 
TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
       91.53        23.05        86.83        48.59        60.49        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       54.74        21.07        62.43        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      140.78        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
        6.08        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-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-7103 TCGA-CV-7104 TCGA-CV-7177 
        7.99         9.01         5.26        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       71.21       130.88        77.16         4.73        47.47        36.00 
TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7255 
       31.36        17.13        95.34         4.96        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       36.13        35.54        17.85       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7425 
        0.46        22.85        25.08        25.94        34.09        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-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       16.64         6.38        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
       48.20        67.86         0.76        56.61        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY 
       35.34         6.38        29.79         6.48        28.01        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-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 
       13.25        25.41         9.60         2.53        16.14        18.67 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EO 
       24.95        17.72        12.36        28.77        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        11.11        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7593 
       33.86        18.02        46.32        46.45        37.58        40.24 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I 
       40.04        41.59        37.18        32.71        21.63         3.02 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 
       18.94        24.95         0.46        11.80        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       15.16        15.06        13.61        20.94         0.07        28.47 
TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
       25.74        27.48        27.48        14.66        22.03        12.66 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
        0.36        13.84         4.27         3.65         6.90        34.75 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       38.53        14.50        37.71         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T 
       13.68        13.84        19.04        15.48        13.35        18.15 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F 
       19.27        10.75        14.37         7.96        30.05        12.62 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QF TCGA-P3-A6SW 
        7.13        16.08        17.98        29.92        10.85        36.82 
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-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.21        23.15         7.30        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J 
       18.64        21.07         6.51        14.76        17.82        15.32 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
        8.32        12.72        16.96         6.87         7.10        32.45 
TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.71        13.55        13.25        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       49.51        48.03        49.45        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36        32.65         2.96        17.03        20.55        14.56 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.07               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            153.86             210.97 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             20.25              21.19 
[1] "0.1 - 153.9 (20.2)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.2"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  17P LOSS MUTATED         2       19        19        48         4         1
  17P LOSS WILD-TYPE      25       57        63       205         8         0
D71V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  2                 25
  STAGE II                19                 57
  STAGE III               19                 63
  STAGE IVA               48                205
  STAGE IVB                4                  8
  STAGE IVC                1                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17P LOSS MUTATED       8  31  25  31
  17P LOSS WILD-TYPE    42 106  75 142
D71V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1                8                 42
  T2                  31                106
  T3                  25                 75
  T4                  31                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
  17P LOSS MUTATED    33  17  36   2
  17P LOSS WILD-TYPE 146  51 132   6
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               33                146
  N1               17                 51
  N2               36                132
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    34   1
  17P LOSS WILD-TYPE 155   0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     34    1
  17P LOSS WILD-TYPE  155    0
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               34                155
  1                1                  0
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    27  80
  17P LOSS WILD-TYPE 113 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     27   80
  17P LOSS WILD-TYPE  113  302
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               27                113
  MALE                 80                302
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    34  57
  17P LOSS WILD-TYPE 117 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     34   57
  17P LOSS WILD-TYPE  117  226
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                34                117
  YES               57                226
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  17P LOSS MUTATED                                     105
  17P LOSS WILD-TYPE                                   406
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  17P LOSS MUTATED                                                             0
  17P LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  17P LOSS MUTATED                                                     2
  17P LOSS WILD-TYPE                                                   8
D71V9, multiclass
                                                             clus
vv                                                            17P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    105
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            17P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      406
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V10, continuous
D71V11, continuous
D71V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0     2
  17P LOSS WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                          14    88
  17P LOSS WILD-TYPE                        34   358
D71V13, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                      14                 34
  WHITE                                          88                358
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V14, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     9  92
  17P LOSS WILD-TYPE  17 367
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      9   92
  17P LOSS WILD-TYPE   17  367
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                 17
  NOT HISPANIC OR LATINO               92                367
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    20  14
  17Q LOSS WILD-TYPE 283 204
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                34                487 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                14                204 
$`17Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A4II 
        9.30        68.48        15.52        14.83         3.55        30.18 
TCGA-BB-4223 TCGA-CN-4739 TCGA-CN-5374 TCGA-CN-6011 TCGA-CQ-6220 TCGA-CQ-6221 
      105.90        45.83        56.94        30.67        32.38        32.88 
TCGA-CQ-6224 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CR-6484 TCGA-CV-5966 TCGA-D6-6823 
       56.58        16.73        11.61        11.64        17.92        23.05 
TCGA-D6-6826 TCGA-F7-A50G TCGA-F7-A620 TCGA-HD-7831 TCGA-HD-8635 TCGA-IQ-7630 
       11.44        20.25        17.85        21.93        22.85        15.95 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       11.84        37.41         6.25        15.42        17.98        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-T2-A6WZ 
       71.74        51.25        47.01        15.91 

$`17Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19        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-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
       65.59        21.17        12.62         4.01        41.85        29.42 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       28.11        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
       16.41         6.15         9.14         4.60         4.41        18.38 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
       22.42        36.72        33.70        50.20        44.98        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-4722 
       27.19        12.92         8.81         6.28        12.69        48.76 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       55.86        38.04         4.67        51.29        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       26.86        32.81        52.14        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       14.33        27.58        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
        8.58        12.39        71.31         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
       11.84        11.57        12.49         8.52        52.08        50.07 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       48.00        23.90        47.44        28.04        19.07        34.13 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        6.74         9.07         9.24        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       32.22        35.05        38.89         3.68        17.42        32.48 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       20.88        19.53        48.20        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
        4.24        41.19        46.95        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
       38.76        70.13        64.87        53.52        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        77.56        44.48        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.49        14.14        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-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-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       10.22        11.34         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        29.82        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58         7.10         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      108.95        76.24        19.20        17.95       107.51        87.55 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       76.50        91.53        80.12        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        2.50         4.14        64.83       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-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
       54.94         3.52        16.27        84.49        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
      153.86        16.64         6.38        22.19        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
      169.38       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       56.61         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
       19.92        22.52        10.42        10.42        10.55        18.84 
TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 
       34.36        51.12        13.25        25.41         9.60         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-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       28.77         7.63        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
       12.79        11.11        58.45        37.25        30.94        33.86 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       18.02        14.04        46.32        46.45        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       40.24        40.04        39.12        41.59        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       21.63         3.02        31.13        18.94        24.95         0.46 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.61        21.11        20.94         0.07        28.47        25.74 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 
       27.48        27.48        14.66        22.03        12.66         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
       13.84         4.27         3.65         6.90        34.75        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       14.50        37.71         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
       13.84        19.04        15.48        13.35        18.15        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 
        7.13        16.08        29.92        10.85        36.82        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        18.64        21.07        19.73         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       12.72        16.96         6.87         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        3.12        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        49.51        48.03        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              3.55               0.07 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            105.90             210.97 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            19.115             21.010 
[1] "3.5 - 105.9 (19.1)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1"  
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  17Q LOSS MUTATED         2        4         8        14         0         0
  17Q LOSS WILD-TYPE      25       72        74       239        12         1
D72V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  2                 25
  STAGE II                 4                 72
  STAGE III                8                 74
  STAGE IVA               14                239
  STAGE IVB                0                 12
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17Q LOSS MUTATED       4  11   7   7
  17Q LOSS WILD-TYPE    46 126  93 166
D72V4, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1                4                 46
  T2                  11                126
  T3                   7                 93
  T4                   7                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
  17Q LOSS MUTATED     9   7  11   0
  17Q LOSS WILD-TYPE 170  61 157   8
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                9                170
  N1                7                 61
  N2               11                157
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    10   0
  17Q LOSS WILD-TYPE 179   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     10    0
  17Q LOSS WILD-TYPE  179    1
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               10                179
  1                0                  1
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     8  26
  17Q LOSS WILD-TYPE 132 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      8   26
  17Q LOSS WILD-TYPE  132  356
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                8                132
  MALE                 26                356
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    13  20
  17Q LOSS WILD-TYPE 138 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     13   20
  17Q LOSS WILD-TYPE  138  263
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                13                138
  YES               20                263
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  17Q LOSS MUTATED                                      33
  17Q LOSS WILD-TYPE                                   478
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  17Q LOSS MUTATED                                                             0
  17Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  17Q LOSS MUTATED                                                     1
  17Q LOSS WILD-TYPE                                                   9
D72V9, multiclass
                                                             clus
vv                                                            17Q LOSS 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                        1
                                                             clus
vv                                                            17Q LOSS 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                          9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V10, continuous
D72V11, continuous
D72V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  0     1
  17Q LOSS WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           3    29
  17Q LOSS WILD-TYPE                        45   417
D72V13, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       3                 45
  WHITE                                          29                417
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V14, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     3  28
  17Q LOSS WILD-TYPE  23 431
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3   28
  17Q LOSS WILD-TYPE   23  431
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               28                431
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    51  53
  18P LOSS WILD-TYPE 252 165
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               104                417 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                53                165 
$`18P LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A6D8 
        9.30        20.48        15.52        14.83        29.42        27.95 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DI TCGA-BB-8601 TCGA-CN-4727 TCGA-CN-4735 
        7.10         5.69        11.05        20.52        51.29        57.11 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6019 TCGA-CN-6994 
       45.83        27.58         8.52        50.07        34.13        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A640 TCGA-CQ-5325 
        3.68        17.42        11.74        23.57         4.41        21.50 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-7072 TCGA-CQ-A4C7 
       32.38        46.95        56.58        13.25        77.56        11.61 
TCGA-CQ-A4CG TCGA-CR-6484 TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7374 TCGA-CV-5435 
       14.14        11.64        47.34        29.23         0.99        76.24 
TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6937 
       17.95        80.12        17.92        54.74        90.12        20.52 
TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6948 TCGA-CV-6953 TCGA-CV-6960 TCGA-CV-6961 
       26.43       140.78        42.38        53.95        28.34         2.50 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7235 TCGA-CV-7236 
      111.16        18.81        52.31        12.92        77.16         4.73 
TCGA-CV-7245 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7416 TCGA-CV-7423 
       26.20        36.13        18.41        35.54        25.08       100.57 
TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7438 TCGA-CV-A45U 
       14.89         3.52        84.49        19.76         6.38        35.47 
TCGA-CV-A460 TCGA-CV-A465 TCGA-CX-7219 TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 
       60.43         7.07        34.36        58.45        30.94        33.86 
TCGA-DQ-7588 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A620 TCGA-F7-A623 
       14.04        37.18        21.63         3.02        17.85        20.25 
TCGA-H7-A6C4 TCGA-HD-7229 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61L 
       13.61         0.07        15.95        37.71        37.41        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A67D TCGA-P3-A6T0 
       13.84        19.04        13.35        14.37         1.84        19.00 
TCGA-P3-A6T5 TCGA-P3-A6T8 TCGA-QK-A6IH TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-T3-A92M 
       29.00        13.15        21.47        19.73        14.76        13.71 
TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A71D TCGA-UF-A7JF TCGA-UF-A7JO TCGA-UF-A7JS 
        3.12        13.25        48.03        55.43        20.75        22.36 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

$`18P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 
       23.74        42.35        57.93        17.10        23.84        65.59 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       68.48        21.17         3.55        12.62         4.01        41.85 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BA-A6DF 
       28.11        20.45        30.18        11.54        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
        2.27        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       33.70        50.20        44.98        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       71.05        25.71        10.55        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        6.28        12.69        48.76        55.86        38.04         4.67 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
       56.68        12.89        26.86        32.81        52.14        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       20.55        14.33        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
        8.58        12.39        71.31         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 
       11.84        11.57        12.49        52.08        56.94        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6020 
       48.00        23.90        47.44        28.04        19.07         6.74 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        9.07         9.24        52.08        11.08        10.45        32.22 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B 
       35.05        32.48        35.01        25.41        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        23.44        19.82        24.39        20.88 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       19.53        48.20        52.37         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       32.88         4.24        14.99        38.76        70.13        64.87 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
       53.52        16.73        43.04        41.88        43.10        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI 
       23.24        29.36        33.60        29.49        12.46        31.23 
TCGA-CR-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-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-7365 TCGA-CR-7368 
       22.78        15.75         9.27        47.18        39.16        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 
       35.84         3.45         3.09        24.95        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        29.82        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58         7.10         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       29.95        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5970 
       19.20       107.51        87.55        76.50        91.53        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-6934 TCGA-CV-6935 TCGA-CV-6936 
       21.07        62.43         9.60         2.14         9.70         5.46 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 
        4.73        21.90        11.24        19.79        12.03        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
       30.08         6.08        65.82        10.98         7.13         8.42 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        4.14        64.83       126.15        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
        5.26         1.84        21.80        71.21        10.75       130.88 
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-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7409 
        4.96        11.87        47.97         2.10        57.47        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 
      210.97        89.33         9.67         0.46        22.85        25.94 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        0.07        34.09        56.48       156.49        54.94        16.27 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
        7.17       153.86        16.64        22.19        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      169.38       180.16       159.65         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 
       88.87        48.20        67.86         0.76        56.61        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        11.11 
TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       37.25        18.02        46.32        46.45        20.45        37.58 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-A50G 
       40.24        40.04        39.12        41.59        32.71        20.25 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A624 
       31.13        18.94        24.95         0.46        11.80        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7753 
       13.38        15.16        15.06        21.11        20.94        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       25.74        21.93        27.48        27.48        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61I 
        6.90        34.75        38.53        14.50        11.84         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A6SH TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       33.57         5.29        15.48        18.15        19.27        10.75 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
        7.96        30.05        12.62         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
       16.08        17.98        29.92        15.78        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       10.85        36.82        47.01        75.55        18.97         2.04 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       12.99        16.01        21.07        21.21        23.15         7.30 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 
        9.34        12.72        18.64        21.07         6.51         5.62 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL 
        6.87        15.91         7.10        32.45        13.55        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
       64.80        54.67         2.83        49.51        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       74.47        17.95        24.30        29.46        18.05        13.94 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       32.65         2.96        17.03 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.07               0.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            140.78             210.97 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            20.535             21.070 
[1] "0.1 - 140.8 (20.5)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.3"
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  18P LOSS MUTATED         5       19        18        50         2         0
  18P LOSS WILD-TYPE      22       57        64       203        10         1
D73V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  5                 22
  STAGE II                19                 57
  STAGE III               18                 64
  STAGE IVA               50                203
  STAGE IVB                2                 10
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  18P LOSS MUTATED       9  28  20  38
  18P LOSS WILD-TYPE    41 109  80 135
D73V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1                9                 41
  T2                  28                109
  T3                  20                 80
  T4                  38                135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18P LOSS MUTATED    41  15  31   1
  18P LOSS WILD-TYPE 138  53 137   7
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               41                138
  N1               15                 53
  N2               31                137
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    36   0
  18P LOSS WILD-TYPE 153   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     36    0
  18P LOSS WILD-TYPE  153    1
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               36                153
  1                0                  1
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    35  69
  18P LOSS WILD-TYPE 105 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     35   69
  18P LOSS WILD-TYPE  105  313
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               35                105
  MALE                 69                313
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    30  53
  18P LOSS WILD-TYPE 121 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     30   53
  18P LOSS WILD-TYPE  121  230
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                30                121
  YES               53                230
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  18P LOSS MUTATED                                     102
  18P LOSS WILD-TYPE                                   409
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  18P LOSS MUTATED                                                             1
  18P LOSS WILD-TYPE                                                           0
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  18P LOSS MUTATED                                                     1
  18P LOSS WILD-TYPE                                                   9
D73V9, multiclass
                                                             clus
vv                                                            18P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    102
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            18P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      409
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V10, continuous
D73V11, continuous
D73V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0     2
  18P LOSS WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                          15    85
  18P LOSS WILD-TYPE                        33   361
D73V13, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                      15                 33
  WHITE                                          85                361
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V14, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    10  85
  18P LOSS WILD-TYPE  16 374
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     10   85
  18P LOSS WILD-TYPE   16  374
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                   10                 16
  NOT HISPANIC OR LATINO               85                374
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   116  95
  18Q LOSS WILD-TYPE 187 123
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               211                310 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                95                123 
$`18Q LOSS MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 
        3.35        15.19         9.30        20.48        65.59        15.52 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4II 
       14.83        12.62         4.01        41.85        29.42        30.18 
TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A6DL 
       27.95         7.10         5.69        14.47        11.05        20.48 
TCGA-BB-4224 TCGA-BB-7862 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A6UO 
        9.14        36.72        38.40        20.52        10.55         8.81 
TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
        6.28        55.86        38.04         4.67        51.29        56.68 
TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5355 TCGA-CN-5363 
       57.11        20.55        45.83        27.58        42.02         8.32 
TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
       16.21        11.84        11.57         8.52        52.08        50.07 
TCGA-CN-6011 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       30.67        34.13         9.24        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 
       11.74        23.57         7.40        31.69        12.39         4.41 
TCGA-CN-A641 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 
       12.07        21.50         2.93        10.42        41.19        32.38 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       64.87        53.52        16.73        77.56        44.48        11.61 
TCGA-CQ-A4CB TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-6493 
       29.36        14.14        11.77        18.54        11.64         9.27 
TCGA-CR-7365 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7386 TCGA-CR-7399 
       39.16        29.23         0.99         9.17        47.01         5.95 
TCGA-CR-7402 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 
       29.95        76.24        17.95       107.51        87.55        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
       17.92        13.35        86.83        48.59        60.49        43.23 
TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6942 
       54.74        90.12         9.70        20.52        26.43       140.78 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7089 
       12.03        42.38        53.95        65.82        28.34        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7104 
      126.15       111.16        18.81        12.66         5.26        12.92 
TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
       10.75        77.16         4.73        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 
       17.13        11.87         2.10        18.41        35.54        17.85 
TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       25.08       100.57        14.89         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45U TCGA-CV-A45X 
       19.76         7.17         6.38        22.19        35.47         6.51 
TCGA-CV-A465 TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CX-7086 
        7.07        28.01         3.62        23.47        22.52        18.84 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-A4Z9 
       34.36        25.41        23.05        16.14        24.95        17.72 
TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7595 TCGA-F7-7848 
       58.45        30.94        33.86        14.04        39.12        37.18 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
       21.63        20.25         3.02         0.46        17.85        20.25 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7831 
       15.16        15.06        13.61        21.11         0.07        21.93 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E 
       27.48        14.66        22.85         3.65        15.95        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
       11.84        37.41        13.68        13.84        19.04        15.48 
TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A7BN 
       13.35        18.15        14.37         7.96         1.84        15.42 
TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T8 TCGA-QK-A64Z 
       71.74        19.00         2.04        29.00        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO 
       21.21        21.47        14.76        12.20         8.32        12.72 
TCGA-T2-A6WZ TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A71B TCGA-UF-A71D 
       15.91        13.71         3.12        13.25        49.51        48.03 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       17.95        24.30        55.43        13.94        20.75        22.36 
TCGA-WA-A7H4 
       14.56 

$`18Q LOSS WILD-TYPE`
TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
       13.64        37.28         9.07        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6871 
       57.93        17.10        23.84        68.48        21.17         3.55 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ 
       28.11        20.45        11.54         7.82         2.27        13.38 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
       16.41         6.15       105.90         4.60         4.41        18.38 
TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
       22.42        33.70        50.20        44.98        66.28        24.66 
TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-C9-A480 TCGA-CN-4722 
       71.05        25.71        27.19        12.92        12.69        48.76 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 
       12.89        26.86        32.81        52.14        12.99        14.33 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       73.61        13.05        46.32         8.58        12.39        71.31 
TCGA-CN-5365 TCGA-CN-5369 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       11.54        12.49        56.94        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 
       28.04        19.07         6.74         9.07        52.08        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A498 
       10.45        32.22        35.05        32.48        35.01        25.41 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A642 
       17.29        29.72        21.21        22.32        16.57         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       23.44        19.82        24.39        20.88        19.53        48.20 
TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
       52.37        54.58        70.45        62.37        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        4.24        32.88        70.13        43.04        41.88        43.10 
TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       23.24        33.60        29.49        12.46        31.23        84.23 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
       34.52        36.99        16.90         6.02        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 
       11.34         7.69        12.46        22.78        15.75        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-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-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        29.82        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7404 
       44.25        30.58         7.10         5.13        35.41        48.39 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5442 
      139.43        17.16       129.21       108.95        19.20        76.50 
TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
       91.53        23.05         7.07        21.07        62.43         9.60 
TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6943 
        2.14         5.46         4.73        21.90        11.24        19.79 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
       15.09        30.08         6.08        10.98         7.13         8.42 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 
        2.50         4.14         7.99         9.01         1.84        52.31 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7250 
       21.80        71.21       130.88        47.47        36.00        95.34 
TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 
        4.96        47.97        36.13        57.47       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        9.67         0.46        22.85        25.94         0.07        34.09 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45O 
       56.48       156.49        54.94       153.86        16.64        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W 
       21.01       169.38       180.16       159.65         1.05        45.96 
TCGA-CV-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-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-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-A4AQ 
       21.24        19.92        10.42        10.42        10.55        51.12 
TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 
       13.25         9.60         2.53        11.44        18.67        25.32 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       12.36        28.77         7.63        22.59        24.95        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7589 
       12.10        12.79        11.11        37.25        18.02        46.32 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 
       46.45        20.45        37.58        40.24        40.04        41.59 
TCGA-F7-8298 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A622 TCGA-F7-A624 
       32.71        31.13        18.94        24.95        11.80        12.43 
TCGA-H7-7774 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8314 
       13.38        20.94        28.47        25.74        27.48        22.03 
TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       12.66         0.36        13.84         4.27         6.90        34.75 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-KU-A6H7 
       38.53        14.50         0.07        33.57         5.29        19.27 
TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 
       10.75        30.05        12.62         6.25         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       17.98        29.92        15.78        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A6IF 
       47.01        75.55        18.97        12.99        16.01        23.15 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
        7.30         9.34        12.72        18.64        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6WX 
        6.51         5.62        17.82        15.32        16.96         6.87 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        7.10        32.45        13.55        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JH TCGA-UF-A7JJ 
        2.83        49.45        44.65        74.47        29.46        18.05 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       32.65         2.96        17.03        20.55 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.07               0.07 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            140.78             210.97 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            18.970             22.505 
[1] "0.1 - 140.8 (19.0)" "0.1 - 211.0 (22.5)"
[1] "hr=" "1.3"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  18Q LOSS MUTATED        11       34        32       112         5         0
  18Q LOSS WILD-TYPE      16       42        50       141         7         1
D74V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                 11                 16
  STAGE II                34                 42
  STAGE III               32                 50
  STAGE IVA              112                141
  STAGE IVB                5                  7
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  18Q LOSS MUTATED      20 58 42 76
  18Q LOSS WILD-TYPE    30 79 58 97
D74V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1               20                 30
  T2                  58                 79
  T3                  42                 58
  T4                  76                 97
[1] 4 2
[1] 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
  18Q LOSS MUTATED    69  29  80   3
  18Q LOSS WILD-TYPE 110  39  88   5
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               69                110
  N1               29                 39
  N2               80                 88
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    72   0
  18Q LOSS WILD-TYPE 117   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     72    0
  18Q LOSS WILD-TYPE  117    1
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               72                117
  1                0                  1
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    54 157
  18Q LOSS WILD-TYPE  86 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     54  157
  18Q LOSS WILD-TYPE   86  225
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               54                 86
  MALE                157                225
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    57 112
  18Q LOSS WILD-TYPE  94 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     57  112
  18Q LOSS WILD-TYPE   94  171
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                57                 94
  YES              112                171
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  18Q LOSS MUTATED                                     209
  18Q LOSS WILD-TYPE                                   302
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  18Q LOSS MUTATED                                                             1
  18Q LOSS WILD-TYPE                                                           0
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  18Q LOSS MUTATED                                                     1
  18Q LOSS WILD-TYPE                                                   9
D74V9, multiclass
                                                             clus
vv                                                            18Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    209
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            18Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      302
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V10, continuous
D74V11, continuous
D74V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0     7
  18Q LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                          27   171
  18Q LOSS WILD-TYPE                        21   275
D74V13, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           7                  4
  BLACK OR AFRICAN AMERICAN                      27                 21
  WHITE                                         171                275
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V14, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    13 181
  18Q LOSS WILD-TYPE  13 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     13  181
  18Q LOSS WILD-TYPE   13  278
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   13                 13
  NOT HISPANIC OR LATINO              181                278
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    48  50
  19P LOSS WILD-TYPE 255 168
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                98                423 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                50                168 
$`19P LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5153 TCGA-BA-6868 TCGA-BA-A4IF TCGA-BA-A6DA 
        9.30        26.50        57.93        15.52        29.42        11.54 
TCGA-BB-4227 TCGA-BB-8596 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4729 
        4.41        71.05        10.55         6.28        38.04        12.89 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-5356 TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-5374 
       20.55        14.33        46.32         8.32         8.52        56.94 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6994 
       48.00        19.07         6.74         9.24        35.05        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A6V7 TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-6220 
        3.68        17.42        19.53         2.93        62.37        32.38 
TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       46.95        13.25        64.87        41.88        11.61        23.24 
TCGA-CR-6477 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7398 
       16.90        47.18        39.16        29.23         9.17         5.13 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 
      108.95        76.24        17.95        43.23        54.74         9.60 
TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 
       90.12        20.52        26.43        11.24        12.03        15.09 
TCGA-CV-6956 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7180 TCGA-CV-7254 TCGA-CV-7416 
        7.13        18.81        12.66        10.75        47.97        25.08 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7440 TCGA-CV-A45U TCGA-CV-A465 TCGA-CV-A6JN 
        3.52        16.27        22.19        35.47         7.07        29.79 
TCGA-CV-A6K1 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A6EM TCGA-D6-A6EQ 
       22.52        16.14        11.44        25.32         7.63        12.10 
TCGA-DQ-5624 TCGA-DQ-7588 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A61W 
       58.45        14.04        37.58        37.18         3.02         0.46 
TCGA-HD-7753 TCGA-HL-7533 TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61L TCGA-IQ-A6SG 
       28.47        34.75        11.84         0.07        13.68        19.04 
TCGA-IQ-A6SH TCGA-MT-A51X TCGA-P3-A6SX TCGA-QK-A652 TCGA-QK-A6IJ TCGA-QK-A8Z9 
       15.48         7.96        47.01        21.21        12.72        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-T3-A92M TCGA-T3-A92N TCGA-UF-A719 TCGA-UF-A7JC 
       12.20        17.82        13.71         3.12        54.67        17.95 
TCGA-UF-A7JK TCGA-UP-A6WW 
       13.94        17.03 

$`19P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 
        3.35        15.19        13.64        37.28         9.07        23.74 
TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       42.35        17.10        23.84        20.48        65.59        68.48 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       21.17        14.83         3.55        12.62         4.01        41.85 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD 
       28.11        20.45        30.18        27.95         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 
       16.41         6.15       105.90         9.14         4.60        18.38 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
       22.42        36.72        33.70        50.20        44.98        66.28 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM 
       24.66        38.40        20.52        25.71        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 
        8.81        12.69        48.76        55.86         4.67        51.29 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       56.68        26.86        32.81        52.14        57.11        12.99 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
       45.83        27.58        73.61        13.05        42.02         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       12.39        71.31        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
       12.49        52.08        50.07        30.67        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
       28.04        34.13         9.07        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       32.22        32.48        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       17.29        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       19.82        24.39        20.88        48.20        52.37        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        70.45        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       41.19        32.88        56.58         4.24        14.99        38.76 
TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 
       70.13        53.52        16.73        43.04        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       44.48        29.36        33.60        29.49        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
       58.42        50.01        39.52        34.52        36.99        18.54 
TCGA-CR-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-7367 TCGA-CR-7368 
       12.46        22.78        15.75         9.27        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 
       35.84         3.45         3.09        24.95         0.99        31.96 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        29.82        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       44.25        30.58         7.10         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5436 TCGA-CV-5440 
       48.39       139.43        17.16       129.21        19.20       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       87.55        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6433 
       23.05        86.83        48.59        60.49         7.07        21.07 
TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 
       62.43         2.14         9.70         5.46         4.73        21.90 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
      140.78        19.79        42.38        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       65.82        10.98         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
       64.83       126.15       111.16         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 
        1.84        52.31        12.92        21.80        71.21       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-7255 
       18.97        17.13        95.34         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-7418 TCGA-CV-7421 
       89.33         9.67         0.46        22.85        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       34.09       100.57        14.89        56.48       156.49        54.94 
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-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V 
       27.98        21.01       169.38       180.16       159.65         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
       45.96         6.51        88.87        48.20        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
        0.76        56.61        15.25         5.98        35.34         6.38 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ 
       10.42        10.42        10.55        18.84        34.36        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6827 
       13.25        25.41         9.60        23.05         2.53        18.67 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EO 
       24.95        17.72        12.36        28.77        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
       13.94        12.79        11.11        37.25        30.94        33.86 
TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 
       18.02        46.32        46.45        20.45        40.24        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J 
       39.12        41.59        32.71        21.63        20.25        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       18.94        24.95        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
        0.07        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       22.03        12.66        22.85         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        3.65         6.90        15.95        38.53        14.50        37.71 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
       37.41        33.57         5.29        13.84        13.35        18.15 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       19.27        10.75        14.37        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        6.25        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 
       15.78        71.74        51.25        10.85        36.82        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-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       13.15        21.07        23.15         7.30        21.47         9.34 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-AA3J 
       18.64        21.07        19.73         6.51         5.62        15.32 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
        8.32        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A 
       32.45        13.55        13.25        20.35        64.80         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD 
       49.51        48.03        49.45        44.65        74.47        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       55.43        29.46        18.05        20.75        22.36        32.65 
TCGA-UF-A7JV TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        20.55        14.56 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.07               0.07 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            108.95             210.97 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             17.62              21.47 
[1] "0.1 - 109.0 (17.6)" "0.1 - 211.0 (21.5)"
[1] "hr=" "1.5"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  19P LOSS MUTATED         2       13        25        46         1         0
  19P LOSS WILD-TYPE      25       63        57       207        11         1
D75V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  2                 25
  STAGE II                13                 63
  STAGE III               25                 57
  STAGE IVA               46                207
  STAGE IVB                1                 11
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19P LOSS MUTATED       5  31  23  30
  19P LOSS WILD-TYPE    45 106  77 143
D75V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1                5                 45
  T2                  31                106
  T3                  23                 77
  T4                  30                143
[1] 4 2
[1] 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
  19P LOSS MUTATED    27  20  33   1
  19P LOSS WILD-TYPE 152  48 135   7
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               27                152
  N1               20                 48
  N2               33                135
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    37   0
  19P LOSS WILD-TYPE 152   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     37    0
  19P LOSS WILD-TYPE  152    1
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               37                152
  1                0                  1
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    20  78
  19P LOSS WILD-TYPE 120 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     20   78
  19P LOSS WILD-TYPE  120  304
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               20                120
  MALE                 78                304
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    33  49
  19P LOSS WILD-TYPE 118 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     33   49
  19P LOSS WILD-TYPE  118  234
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                33                118
  YES               49                234
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  19P LOSS MUTATED                                      98
  19P LOSS WILD-TYPE                                   413
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  19P LOSS MUTATED                                                             0
  19P LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  19P LOSS MUTATED                                                     0
  19P LOSS WILD-TYPE                                                  10
D75V9, multiclass
                                                             clus
vv                                                            19P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     98
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            19P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      413
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V10, continuous
D75V11, continuous
D75V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  1     2
  19P LOSS WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                          13    78
  19P LOSS WILD-TYPE                        35   368
D75V13, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                      13                 35
  WHITE                                          78                368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V14, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     8  85
  19P LOSS WILD-TYPE  18 374
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      8   85
  19P LOSS WILD-TYPE   18  374
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                 18
  NOT HISPANIC OR LATINO               85                374
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    44  42
  19Q LOSS WILD-TYPE 259 176
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                86                435 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                42                176 
$`19Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 
        9.30        26.50        17.10        15.52        14.83         3.55 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BB-4227 TCGA-BB-8596 TCGA-BB-8601 
        4.01        29.42        11.54         4.41        71.05        20.52 
TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4737 TCGA-CN-5356 TCGA-CN-5363 
       10.55         6.28        38.04        20.55        46.32         8.32 
TCGA-CN-5374 TCGA-CN-6018 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
       56.94        19.07        32.22        35.05        38.89        17.42 
TCGA-CN-6997 TCGA-CN-A49A TCGA-CN-A6V7 TCGA-CQ-5326 TCGA-CQ-6220 TCGA-CQ-7064 
       32.48        17.29        19.53         2.93        32.38        64.87 
TCGA-CQ-7069 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-6477 TCGA-CR-7365 
       41.88        11.61        23.24        31.23        16.90        39.16 
TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7398 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       29.23         9.17         5.13       129.21       108.95        76.24 
TCGA-CV-5439 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6940 
       17.95        43.23        54.74         9.60        90.12        26.43 
TCGA-CV-6941 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-7097 TCGA-CV-7180 TCGA-CV-7254 
       11.24         7.13        28.34        12.66        10.75        47.97 
TCGA-CV-7261 TCGA-CV-7416 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-A45U TCGA-CV-A465 
       36.13        25.08         3.52        16.27        35.47         7.07 
TCGA-CV-A6JN TCGA-CV-A6K1 TCGA-D6-6517 TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A6EM 
       29.79        22.52         9.60        11.44        25.32         7.63 
TCGA-D6-A6EP TCGA-DQ-7588 TCGA-F7-A61W TCGA-HD-7753 TCGA-IQ-A61I TCGA-IQ-A61L 
       13.94        14.04         0.46        28.47         0.07        13.68 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A51X TCGA-P3-A6T2 TCGA-QK-A652 TCGA-QK-A6IJ 
       19.04        15.48         7.96        75.55        21.21        12.72 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-T3-A92M TCGA-T3-A92N TCGA-UF-A719 TCGA-UF-A71D 
       12.20        17.82        13.71         3.12        54.67        48.03 
TCGA-UF-A7JC TCGA-UF-A7JK 
       17.95        13.94 

$`19Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 
        3.35        15.19        13.64        37.28         9.07        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       42.35        57.93        23.84        20.48        65.59        68.48 
TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
       21.17        12.62        41.85        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-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        9.14         4.60        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HU 
       50.20        44.98        66.28        24.66        38.40        25.71 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
       27.19        12.92         8.81        12.69        48.76        55.86 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
        4.67        51.29        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       52.14        57.11        12.99        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       73.61        13.05        42.02         8.58        12.39        71.31 
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-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       52.08        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       28.04        34.13         6.74         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       11.08        10.45         3.68        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       23.57        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       19.82        24.39        20.88        48.20        52.37        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
        4.24        41.19        32.88        46.95        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 
        4.24        14.99        38.76        70.13        53.52        16.73 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.04        43.10        77.56        44.48        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       29.49        14.14        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-6492 TCGA-CR-6493 
       11.64         7.69        12.46        22.78        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-7374 TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
       24.95         0.99        31.96        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       17.13        32.78        47.01        27.06        12.89        29.82 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58         7.10 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        5.95        35.41        29.95        48.39       139.43        17.16 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       19.20       107.51        87.55        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
        7.07        21.07        62.43         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       20.52         4.73        21.90       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       42.38        15.09        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
       10.98         8.42         2.50         4.14        64.83       126.15 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
      111.16        18.81         7.99         9.01         5.26         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 
       52.31        12.92        21.80        71.21       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-7255 TCGA-CV-7263 
       17.13        95.34         4.96        11.87         2.10        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-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
        0.46        22.85        25.94         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 
       14.89        56.48       156.49        54.94        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
        7.17       153.86        16.64         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W 
       21.01       169.38       180.16       159.65         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JO 
       56.61        15.25         5.98        35.34         6.38         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 
       28.01         3.62        21.24        23.47        19.92        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 
       10.42        10.55        18.84        34.36        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 
       25.41        23.05         2.53        16.14        18.67        24.95 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ 
       17.72        12.36        28.77        22.59        24.95        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
       12.79        11.11        58.45        37.25        30.94        33.86 
TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       18.02        46.32        46.45        20.45        37.58        40.24 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       40.04        39.12        41.59        37.18        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 
       20.25         3.02        31.13        18.94        24.95        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 
       13.61        21.11        20.94         0.07        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       27.48        27.48        14.66        22.03        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
        0.36        13.84         4.27         3.65         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
       33.57         5.29        13.84        13.35        18.15        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       10.75        14.37        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-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-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 
       21.07        23.15         7.30        21.47         9.34        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-AA3J 
       21.07        19.73         6.51         5.62        14.76        15.32 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
        8.32        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A 
       32.45        13.55        13.25        20.35        64.80         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF 
       49.51        49.45        44.65        74.47        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       29.46        18.05        20.75        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.07               0.07 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            129.21             210.97 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             17.95              21.17 
[1] "0.1 - 129.2 (17.9)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.4"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  19Q LOSS MUTATED         1        9        25        41         2         0
  19Q LOSS WILD-TYPE      26       67        57       212        10         1
D76V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  1                 26
  STAGE II                 9                 67
  STAGE III               25                 57
  STAGE IVA               41                212
  STAGE IVB                2                 10
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19Q LOSS MUTATED       4  24  26  25
  19Q LOSS WILD-TYPE    46 113  74 148
D76V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1                4                 46
  T2                  24                113
  T3                  26                 74
  T4                  25                148
[1] 4 2
[1] 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
  19Q LOSS MUTATED    26  15  32   1
  19Q LOSS WILD-TYPE 153  53 136   7
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               26                153
  N1               15                 53
  N2               32                136
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    32   0
  19Q LOSS WILD-TYPE 157   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     32    0
  19Q LOSS WILD-TYPE  157    1
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               32                157
  1                0                  1
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    19  67
  19Q LOSS WILD-TYPE 121 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     19   67
  19Q LOSS WILD-TYPE  121  315
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               19                121
  MALE                 67                315
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    31  43
  19Q LOSS WILD-TYPE 120 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     31   43
  19Q LOSS WILD-TYPE  120  240
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                31                120
  YES               43                240
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  19Q LOSS MUTATED                                      85
  19Q LOSS WILD-TYPE                                   426
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  19Q LOSS MUTATED                                                             0
  19Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  19Q LOSS MUTATED                                                     1
  19Q LOSS WILD-TYPE                                                   9
D76V9, multiclass
                                                             clus
vv                                                            19Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     85
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            19Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      426
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V10, continuous
D76V11, continuous
D76V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     2
  19Q LOSS WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                          15    66
  19Q LOSS WILD-TYPE                        33   380
D76V13, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                      15                 33
  WHITE                                          66                380
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V14, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     6  73
  19Q LOSS WILD-TYPE  20 386
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6   73
  19Q LOSS WILD-TYPE   20  386
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 20
  NOT HISPANIC OR LATINO               73                386
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    25  22
  20P LOSS WILD-TYPE 278 196
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                47                474 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                22                196 
$`20P LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5152 TCGA-BA-5555 
       15.19         9.30        13.64        37.28        42.35        17.10 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BB-4227 TCGA-BB-7866 TCGA-BB-8601 
       14.83         3.55         4.01         4.41        44.98        20.52 
TCGA-BB-A6UO TCGA-CN-6011 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A63W 
        8.81        30.67        35.05        38.89         3.68        12.39 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-7364 TCGA-CR-7374 
       33.60        14.14        18.54         6.02        47.18         0.99 
TCGA-CR-7379 TCGA-CR-7383 TCGA-CV-5440 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7104 
       34.06        17.13       107.51       111.16         5.26        12.92 
TCGA-CV-7235 TCGA-CV-7247 TCGA-CV-7254 TCGA-CV-7407 TCGA-CV-7418 TCGA-CV-7435 
       77.16        18.97        47.97        35.54        25.94       153.86 
TCGA-CV-A460 TCGA-D6-6823 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-F7-7848 TCGA-F7-8298 
       60.43        23.05        46.32        46.45        37.18        32.71 
TCGA-F7-A623 TCGA-HD-7917 TCGA-IQ-7630 TCGA-QK-A6V9 TCGA-UF-A719 
       20.25        27.48        15.95        18.64        54.67 

$`20P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5556 
        3.35         9.07        26.50        23.74        57.93        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 
       20.48        65.59        68.48        15.52        21.17        12.62 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
       41.85        29.42        28.11        20.45        30.18        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        9.14         4.60        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A5HU 
       50.20        66.28        24.66        38.40        71.05        25.71 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
       10.55        27.19        12.92         6.28        12.69        48.76 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       55.86        38.04         4.67        51.29        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       26.86        32.81        52.14        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 
       46.32         8.58        12.39        71.31         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       56.94        50.07        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        34.13         6.74         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       11.08        10.45        32.22        17.42        32.48        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
        7.40        31.69        22.32        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
        2.70        23.44        19.82        24.39        20.88        19.53 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.38        32.88        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
       14.99        38.76        70.13        64.87        53.52        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       43.04        41.88        43.10        77.56        44.48        11.61 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       23.24        29.36        29.49        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-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        34.52        36.99        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       11.34        11.64         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-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-7376 TCGA-CR-7377 TCGA-CR-7380 
        3.09        24.95        29.23        31.96         9.17        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-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58         7.10 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       17.16       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       87.55        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       54.74        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        9.70         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       140.78        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        8.42        28.34         2.50         4.14        64.83       126.15 
TCGA-CV-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-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 
       21.80        71.21        10.75       130.88         4.73        47.47 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       36.00        31.36        26.20        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 
       11.87         2.10        36.13        18.41        57.47        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
      210.97        89.33         9.67         0.46        22.85        25.08 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
        0.07        34.09       100.57        14.89        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
       54.94         3.52        16.27        84.49        19.76         7.17 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       16.64         6.38        22.19        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       88.87        48.20        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ 
       10.42        10.42        10.55        18.84        34.36        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       13.25        25.41         9.60         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        7.63        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
       11.11        58.45        37.25        30.94        33.86        18.02 
TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       14.04        20.45        37.58        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       41.59        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 
       24.95         0.46        17.85        11.80        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       15.16        15.06        13.61        21.11        20.94         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       28.47        25.74        21.93        27.48        14.66        22.03 
TCGA-HD-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        38.53        14.50        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       37.41         0.07        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       19.04        15.48        13.35        18.15        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
        9.34        12.72        21.07        19.73         6.51         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       16.96         6.87        15.91         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A 
        3.12        13.55        13.25        20.35        64.80         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       49.51        48.03        49.45        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36        32.65         2.96        17.03        20.55        14.56 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.99               0.07 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            153.86             210.97 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             23.05              20.91 
[1] "1.0 - 153.9 (23.1)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1.1"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  20P LOSS MUTATED         3       10         5        21         0         0
  20P LOSS WILD-TYPE      24       66        77       232        12         1
D77V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  3                 24
  STAGE II                10                 66
  STAGE III                5                 77
  STAGE IVA               21                232
  STAGE IVB                0                 12
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  20P LOSS MUTATED       5  12   8  14
  20P LOSS WILD-TYPE    45 125  92 159
D77V4, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1                5                 45
  T2                  12                125
  T3                   8                 92
  T4                  14                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
  20P LOSS MUTATED    18   2  15   0
  20P LOSS WILD-TYPE 161  66 153   8
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               18                161
  N1                2                 66
  N2               15                153
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    17   0
  20P LOSS WILD-TYPE 172   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     17    0
  20P LOSS WILD-TYPE  172    1
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               17                172
  1                0                  1
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    12  35
  20P LOSS WILD-TYPE 128 347
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     12   35
  20P LOSS WILD-TYPE  128  347
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               12                128
  MALE                 35                347
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    18  21
  20P LOSS WILD-TYPE 133 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     18   21
  20P LOSS WILD-TYPE  133  262
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                18                133
  YES               21                262
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  20P LOSS MUTATED                                      47
  20P LOSS WILD-TYPE                                   464
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  20P LOSS MUTATED                                                             0
  20P LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  20P LOSS MUTATED                                                     0
  20P LOSS WILD-TYPE                                                  10
D77V9, multiclass
                                                             clus
vv                                                            20P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     47
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            20P LOSS 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                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V10, continuous
D77V11, continuous
D77V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     0
  20P LOSS WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           5    41
  20P LOSS WILD-TYPE                        43   405
D77V13, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       5                 43
  WHITE                                          41                405
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V14, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     2  43
  20P LOSS WILD-TYPE  24 416
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   43
  20P LOSS WILD-TYPE   24  416
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 24
  NOT HISPANIC OR LATINO               43                416
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    17  11
  20Q LOSS WILD-TYPE 286 207
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                28                493 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                11                207 
$`20Q LOSS MUTATED`
TCGA-BA-5152 TCGA-BA-6870 TCGA-BA-6871 TCGA-BB-7866 TCGA-BB-8601 TCGA-CN-4729 
       42.35        14.83         3.55        44.98        20.52        12.89 
TCGA-CN-5360 TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-6473 TCGA-CR-7370 TCGA-CR-7402 
       71.31        31.23        84.23        36.99         3.45        29.95 
TCGA-CV-5440 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7247 TCGA-CV-7254 
      107.51       111.16         5.26        77.16        18.97        47.97 
TCGA-CV-7407 TCGA-CV-7418 TCGA-CV-7435 TCGA-CV-A460 TCGA-D6-6826 TCGA-DQ-7590 
       35.54        25.94       153.86        60.43        11.44        46.45 
TCGA-HD-7917 TCGA-IQ-7630 TCGA-KU-A6H7 TCGA-UF-A719 
       27.48        15.95        19.27        54.67 

$`20Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       26.50        23.74        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 
       65.59        68.48        15.52        21.17        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
       41.85        29.42        28.11        20.45        30.18        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.60         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       33.70        50.20        66.28        24.66        38.40        71.05 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       25.71        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
       12.69        48.76        55.86        38.04         4.67        51.29 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       56.68        26.86        32.81        52.14        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        45.83        27.58        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5364 
       42.02        46.32         8.58        12.39         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       56.94        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       28.04        19.07        34.13         6.74         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
       52.08        11.08        10.45        32.22        35.05        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        3.68        17.42        32.48        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       23.57        17.29        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       23.44        19.82        24.39        20.88        19.53        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       45.99        10.42        11.21         4.24        41.19        32.38 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       32.88        46.95        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       38.76        70.13        64.87        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        43.10        77.56        44.48        11.61        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5247 
       29.36        33.60        29.49        14.14        12.46        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-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
       34.52        18.54        16.90         6.02        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       11.34        11.64         7.69        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.09        24.95        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        29.82        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58         7.10         5.13         5.95        35.41 
TCGA-CR-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        87.55        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        7.07        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       90.12         2.14         9.70         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       21.90        26.43        11.24       140.78        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       42.38        15.09        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       10.98         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
       64.83       126.15        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-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
      130.88         4.73        47.47        36.00        31.36        26.20 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 
       17.13        95.34         4.96        11.87         2.10        36.13 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       18.41        57.47        17.85       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
        0.46        22.85        25.08         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
       14.89        56.48       156.49        54.94         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       84.49        19.76         7.17        16.64         6.38        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        21.01       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 
        1.05        45.96         6.51        88.87        48.20        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        0.76        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
       23.47        19.92        22.52        10.42        10.42        10.55 
TCGA-CX-7086 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       18.84        34.36        51.12        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
       23.05         2.53        16.14        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        11.11        58.45        37.25 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 
       30.94        33.86        18.02        14.04        46.32        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       37.58        40.24        40.04        39.12        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       24.95         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
        0.07        28.47        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       22.03        12.66        22.85         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        3.65         6.90        34.75        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        37.41         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H8 
       13.84        19.04        15.48        13.35        18.15        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        18.64        21.07        19.73         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.72        16.96         6.87        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       13.71         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        49.51        48.03        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              3.45               0.07 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            153.86             210.97 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            33.385             20.550 
[1] "3.5 - 153.9 (33.4)" "0.1 - 211.0 (20.6)"
[1] "hr=" "1.5"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  20Q LOSS MUTATED         1        8         4         7         0         0
  20Q LOSS WILD-TYPE      26       68        78       246        12         1
D78V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  1                 26
  STAGE II                 8                 68
  STAGE III                4                 78
  STAGE IVA                7                246
  STAGE IVB                0                 12
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  20Q LOSS MUTATED       2  10   3   5
  20Q LOSS WILD-TYPE    48 127  97 168
D78V4, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1                2                 48
  T2                  10                127
  T3                   3                 97
  T4                   5                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
  20Q LOSS MUTATED     8   3   6   0
  20Q LOSS WILD-TYPE 171  65 162   8
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                8                171
  N1                3                 65
  N2                6                162
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     7   0
  20Q LOSS WILD-TYPE 182   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      7    0
  20Q LOSS WILD-TYPE  182    1
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                7                182
  1                0                  1
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     6  22
  20Q LOSS WILD-TYPE 134 360
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6   22
  20Q LOSS WILD-TYPE  134  360
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                6                134
  MALE                 22                360
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     6  16
  20Q LOSS WILD-TYPE 145 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6   16
  20Q LOSS WILD-TYPE  145  267
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 6                145
  YES               16                267
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  20Q LOSS MUTATED                                      27
  20Q LOSS WILD-TYPE                                   484
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  20Q LOSS MUTATED                                                             0
  20Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  20Q LOSS MUTATED                                                     1
  20Q LOSS WILD-TYPE                                                   9
D78V9, multiclass
                                                             clus
vv                                                            20Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     27
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            20Q LOSS 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                          9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V10, continuous
D78V11, continuous
D78V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     0
  20Q LOSS WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           3    24
  20Q LOSS WILD-TYPE                        45   422
D78V13, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       3                 45
  WHITE                                          24                422
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V14, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1  25
  20Q LOSS WILD-TYPE  25 434
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1   25
  20Q LOSS WILD-TYPE   25  434
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               25                434
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   102  81
  21Q LOSS WILD-TYPE 201 137
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               183                338 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                81                137 
$`21Q LOSS MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 
        3.35         9.30        65.59        68.48        15.52        14.83 
TCGA-BA-6871 TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-8596 
        3.55        27.95        11.54        36.72        50.20        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-CN-4725 
       20.52        25.71        10.55        27.19         6.28        38.04 
TCGA-CN-4728 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 
       56.68        12.99        14.33        45.83        73.61        13.05 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 
        8.32        11.54         8.52        56.94        50.07        48.00 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6994 TCGA-CN-6996 
       19.07        34.13         9.07         9.24        38.89        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63W 
       32.48        11.74        23.57        29.72         7.40        12.39 
TCGA-CQ-5323 TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6220 TCGA-CQ-6223 
       48.20         2.93        62.37        10.42        32.38        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
       56.58        13.25        38.76        64.87        53.52        16.73 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CE 
       41.88        77.56        44.48        11.61        23.24        29.49 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6491 
       12.46        31.23        11.77        16.90        11.64        22.78 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 
       39.16        47.34        35.84         3.45         3.09        29.23 
TCGA-CR-7388 TCGA-CR-7399 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5444 
       27.06         5.95        17.16        17.95       107.51        80.12 
TCGA-CV-5966 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       17.92        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6934 TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 
        2.14        20.52        11.24        65.82         7.13         8.42 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 
        2.50         4.14        64.83       126.15       111.16        12.66 
TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7235 
        5.26        52.31        12.92        21.80        10.75        77.16 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 
       36.00        26.20        18.97        17.13        47.97        36.13 
TCGA-CV-7263 TCGA-CV-7409 TCGA-CV-7416 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 
       18.41        17.85        25.08        34.09       100.57        14.89 
TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45W TCGA-CV-A465 TCGA-CV-A6JN 
       84.49       153.86        22.19        45.96         7.07        29.79 
TCGA-CV-A6JU TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 
        3.62        10.42        18.84        34.36        25.41        23.05 
TCGA-D6-6826 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-D6-A74Q 
       11.44        17.72        12.36         7.63        12.10        11.11 
TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7592 TCGA-F7-A50G TCGA-F7-A50I 
       58.45        30.94        14.04        37.58        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 
       31.13         0.46        17.85        15.16        15.06         0.07 
TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-8634 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-A61E 
       28.47        21.93        12.66        13.84         3.65        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-KU-A66T 
       11.84        37.41        33.57        13.68        15.48        18.15 
TCGA-MT-A51X TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SX 
        7.96        17.98        15.78        71.74        10.85        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T8 
       19.00        75.55        18.97         2.04        29.00        13.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-AA3J 
        7.30        21.47        12.72         6.51        14.76        15.32 
TCGA-QK-AA3K TCGA-T3-A92N TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JD 
        8.32         3.12         2.83        49.45        44.65        24.30 
TCGA-UF-A7JH TCGA-UF-A7JK TCGA-WA-A7H4 
       29.46        13.94        14.56 

$`21Q LOSS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
       15.19        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-6869 
       42.35        57.93        17.10        23.84        20.48        21.17 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       12.62         4.01        41.85        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       30.18         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 
        9.14         4.60         4.41        18.38        22.42        33.70 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A6UM TCGA-BB-A6UO 
       44.98        66.28        24.66        38.40        12.92         8.81 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 
       12.69        48.76        55.86         4.67        51.29        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4740 
       26.86        32.81        52.14        57.11        20.55        27.58 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5364 
       42.02        46.32         8.58        12.39        71.31        16.21 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-6011 TCGA-CN-6013 
       11.84        11.57        12.49        52.08        30.67        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
       47.44        28.04         6.74        52.08        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A 
       32.22        35.05         3.68        35.01        25.41        17.29 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       21.21        31.69        22.32        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
        2.70        23.44        19.82        24.39        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 
       52.37        21.50        54.58        70.45        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 
        4.24        41.19        32.88         4.24        14.99        70.13 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-5243 
       43.04        43.10        29.36        33.60        14.14        84.23 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
       34.52        36.99        18.54         6.02        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
       11.34         7.69        12.46        15.75         9.27        47.18 
TCGA-CR-7368 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       40.93        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-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        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        7.10         5.13        35.41        29.95        48.39       139.43 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 
      129.21       108.95        76.24        19.20        87.55        76.50 
TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-6433 TCGA-CV-6436 
       91.53        13.35        23.05        86.83        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 
        9.60        90.12         9.70         5.46         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       26.43       140.78        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6960 TCGA-CV-7095 
       30.08         6.08        53.95        10.98        28.34        18.81 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7236 
        7.99         9.01         1.84        71.21       130.88         4.73 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 
       47.47        31.36        95.34         4.96        11.87         2.10 
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-7418 TCGA-CV-7421 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       22.85        25.94         0.07        56.48       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 
        3.52        16.27        19.76         7.17        16.64         6.38 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        21.01       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
        1.05         6.51        88.87        48.20        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
        0.76        56.61        15.25         5.98        35.34         6.38 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
        6.48        28.01        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6824 
       10.42        10.55        51.12        13.25         9.60         2.53 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EN 
       16.14        18.67        24.95        25.32        28.77        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       24.95        13.94        12.79        37.25        33.86        18.02 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       46.32        46.45        20.45        40.24        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A61S TCGA-F7-A61V 
       41.59        37.18        32.71        21.63        18.94        24.95 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-A6C4 TCGA-H7-A6C5 
       11.80        20.25        12.43        13.38        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       20.94        25.74        27.48        27.48        14.66        22.03 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
       22.85         0.36         4.27         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG 
       38.53        14.50         0.07         5.29        13.84        19.04 
TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D 
       13.35        19.27        10.75        14.37        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       12.62         6.25        15.42         7.13        16.08        29.92 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 
       51.25        36.82        12.99        16.01        21.07        21.21 
TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 
       23.15         9.34        18.64        21.07        19.73         5.62 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       12.20        17.82        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
        7.10        32.45        13.71        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JC 
       64.80        54.67        49.51        48.03        74.47        17.95 
TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       55.43        18.05        20.75        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ 
       17.03        20.55 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.07               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            153.86             210.97 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             18.97              21.14 
[1] "0.1 - 153.9 (19.0)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.2"
D79V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  21Q LOSS MUTATED         8       30        31        93         6         0
  21Q LOSS WILD-TYPE      19       46        51       160         6         1
D79V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  8                 19
  STAGE II                30                 46
  STAGE III               31                 51
  STAGE IVA               93                160
  STAGE IVB                6                  6
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  21Q LOSS MUTATED      10  54  41  64
  21Q LOSS WILD-TYPE    40  83  59 109
D79V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1               10                 40
  T2                  54                 83
  T3                  41                 59
  T4                  64                109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  21Q LOSS MUTATED    58  30  62   4
  21Q LOSS WILD-TYPE 121  38 106   4
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               58                121
  N1               30                 38
  N2               62                106
  N3                4                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    64   0
  21Q LOSS WILD-TYPE 125   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     64    0
  21Q LOSS WILD-TYPE  125    1
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               64                125
  1                0                  1
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    47 137
  21Q LOSS WILD-TYPE  93 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     47  137
  21Q LOSS WILD-TYPE   93  245
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               47                 93
  MALE                137                245
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    46 101
  21Q LOSS WILD-TYPE 105 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     46  101
  21Q LOSS WILD-TYPE  105  182
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                46                105
  YES              101                182
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  21Q LOSS MUTATED                                     180
  21Q LOSS WILD-TYPE                                   331
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  21Q LOSS MUTATED                                                             0
  21Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  21Q LOSS MUTATED                                                     4
  21Q LOSS WILD-TYPE                                                   6
D79V9, multiclass
                                                             clus
vv                                                            21Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    180
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        4
                                                             clus
vv                                                            21Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      331
  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"
D79V10, continuous
D79V11, continuous
D79V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  1     7
  21Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                          25   145
  21Q LOSS WILD-TYPE                        23   301
D79V13, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           7                  4
  BLACK OR AFRICAN AMERICAN                      25                 23
  WHITE                                         145                301
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V14, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     8 161
  21Q LOSS WILD-TYPE  18 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      8  161
  21Q LOSS WILD-TYPE   18  298
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                 18
  NOT HISPANIC OR LATINO              161                298
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    49  25
  22Q LOSS WILD-TYPE 254 193
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                74                447 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                25                193 
$`22Q LOSS MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5558 TCGA-BA-6870 TCGA-BA-6871 
        3.35         9.30        26.50        65.59        14.83         3.55 
TCGA-BA-A6DE TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-A5HY 
       14.47       105.90         9.14         4.60        22.42        10.55 
TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4730 TCGA-CN-5355 TCGA-CN-5370 TCGA-CN-6018 
        6.28        38.04        26.86        42.02         8.52        19.07 
TCGA-CN-6021 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A63W TCGA-CN-A6V7 TCGA-CQ-5327 
        9.07         3.68        11.74        12.39        19.53        54.58 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-A4C7 TCGA-CQ-A4CE TCGA-CR-5248 TCGA-CR-6488 
       64.87        53.52        11.61        29.49        54.67        12.46 
TCGA-CR-6493 TCGA-CR-7373 TCGA-CR-7379 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5973 
        9.27        29.23        34.06         5.13         5.95        86.83 
TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6945 TCGA-CV-6962 TCGA-CV-7091 
       60.49        54.74         9.60        12.03         4.14       111.16 
TCGA-CV-7180 TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7432 TCGA-CV-A465 
       10.75         9.67        25.08         0.07        84.49         7.07 
TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CX-7086 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EM 
       21.24        22.52        18.84        25.32        17.72         7.63 
TCGA-DQ-5631 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A623 
       18.02        37.58        40.24        20.25        31.13        20.25 
TCGA-HD-A633 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A6SG TCGA-MT-A51W 
       13.84        15.95        37.71        11.84        19.04        14.37 
TCGA-MT-A67G TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VB 
        6.25        71.74        19.00        21.47        12.72        21.07 
TCGA-T3-A92M TCGA-T3-A92N 
       13.71         3.12 

$`22Q LOSS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
       15.19        13.64        37.28         9.07        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 
       57.93        17.10        23.84        20.48        68.48        15.52 
TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG 
       21.17        12.62         4.01        41.85        29.42        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-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
        7.82         2.27        11.05        13.38        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        6.15         4.41        18.38        36.72        33.70        50.20 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       44.98        66.28        24.66        38.40        71.05        20.52 
TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 
       25.71        27.19        12.92         8.81        12.69        48.76 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 
       55.86         4.67        51.29        56.68        12.89        32.81 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       52.14        57.11        12.99        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       27.58        73.61        13.05        46.32         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       71.31         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
       12.49        52.08        56.94        50.07        30.67        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 
       23.90        47.44        28.04        34.13         6.74         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
       52.08        11.08        10.45        32.22        35.05        38.89 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       17.42        32.48        35.01        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
       29.72        21.21         7.40        31.69        22.32        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 
       20.88        48.20        52.37        21.50         2.93        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.38        32.88        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
       14.99        38.76        70.13        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        77.56        44.48        23.24        29.36        33.60 
TCGA-CQ-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-6481 TCGA-CR-6482 
       18.54        16.90         6.02        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 
       11.64         7.69        22.78        15.75        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-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
        0.99        31.96         9.17        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-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-7401 
       46.85        32.65        44.25        30.58         7.10        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       29.95        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       76.24        19.20        17.95       107.51        87.55        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 
       91.53        80.12        17.92        13.35        23.05        48.59 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 
        7.07        43.23        21.07        62.43        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-6948 TCGA-CV-6950 TCGA-CV-6951 
       11.24       140.78        19.79        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-7089 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 
       28.34         2.50        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-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       21.80        71.21       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-7414 
       57.47        35.54        17.85       210.97        89.33         0.46 
TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
       22.85        25.94        34.09       100.57        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 
      156.49        54.94         3.52        16.27        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
      153.86        16.64         6.38        22.19        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
      169.38       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
       56.61        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-A6K2 
        6.48        28.01         3.62        23.47        19.92        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        34.36        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       24.95        12.36        28.77        22.59        24.95        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
       12.10        12.79        11.11        58.45        37.25        30.94 
TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 
       33.86        14.04        46.32        46.45        20.45        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I 
       39.12        41.59        37.18        32.71        21.63         3.02 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 
       18.94        24.95         0.46        17.85        11.80        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-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-A61H 
        3.65         6.90        34.75        38.53        14.50        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SH 
        0.07        33.57         5.29        13.68        13.84        15.48 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A 
       13.35        18.15        19.27        10.75         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
        1.84        12.62        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       29.92        15.78        51.25        10.85        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-A6II 
       13.15        21.07        21.21        23.15         7.30         9.34 
TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       18.64        19.73         6.51         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       17.82        15.32         8.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       15.91         7.10        32.45        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       64.80        54.67         2.83        49.51        48.03        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       18.05        13.94        20.75        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.07               0.07 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            111.16             210.97 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             18.43              21.21 
[1] "0.1 - 111.2 (18.4)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.1"
D80V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  22Q LOSS MUTATED         3       12        17        33         1         0
  22Q LOSS WILD-TYPE      24       64        65       220        11         1
D80V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  3                 24
  STAGE II                12                 64
  STAGE III               17                 65
  STAGE IVA               33                220
  STAGE IVB                1                 11
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  22Q LOSS MUTATED       6  22  19  19
  22Q LOSS WILD-TYPE    44 115  81 154
D80V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1                6                 44
  T2                  22                115
  T3                  19                 81
  T4                  19                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
  22Q LOSS MUTATED    27  13  22   0
  22Q LOSS WILD-TYPE 152  55 146   8
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               27                152
  N1               13                 55
  N2               22                146
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    28   0
  22Q LOSS WILD-TYPE 161   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     28    0
  22Q LOSS WILD-TYPE  161    1
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               28                161
  1                0                  1
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    25  50
  22Q LOSS WILD-TYPE 115 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     25   50
  22Q LOSS WILD-TYPE  115  332
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               25                115
  MALE                 50                332
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    24  43
  22Q LOSS WILD-TYPE 127 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     24   43
  22Q LOSS WILD-TYPE  127  240
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                24                127
  YES               43                240
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  22Q LOSS MUTATED                                      75
  22Q LOSS WILD-TYPE                                   436
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  22Q LOSS MUTATED                                                             0
  22Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  22Q LOSS MUTATED                                                     0
  22Q LOSS WILD-TYPE                                                  10
D80V9, multiclass
                                                             clus
vv                                                            22Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     75
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            22Q LOSS 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                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V10, continuous
D80V11, continuous
D80V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  1     3
  22Q LOSS WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                           8    60
  22Q LOSS WILD-TYPE                        40   386
D80V13, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                       8                 40
  WHITE                                          60                386
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V14, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     6  64
  22Q LOSS WILD-TYPE  20 395
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6   64
  22Q LOSS WILD-TYPE   20  395
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 20
  NOT HISPANIC OR LATINO               64                395
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    69  65
  XP LOSS WILD-TYPE 234 153
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              134               387 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               65               153 
$`XP LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-6868 TCGA-BA-6872 
       15.19        13.64         9.07        26.50        15.52        12.62 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7862 
       20.45        27.95        14.47        20.48        16.41        36.72 
TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A6UM TCGA-BB-A6UO 
       24.66        71.05        25.71        10.55        12.92         8.81 
TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-5359 
       38.04        56.68        57.11        12.99        20.55        12.39 
TCGA-CN-5360 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6024 TCGA-CN-6988 
       71.31        50.07        48.00        19.07        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A49A TCGA-CN-A49B 
       32.22        35.05        17.42        32.48        17.29        29.72 
TCGA-CN-A6V7 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6227 
       19.53        10.42        41.19        32.38        32.88         4.24 
TCGA-CQ-6229 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 
       38.76        77.56        11.61        31.23        11.77        54.67 
TCGA-CR-6472 TCGA-CR-6487 TCGA-CR-6493 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7380 
       34.52         7.69         9.27         3.09         0.99        19.92 
TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       17.13        27.06        29.82         7.10         5.13         5.95 
TCGA-CV-5430 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5976 TCGA-CV-6441 TCGA-CV-6935 
      139.43        76.24        17.95        48.59         9.60         9.70 
TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6948 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-7095 
        5.46        26.43        42.38         8.42        28.34        18.81 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7243 TCGA-CV-7245 
        5.26         1.84        77.16         4.73        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7255 TCGA-CV-7418 TCGA-CV-7425 TCGA-CV-7430 TCGA-CV-7432 
       18.97         2.10        25.94        56.48        16.27        84.49 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45Q TCGA-CV-A460 TCGA-CV-A465 TCGA-CV-A6JY 
       16.64         6.38       169.38        60.43         7.07        21.24 
TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6827 TCGA-D6-8568 
       22.52        10.42        18.84        25.41        18.67        24.95 
TCGA-D6-A6EM TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7592 
        7.63        37.25        30.94        18.02        14.04        37.58 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-A6C5 
       37.18        21.63        20.25         0.46        17.85        21.11 
TCGA-HD-7917 TCGA-HD-8635 TCGA-IQ-A6SG TCGA-MT-A51X TCGA-MT-A7BN TCGA-MZ-A6I9 
       27.48        22.85        19.04         7.96        15.42        16.08 
TCGA-P3-A5QE TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-QK-A6IH TCGA-QK-A8Z8 TCGA-QK-A8ZB 
       51.25        18.97         2.04        21.47         5.62        17.82 
TCGA-QK-AA3J TCGA-T2-A6WZ TCGA-T3-A92M TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A71E 
       15.32        15.91        13.71        13.25        54.67        49.45 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UP-A6WW 
       17.95        24.30        29.46        20.75        22.36        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

$`XP LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
        3.35         9.30        37.28        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 
       17.10        23.84        20.48        65.59        68.48        21.17 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG 
       14.83         3.55         4.01        41.85        29.42        28.11 
TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG 
       30.18        11.54         7.10         5.69         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       11.05        13.38         6.15       105.90         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
        4.41        18.38        22.42        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-C9-A480 
       66.28        38.40        20.52        27.19         6.28        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 
       48.76        55.86         4.67        51.29        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       32.81        52.14        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5364 
       13.05        42.02        46.32         8.58         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        52.08 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
       56.94        30.67        23.90        47.44        28.04        34.13 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6995 
        6.74         9.07         9.24        52.08        38.89         3.68 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63T 
       11.74        35.01        25.41        23.57        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5323 
        2.70        23.44        19.82        24.39        20.88        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       45.99        11.21         4.24        46.95        56.58        13.25 
TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       14.99        70.13        64.87        53.52        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       41.88        43.10        44.48        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-5250 
       29.49        14.14        12.46        84.23        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       58.42        50.01        39.52        36.99        18.54        16.90 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 
        6.02        11.90        10.22        11.34        11.64        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       22.78        15.75        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 
       35.84         3.45        24.95        29.23        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 
       34.06        26.17        32.78        47.01        12.89        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7401 TCGA-CR-7402 
       46.85        32.65        44.25        30.58        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5440 
       48.39        17.16       129.21       108.95        19.20       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       87.55        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       23.05        86.83        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6937 TCGA-CV-6938 
       21.07        62.43        90.12         2.14        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 
       21.90        11.24       140.78        19.79        12.03        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-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 
        2.50         4.14        64.83       126.15       111.16        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        7.99         9.01        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7248 TCGA-CV-7250 
       10.75       130.88        47.47        36.00        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
        4.96        11.87        47.97        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-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 
       22.85        25.08         0.07        34.09       100.57        14.89 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
      156.49        54.94         3.52        19.76         7.17       153.86 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       22.19        27.98        21.01       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 
        1.05        45.96         6.51        88.87        48.20        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
        0.76        56.61        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 
       29.79         6.48        28.01         3.62        23.47        19.92 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 
       10.42        10.55        34.36        51.12        13.25         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A4Z9 
       23.05         2.53        16.14        11.44        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       12.36        28.77        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 
       12.79        11.11        58.45        33.86        46.32        46.45 
TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 
       20.45        40.24        40.04        39.12        41.59        32.71 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A622 TCGA-F7-A623 
        3.02        31.13        18.94        24.95        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A 
       12.43        13.38        15.16        15.06        13.61        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
        0.07        28.47        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       22.03        12.66         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        37.41         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.84        15.48        13.35        18.15        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI 
       14.37        30.05         1.84        12.62         6.25         7.13 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SW 
       17.98        29.92        15.78        71.74        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       47.01        19.00        75.55        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
       13.15        21.07        21.21        23.15         7.30         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 
       12.72        18.64        21.07        19.73         6.51        14.76 
TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
       12.20         8.32        12.72        16.96         6.87         7.10 
TCGA-T2-A6X2 TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A 
       32.45         3.12        13.55        20.35        64.80         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JJ 
       49.51        48.03        44.65        74.47        55.43        18.05 
TCGA-UF-A7JK TCGA-UF-A7JT TCGA-UF-A7JV 
       13.94        32.65         2.96 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.46              0.07 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           169.38            210.97 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
             19.3              21.5 
[1] "0.5 - 169.4 (19.3)" "0.1 - 211.0 (21.5)"
[1] "hr=" "1.4"
D81V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  XP LOSS MUTATED         6       17        22        61         5         1
  XP LOSS WILD-TYPE      21       59        60       192         7         0
D81V3, multiclass
           clus
vv          XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 6                21
  STAGE II               17                59
  STAGE III              22                60
  STAGE IVA              61               192
  STAGE IVB               5                 7
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  XP LOSS MUTATED      12  29  38  37
  XP LOSS WILD-TYPE    38 108  62 136
D81V4, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  T0+T1              12                38
  T2                 29               108
  T3                 38                62
  T4                 37               136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XP LOSS MUTATED    41  16  49   2
  XP LOSS WILD-TYPE 138  52 119   6
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              41               138
  N1              16                52
  N2              49               119
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    45   1
  XP LOSS WILD-TYPE 144   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     45    1
  XP LOSS WILD-TYPE  144    0
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              45               144
  1               1                 0
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    31 103
  XP LOSS WILD-TYPE 109 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     31  103
  XP LOSS WILD-TYPE  109  279
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              31               109
  MALE               103               279
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    35  73
  XP LOSS WILD-TYPE 116 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     35   73
  XP LOSS WILD-TYPE  116  210
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               35               116
  YES              73               210
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  XP LOSS MUTATED                                     129
  XP LOSS WILD-TYPE                                   382
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  XP LOSS MUTATED                                                             0
  XP LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  XP LOSS MUTATED                                                     5
  XP LOSS WILD-TYPE                                                   5
D81V9, multiclass
                                                             clus
vv                                                            XP LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   129
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       5
                                                             clus
vv                                                            XP LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     382
  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"
D81V10, continuous
D81V11, continuous
D81V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP LOSS MUTATED                                  1     1
  XP LOSS WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED                          13   115
  XP LOSS WILD-TYPE                        35   331
D81V13, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                     13                35
  WHITE                                        115               331
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V14, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     7 116
  XP LOSS WILD-TYPE  19 343
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      7  116
  XP LOSS WILD-TYPE   19  343
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                19
  NOT HISPANIC OR LATINO             116               343
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    44  39
  XQ LOSS WILD-TYPE 259 179
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               83               438 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               39               179 
$`XQ LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-6868 TCGA-BA-A4IH TCGA-BA-A6D8 
       15.19        13.64         9.07        15.52        20.45        27.95 
TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7862 TCGA-BB-7871 TCGA-BB-8596 
       14.47        20.48        16.41        36.72        24.66        71.05 
TCGA-BB-A5HY TCGA-BB-A6UM TCGA-CN-4725 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-5360 
       10.55        12.92        38.04        57.11        12.99        71.31 
TCGA-CN-6010 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A49A TCGA-CN-A6V7 TCGA-CQ-6218 
       50.07        35.05        32.48        17.29        19.53        41.19 
TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-A4CI TCGA-CR-5248 
       32.88         4.24        64.87        16.73        31.23        54.67 
TCGA-CR-6472 TCGA-CR-6487 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7388 
       34.52         7.69         3.09         0.99        17.13        27.06 
TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5439 TCGA-CV-5973 
       29.82         7.10         5.13         5.95        17.95        86.83 
TCGA-CV-5976 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6940 TCGA-CV-6948 TCGA-CV-6960 
       48.59         9.60         9.70        26.43        42.38        28.34 
TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7236 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
       18.81         5.26         4.73        25.08        25.94         0.07 
TCGA-CV-7425 TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-A460 TCGA-CV-A6K1 TCGA-CX-7082 
       56.48        16.27       153.86        60.43        22.52        10.42 
TCGA-D6-6827 TCGA-DQ-7588 TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A61W TCGA-H7-A6C5 
       18.67        14.04        37.18        20.25         0.46        21.11 
TCGA-MZ-A6I9 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-QK-A6IH 
       16.08        71.74        51.25        18.97         2.04        21.47 
TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A7JC 
        5.62        17.82        15.32        15.91        13.25        17.95 
TCGA-UF-A7JD TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ 
       24.30        20.75        22.36        17.03        20.55 

$`XQ LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
        3.35         9.30        37.28        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       57.93        17.10        23.84        20.48        65.59        68.48 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       21.17        14.83         3.55        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        28.11        30.18        11.54         7.10         5.69 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 
        7.82         2.27        11.05        13.38         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 
        9.14         4.60         4.41        18.38        22.42        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HU 
       50.20        44.98        66.28        38.40        20.52        25.71 
TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
       27.19         8.81         6.28        12.69        48.76        55.86 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
        4.67        51.29        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       52.14        20.55        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 
       13.05        42.02        46.32         8.58        12.39         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-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       52.08        56.94        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       28.04        19.07        34.13         6.74         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 
       52.08        11.08        10.45        32.22        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B 
       17.42        11.74        35.01        25.41        23.57        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        23.44        19.82        24.39 
TCGA-CN-A6V6 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        48.20        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       70.45        62.37        45.99        10.42        11.21         4.24 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-6229 
       32.38        46.95        56.58        13.25        14.99        38.76 
TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       70.13        53.52        43.04        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 
       14.14        12.46        84.23        11.77        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       58.42        50.01        39.52        36.99        18.54        16.90 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 
        6.02        11.90        10.22        11.34        11.64        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       22.78        15.75         9.27        47.18        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 
       40.93        35.84         3.45        24.95        29.23        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
        9.17        34.06        19.92        26.17        32.78        47.01 
TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       12.89        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
      108.95        76.24        19.20       107.51        87.55        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5977 
       91.53        80.12        17.92        13.35        23.05        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-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 
        2.14         5.46        20.52         4.73        21.90        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
      140.78        19.79        12.03        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6961 
       53.95        65.82        10.98         7.13         8.42         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 
        4.14        64.83       126.15       111.16        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        9.01         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
       10.75       130.88        77.16        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-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 
       34.09       100.57        14.89       156.49        54.94         3.52 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       84.49        19.76         7.17        16.64         6.38        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        21.01       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 
        1.05        45.96         6.51        88.87        48.20        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        0.76        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
       23.47        19.92        10.42        10.55        18.84        34.36 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       16.14        11.44        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       28.77         7.63        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
       12.79        11.11        58.45        37.25        30.94        33.86 
TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       18.02        46.32        46.45        20.45        37.58        40.24 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I 
       40.04        39.12        41.59        32.71        21.63         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       31.13        18.94        24.95        17.85        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A 
       12.43        13.38        15.16        15.06        13.61        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
        4.27         3.65         6.90        34.75        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        37.71        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S 
        5.29        13.68        13.84        19.04        15.48        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A7D7 
        1.84        12.62         6.25        15.42         7.13        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       29.92        15.78        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       75.55        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.21        23.15         7.30         9.34        12.72        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K 
       21.07        19.73         6.51        14.76        12.20         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       12.72        16.96         6.87         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
        3.12        13.55        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF 
       49.51        48.03        49.45        44.65        74.47        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JT TCGA-UF-A7JV TCGA-WA-A7H4 
       29.46        18.05        13.94        32.65         2.96        14.56 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.07              0.07 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           153.86            210.97 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            19.53             21.19 
[1] "0.1 - 153.9 (19.5)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.3"
D82V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  XQ LOSS MUTATED         6        7        11        39         4         1
  XQ LOSS WILD-TYPE      21       69        71       214         8         0
D82V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 6                21
  STAGE II                7                69
  STAGE III              11                71
  STAGE IVA              39               214
  STAGE IVB               4                 8
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  XQ LOSS MUTATED      10  16  24  23
  XQ LOSS WILD-TYPE    40 121  76 150
D82V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1              10                40
  T2                 16               121
  T3                 24                76
  T4                 23               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
  XQ LOSS MUTATED    21  11  31   2
  XQ LOSS WILD-TYPE 158  57 137   6
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              21               158
  N1              11                57
  N2              31               137
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    30   1
  XQ LOSS WILD-TYPE 159   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     30    1
  XQ LOSS WILD-TYPE  159    0
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              30               159
  1               1                 0
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    25  58
  XQ LOSS WILD-TYPE 115 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     25   58
  XQ LOSS WILD-TYPE  115  324
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              25               115
  MALE                58               324
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    20  46
  XQ LOSS WILD-TYPE 131 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     20   46
  XQ LOSS WILD-TYPE  131  237
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               20               131
  YES              46               237
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  XQ LOSS MUTATED                                      79
  XQ LOSS WILD-TYPE                                   432
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  XQ LOSS MUTATED                                                             0
  XQ LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  XQ LOSS MUTATED                                                     4
  XQ LOSS WILD-TYPE                                                   6
D82V9, multiclass
                                                             clus
vv                                                            XQ LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    79
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       4
                                                             clus
vv                                                            XQ LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     432
  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"
D82V10, continuous
D82V11, continuous
D82V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0     1
  XQ LOSS WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           8    71
  XQ LOSS WILD-TYPE                        40   375
D82V13, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      8                40
  WHITE                                         71               375
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V14, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     3  73
  XQ LOSS WILD-TYPE  23 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3   73
  XQ LOSS WILD-TYPE   23  386
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                23
  NOT HISPANIC OR LATINO              73               386
[1] 2 2
[1] FALSE
